ERROR [2016-09-26 16:27:28,719] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-26 16:27:28,719] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-26 16:27:28,719] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-26 16:27:28,729] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-26 16:27:28,729] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-26 16:27:28,729] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-26 16:27:28,729] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-26 16:27:28,739] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508/mut1-1474747508-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 16:27:29,255] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-26 16:27:29,255] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-bowtie2.bam.sort.bam INFO [2016-09-26 16:27:29,315] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-bowtie2.bam.sort.bam.vcf INFO [2016-09-26 16:27:29,455] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-zero_coverage_gaps.bedgraph INFO [2016-09-26 16:27:29,485] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-below_threshold_coverage_gaps.bedgraph INFO [2016-09-26 16:27:29,545] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-soft_clipping.bedgraph INFO [2016-09-26 16:27:29,575] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-non-ref_freq.bedgraph INFO [2016-09-26 16:27:29,695] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-strand_bias.xls INFO [2016-09-26 16:27:29,815] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-avg-ref-basequality.bedgraph INFO [2016-09-26 16:27:29,936] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-inverse-avg-ref-basequality.bedgraph ERROR [2016-09-26 16:29:16,589] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508/mut1-1474747508-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 16:29:16,589] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-26 16:29:16,589] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-26 16:29:16,589] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-26 16:29:16,589] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-26 16:29:16,589] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-26 16:29:16,599] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-26 16:29:16,599] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-26 16:29:16,599] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-26 16:29:16,609] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508/mut1-1474747508-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 16:29:17,171] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-26 16:29:17,181] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-bowtie2.bam.sort.bam INFO [2016-09-26 16:29:17,251] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-bowtie2.bam.sort.bam.vcf INFO [2016-09-26 16:29:17,351] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-zero_coverage_gaps.bedgraph INFO [2016-09-26 16:29:17,391] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-below_threshold_coverage_gaps.bedgraph INFO [2016-09-26 16:29:17,451] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-soft_clipping.bedgraph INFO [2016-09-26 16:29:17,481] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-non-ref_freq.bedgraph INFO [2016-09-26 16:29:17,601] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-strand_bias.xls INFO [2016-09-26 16:29:17,691] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-avg-ref-basequality.bedgraph INFO [2016-09-26 16:29:17,831] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474747508//mut1-1474747508-inverse-avg-ref-basequality.bedgraph ERROR [2016-09-26 17:07:07,480] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732/mut1-1474923732-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 17:07:07,480] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-26 17:07:07,480] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-26 17:07:07,480] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-26 17:07:07,480] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-26 17:07:07,490] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-26 17:07:07,490] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-26 17:07:07,490] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-26 17:07:07,490] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-26 17:07:08,520] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732/mut1-1474923732-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 17:07:09,271] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-26 17:07:09,271] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-bowtie2.bam.sort.bam INFO [2016-09-26 17:07:09,348] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-bowtie2.bam.sort.bam.vcf INFO [2016-09-26 17:07:09,458] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-zero_coverage_gaps.bedgraph INFO [2016-09-26 17:07:09,518] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-below_threshold_coverage_gaps.bedgraph INFO [2016-09-26 17:07:09,568] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-soft_clipping.bedgraph INFO [2016-09-26 17:07:09,638] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-non-ref_freq.bedgraph INFO [2016-09-26 17:07:09,778] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-strand_bias.bedgraph INFO [2016-09-26 17:07:09,948] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-avg-ref-basequality.bedgraph INFO [2016-09-26 17:07:10,058] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-inverse-avg-ref-basequality.bedgraph ERROR [2016-09-26 17:46:53,457] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732/mut1-1474923732-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 17:46:53,457] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-26 17:46:53,457] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-26 17:46:53,457] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-26 17:46:53,457] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-26 17:46:53,467] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-26 17:46:53,467] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-26 17:46:53,467] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-26 17:46:53,467] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-26 17:46:54,497] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732/mut1-1474923732-igv_session_file.xml HTTP/1.1 ERROR [2016-09-26 17:46:55,235] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-26 17:46:55,235] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-bowtie2.bam.sort.bam INFO [2016-09-26 17:46:55,285] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-bowtie2.bam.sort.bam.vcf INFO [2016-09-26 17:46:55,395] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-zero_coverage_gaps.bedgraph INFO [2016-09-26 17:46:55,425] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-below_threshold_coverage_gaps.bedgraph INFO [2016-09-26 17:46:55,475] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-soft_clipping.bedgraph INFO [2016-09-26 17:46:55,515] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-non-ref_freq.bedgraph INFO [2016-09-26 17:46:55,645] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-strand_bias.bedgraph INFO [2016-09-26 17:46:55,805] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-avg-ref-basequality.bedgraph INFO [2016-09-26 17:46:55,925] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1474923732//mut1-1474923732-inverse-avg-ref-basequality.bedgraph INFO [2016-09-28 11:04:07,296] [ShutdownThread.java:51] Shutting down INFO [2016-09-28 17:12:09,033] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-09-28 17:12:09,033] [Main.java:100] Java 1.8.0_91 INFO [2016-09-28 17:12:09,033] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-09-28 17:12:09,033] [Main.java:102] OS: Windows 7 INFO [2016-09-28 17:12:12,168] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-09-28 17:12:27,320] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1472658733//baseclear_GA21_ref_mut1.fa INFO [2016-09-28 17:12:27,524] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1472658733//baseclear_GA21_ref_mut1.fa INFO [2016-09-28 17:12:27,724] [CommandListener.java:106] Listening on port 60151 INFO [2016-09-28 17:12:39,242] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1472675325/NGS16013_VLHP1_A01_USR01308598/VLHP1.fa INFO [2016-09-28 17:12:39,402] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1472675325/NGS16013_VLHP1_A01_USR01308598/VLHP1.fa INFO [2016-09-28 17:12:39,552] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-09-28 17:13:37,433] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478-igv_session_file.xml HTTP/1.1 ERROR [2016-09-28 17:13:37,855] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-28 17:13:37,855] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-09-28 17:13:38,315] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-09-28 17:13:38,515] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478-soft_clip.bedgraph INFO [2016-09-28 17:15:13,767] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/VLHP1_sub-sequence_2214-2587.fa INFO [2016-09-28 17:15:13,822] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-09-28 17:15:33,652] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478-igv_session_file.xml HTTP/1.1 ERROR [2016-09-28 17:15:33,652] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-28 17:15:33,652] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-28 17:15:33,662] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-28 17:15:33,662] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-28 17:15:33,662] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-28 17:15:33,672] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-28 17:15:33,672] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-28 17:15:33,682] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-28 17:15:33,692] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478-igv_session_file.xml HTTP/1.1 ERROR [2016-09-28 17:15:34,118] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-28 17:15:34,118] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-09-28 17:15:34,178] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-09-28 17:15:34,308] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/NGS16011_VLHP1_D07_USR01308478-soft_clip.bedgraph ERROR [2016-09-28 17:24:39,976] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_F10_USR01308593/NGS16011_VLHP1_F10_USR01308593-igv_session_file.xml HTTP/1.1 ERROR [2016-09-28 17:24:39,976] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-28 17:24:39,976] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-28 17:24:39,976] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-28 17:24:39,986] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-28 17:24:39,986] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-28 17:24:39,986] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-28 17:24:39,986] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-28 17:24:39,986] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-28 17:24:41,016] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_F10_USR01308593/NGS16011_VLHP1_F10_USR01308593-igv_session_file.xml HTTP/1.1 ERROR [2016-09-28 17:24:41,358] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-28 17:24:41,358] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_F10_USR01308593/NGS16011_VLHP1_F10_USR01308593.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-09-28 17:24:42,008] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_F10_USR01308593/NGS16011_VLHP1_F10_USR01308593.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-09-28 17:24:42,168] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_F10_USR01308593/NGS16011_VLHP1_F10_USR01308593-soft_clip.bedgraph ERROR [2016-09-29 11:02:48,153] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787/mut1-1475077787-igv_session_file.xml HTTP/1.1 ERROR [2016-09-29 11:02:48,153] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-29 11:02:48,163] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-29 11:02:48,163] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-29 11:02:48,163] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-29 11:02:48,163] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-29 11:02:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-29 11:02:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-29 11:02:48,173] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-29 11:02:49,193] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787/mut1-1475077787-igv_session_file.xml HTTP/1.1 ERROR [2016-09-29 11:02:53,051] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-29 11:02:53,051] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-bowtie2.bam.sort.bam INFO [2016-09-29 11:02:55,371] [MessageUtils.java:74] File: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-bowtie2.bam.sort.bam
does not contain any sequence names which match the current genome.

File:      baseclear_GA21_ref_mut1,
Genome: VLHP1, INFO [2016-09-29 11:03:01,008] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-bowtie2.bam.sort.bam.vcf INFO [2016-09-29 11:03:04,968] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1472658733//baseclear_GA21_ref_mut1.fa INFO [2016-09-29 11:03:10,648] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1472658733//baseclear_GA21_ref_mut1.fa INFO [2016-09-29 11:03:24,220] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-zero_coverage_gaps.bedgraph INFO [2016-09-29 11:03:30,900] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-below_threshold_coverage_gaps.bedgraph INFO [2016-09-29 11:03:35,120] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-soft_clipping.bedgraph INFO [2016-09-29 11:03:35,560] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-non-ref_freq.bedgraph INFO [2016-09-29 11:03:36,405] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-strand_bias.bedgraph INFO [2016-09-29 11:03:36,704] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-avg-ref-basequality.bedgraph INFO [2016-09-29 11:03:37,172] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-inverse-avg-ref-basequality.bedgraph ERROR [2016-09-29 11:03:37,812] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787/mut1-1475077787-igv_session_file.xml HTTP/1.1 ERROR [2016-09-29 11:03:37,812] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-29 11:03:37,822] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-29 11:03:37,822] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-29 11:03:37,822] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-29 11:03:37,822] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-29 11:03:37,822] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-29 11:03:37,822] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-29 11:03:37,822] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-29 11:03:37,843] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787/mut1-1475077787-igv_session_file.xml HTTP/1.1 ERROR [2016-09-29 11:03:38,530] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-29 11:03:38,530] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-bowtie2.bam.sort.bam INFO [2016-09-29 11:03:38,980] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-bowtie2.bam.sort.bam.vcf INFO [2016-09-29 11:03:39,990] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-zero_coverage_gaps.bedgraph INFO [2016-09-29 11:03:40,080] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-below_threshold_coverage_gaps.bedgraph INFO [2016-09-29 11:03:40,210] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-soft_clipping.bedgraph INFO [2016-09-29 11:03:40,250] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-non-ref_freq.bedgraph INFO [2016-09-29 11:03:40,450] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-strand_bias.bedgraph INFO [2016-09-29 11:03:40,590] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-avg-ref-basequality.bedgraph INFO [2016-09-29 11:03:40,840] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test2/mut1/1475077787//mut1-1475077787-inverse-avg-ref-basequality.bedgraph INFO [2016-09-29 11:43:47,127] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-09-29 11:43:47,187] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-09-29 11:44:11,927] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_D12_Empty/NGS16011_VLHP1_D12_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-09-29 11:44:11,927] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-09-29 11:44:11,927] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-09-29 11:44:11,937] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-09-29 11:44:11,937] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-09-29 11:44:11,937] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-09-29 11:44:11,937] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-09-29 11:44:11,937] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-09-29 11:44:11,937] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-09-29 11:44:12,956] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_D12_Empty/NGS16011_VLHP1_D12_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-09-29 11:44:13,255] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-09-29 11:44:13,255] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D12_Empty/NGS16011_VLHP1_D12_Empty.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-09-29 11:44:13,345] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D12_Empty/NGS16011_VLHP1_D12_Empty.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-09-29 11:44:13,495] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D12_Empty/NGS16011_VLHP1_D12_Empty-soft_clip.bedgraph INFO [2016-09-29 17:44:31,662] [ShutdownThread.java:51] Shutting down INFO [2016-10-01 10:13:43,757] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-01 10:13:43,767] [Main.java:100] Java 1.8.0_91 INFO [2016-10-01 10:13:43,767] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-01 10:13:43,767] [Main.java:102] OS: Windows 7 INFO [2016-10-01 10:13:45,267] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-01 10:14:04,211] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-01 10:14:04,880] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-01 10:14:05,132] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-01 10:14:05,422] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-01 10:14:14,572] [GenomeManager.java:145] Loading genome: http://localhost:60151/load?file=http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml ERROR [2016-10-01 10:14:14,608] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http%3A%2F%2Fdemeter%2F%2Fproject%2FGED2458%2Fdelivered%2F1475330633%2FNGS16004_B1_MZET160411A007A%2FNGS16004_B1_MZET160411A007A-igv_session_file.xml.fai HTTP/1.1 ERROR [2016-10-01 10:14:14,608] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: IGV Version 2.3.78 (117)06/28/2016 12:08 PM ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: Cache-Control: no-cache ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: Pragma: no-cache ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: Accept: text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2 ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: keep-alive ERROR [2016-10-01 10:14:14,618] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http%3A%2F%2Fdemeter%2F%2Fproject%2FGED2458%2Fdelivered%2F1475330633%2FNGS16004_B1_MZET160411A007A%2FNGS16004_B1_MZET160411A007A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-01 10:14:14,618] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: IGV Version 2.3.78 (117)06/28/2016 12:08 PM ERROR [2016-10-01 10:14:14,628] [CommandExecutor.java:199] UNKOWN COMMAND: Cache-Control: no-cache ERROR [2016-10-01 10:14:14,628] [CommandExecutor.java:199] UNKOWN COMMAND: Pragma: no-cache ERROR [2016-10-01 10:14:14,628] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-01 10:14:14,628] [CommandExecutor.java:199] UNKOWN COMMAND: Accept: text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2 ERROR [2016-10-01 10:14:14,628] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: keep-alive ERROR [2016-10-01 10:14:14,628] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-01 10:14:14,628] [CommandListener.java:167] GET /load?file=http%3A%2F%2Fdemeter%2F%2Fproject%2FGED2458%2Fdelivered%2F1475330633%2FNGS16004_B1_MZET160411A007A%2FNGS16004_B1_MZET160411A007A-igv_session_file.xml.fai HTTP/1.1 INFO [2016-10-01 10:14:14,638] [IGV.java:1700] Loading 1 resources. INFO [2016-10-01 10:14:14,648] [TrackLoader.java:118] Loading resource, path http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml.fai ERROR [2016-10-01 10:14:14,948] [TrackLoader.java:256] File not found: http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml.fai java.io.FileNotFoundException: File not found: http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml.fai at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:739) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:614) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:220) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:214) at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:111) at org.broad.igv.util.ParsingUtils.openAsciiReader(ParsingUtils.java:90) at org.broad.igv.data.expression.ExpressionFileParser.parsableMAGE_TAB(ExpressionFileParser.java:134) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:202) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.ui.IGV$13.run(IGV.java:1721) at org.broad.igv.ui.IGV.loadResources(IGV.java:1734) at org.broad.igv.ui.IGV$5.run(IGV.java:738) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGV.loadTracks(IGV.java:750) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:566) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) ERROR [2016-10-01 10:14:14,948] [IGV.java:1725] Error loading track org.broad.igv.exceptions.DataLoadException: File not found: http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml.fai at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.ui.IGV$13.run(IGV.java:1721) at org.broad.igv.ui.IGV.loadResources(IGV.java:1734) at org.broad.igv.ui.IGV$5.run(IGV.java:738) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGV.loadTracks(IGV.java:750) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:566) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-01 10:14:14,958] [MessageUtils.java:74] Error loading http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml.fai: File not found: http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml.fai INFO [2016-10-01 10:15:42,628] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-01 10:15:42,628] [Main.java:100] Java 1.8.0_91 INFO [2016-10-01 10:15:42,628] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-01 10:15:42,628] [Main.java:102] OS: Windows 7 INFO [2016-10-01 10:15:43,730] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-01 10:16:01,480] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-01 10:16:02,154] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-01 10:16:02,324] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-01 10:16:02,584] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-01 10:16:57,806] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa INFO [2016-10-01 10:16:58,477] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-01 10:17:09,194] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-01 10:17:09,194] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-01 10:17:10,223] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-01 10:17:10,754] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-01 10:17:10,754] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-01 10:17:11,955] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-01 10:17:14,264] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/NGS16004_B1_MZET160411A007A-soft_clip.bedgraph ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475331740/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 09:22:11,113] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 09:22:11,113] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 09:22:12,153] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475331740/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 09:22:12,499] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-02 09:22:14,039] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 09:22:14,039] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475331740/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-02 09:22:20,788] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475331740/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-02 09:22:34,047] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475331740/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph INFO [2016-10-02 10:50:14,431] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa INFO [2016-10-02 10:50:18,143] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_D12_JHAX/NGS16004_D12_JHAX-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 10:50:48,173] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 10:50:48,173] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 10:50:49,213] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_D12_JHAX/NGS16004_D12_JHAX-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 10:50:50,537] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 10:50:50,537] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_D12_JHAX/NGS16004_D12_JHAX.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 10:50:54,337] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_D12_JHAX/NGS16004_D12_JHAX.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 10:51:00,437] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_D12_JHAX/NGS16004_D12_JHAX-soft_clip.bedgraph ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 10:51:32,790] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 10:51:32,790] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 10:51:32,800] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 10:51:34,332] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 10:51:34,342] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 10:51:38,022] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 10:51:46,712] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 10:52:37,734] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 10:52:37,754] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 10:52:37,754] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 10:52:38,988] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 10:52:38,988] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 10:52:42,958] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 10:52:51,078] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A-soft_clip.bedgraph ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 11:30:12,275] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 11:30:12,275] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 11:30:13,295] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 11:30:14,189] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 11:30:14,189] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 11:30:17,100] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: ZmpylD, INFO [2016-10-02 11:30:21,790] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 11:30:26,841] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-02 11:30:27,461] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-02 11:30:28,612] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 11:30:35,823] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 11:30:35,823] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 11:30:35,833] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 11:30:37,175] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 11:30:37,175] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 11:30:40,305] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 11:30:48,587] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475424458/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 12:12:38,951] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 12:12:38,951] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 12:12:39,971] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475424458/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:12:41,333] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 12:12:41,333] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475424458/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 12:12:46,583] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475424458/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 12:12:50,663] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475424458/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_A02_USR01308293/NGS16011_VLHP1_A02_USR01308293-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 12:46:16,326] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 12:46:16,326] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 12:46:17,406] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_A02_USR01308293/NGS16011_VLHP1_A02_USR01308293-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:46:18,577] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 12:46:18,577] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A02_USR01308293/NGS16011_VLHP1_A02_USR01308293.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 12:46:23,567] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A02_USR01308293/NGS16011_VLHP1_A02_USR01308293.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 12:46:33,666] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_A02_USR01308293/NGS16011_VLHP1_A02_USR01308293-soft_clip.bedgraph ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_A01_USR01308292/NGS16012_VLHP2_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 12:49:43,794] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 12:49:43,794] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 12:49:43,814] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_A01_USR01308292/NGS16012_VLHP2_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:49:44,918] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 12:49:44,918] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_A01_USR01308292/NGS16012_VLHP2_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-02 12:49:48,188] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_A01_USR01308292/NGS16012_VLHP2_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP2,
Genome: VLHP1, INFO [2016-10-02 12:49:50,688] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_A01_USR01308292/NGS16012_VLHP2_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-02 12:49:57,048] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_A01_USR01308292/NGS16012_VLHP2_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-02 12:50:15,727] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1474386940/NGS16013_VLHP2_C07_USR01308688/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-02 12:50:18,497] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1474386940/NGS16013_VLHP2_C07_USR01308688/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-02 12:50:30,118] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1472675325/NGS16013_VLHP1_A01_USR01308598/VLHP1.fa INFO [2016-10-02 12:50:36,159] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1472675325/NGS16013_VLHP1_A01_USR01308598/VLHP1.fa INFO [2016-10-02 12:50:39,910] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-02 12:50:44,110] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-02 12:52:41,713] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa INFO [2016-10-02 12:52:43,653] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474408060/NGS16010_GW2-1_D03_USR01308777/NGS16010_GW2-1_D03_USR01308777-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 12:53:04,013] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 12:53:04,013] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 12:53:04,013] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474408060/NGS16010_GW2-1_D03_USR01308777/NGS16010_GW2-1_D03_USR01308777-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 12:53:05,343] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 12:53:05,343] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D03_USR01308777/NGS16010_GW2-1_D03_USR01308777.extendedFrags.mod.fastq-vs-GW2-1_sub-sequence_1836-2240.sort.bam INFO [2016-10-02 12:53:14,023] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D03_USR01308777/NGS16010_GW2-1_D03_USR01308777.extendedFrags.mod.fastq-vs-GW2-1_sub-sequence_1836-2240.sort.bam.mod.vcf INFO [2016-10-02 12:53:19,803] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D03_USR01308777/NGS16010_GW2-1_D03_USR01308777-soft_clip.bedgraph INFO [2016-10-02 13:26:50,497] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa INFO [2016-10-02 13:26:54,537] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 13:27:09,297] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 13:27:09,327] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 13:27:10,337] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 13:27:11,499] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 13:27:11,499] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 13:27:15,229] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 13:27:24,039] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph ERROR [2016-10-02 14:04:29,158] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:04:29,158] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 14:04:29,158] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 14:04:29,158] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 14:04:29,158] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 14:04:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 14:04:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 14:04:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 14:04:29,168] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 14:04:30,198] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:04:30,720] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 14:04:30,720] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 14:04:31,560] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 14:04:33,610] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H1_MZET160408A032A/NGS16004_H1_MZET160408A032A-soft_clip.bedgraph INFO [2016-10-02 14:22:15,681] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1474386940/NGS16013_VLHP1_A10_USR01308695/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-02 14:22:16,381] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1474386940/NGS16013_VLHP1_A10_USR01308695/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 14:22:40,061] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 14:22:40,061] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 14:22:41,071] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:22:41,481] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 14:22:41,481] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 14:22:42,481] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: VLHP1_sub-sequence_2214-2587, INFO [2016-10-02 14:22:50,151] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 14:22:52,281] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-soft_clip.bedgraph ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 14:23:15,997] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 14:23:15,997] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 14:23:16,027] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:23:16,533] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 14:23:16,533] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 14:23:16,963] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: VLHP1_sub-sequence_2214-2587, INFO [2016-10-02 14:23:33,410] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 14:23:35,460] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-soft_clip.bedgraph INFO [2016-10-02 14:23:58,946] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-02 14:23:59,786] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 14:24:11,636] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 14:24:11,636] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 14:24:11,646] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:24:12,115] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 14:24:12,115] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-02 14:24:12,765] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-02 14:24:14,845] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/NGS16011_VLHP1_A03_USR01308296-soft_clip.bedgraph INFO [2016-10-02 14:28:03,575] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa INFO [2016-10-02 14:28:04,335] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 14:28:29,063] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 14:28:29,063] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 14:28:30,093] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 14:28:30,523] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 14:28:30,523] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 14:28:31,193] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 14:28:33,353] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 16:07:14,801] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 16:07:14,801] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 16:07:15,841] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:07:16,795] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 16:07:16,795] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 16:07:17,835] [MessageUtils.java:74] File: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam
does not contain any sequence names which match the current genome.

File:      ZmpylD.w_AR,
Genome: ZmpylD, INFO [2016-10-02 16:07:19,795] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 16:07:22,165] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-soft_clip.bedgraph ERROR [2016-10-02 16:09:34,134] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:09:34,134] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 16:09:34,134] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 16:09:34,134] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 16:09:34,134] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 16:09:34,134] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 16:09:34,144] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 16:09:34,144] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 16:09:34,144] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 16:09:34,154] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:09:34,696] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 16:09:34,696] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 16:09:35,316] [MessageUtils.java:74] File: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam
does not contain any sequence names which match the current genome.

File:      ZmpylD.w_AR,
Genome: ZmpylD, INFO [2016-10-02 16:09:39,936] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 16:09:43,126] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-soft_clip.bedgraph INFO [2016-10-02 16:10:21,115] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-02 16:10:21,885] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 16:10:47,337] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 16:10:47,337] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 16:10:47,347] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:10:47,979] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 16:10:47,979] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 16:10:48,861] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 16:10:52,041] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/NGS16004_F1_MZET160506A120A-soft_clip.bedgraph ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_G1_MZET160600A138A/NGS16004_G1_MZET160600A138A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-02 16:11:42,812] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-02 16:11:42,812] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-02 16:11:42,812] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475433321/NGS16004_G1_MZET160600A138A/NGS16004_G1_MZET160600A138A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-02 16:11:42,974] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-02 16:11:43,426] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-02 16:11:43,436] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_G1_MZET160600A138A/NGS16004_G1_MZET160600A138A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam INFO [2016-10-02 16:11:45,195] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_G1_MZET160600A138A/NGS16004_G1_MZET160600A138A.extendedFrags.mod.fastq-vs-ZmpylD.w_AR.sort.bam.mod.vcf INFO [2016-10-02 16:11:48,405] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475433321/NGS16004_G1_MZET160600A138A/NGS16004_G1_MZET160600A138A-soft_clip.bedgraph INFO [2016-10-02 19:04:14,830] [ShutdownThread.java:51] Shutting down INFO [2016-10-03 05:27:02,498] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-03 05:27:02,498] [Main.java:100] Java 1.8.0_91 INFO [2016-10-03 05:27:02,498] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-03 05:27:02,498] [Main.java:102] OS: Windows 7 INFO [2016-10-03 05:27:04,318] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-03 05:27:22,950] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-03 05:27:23,634] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-03 05:27:23,804] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-03 05:27:24,145] [HttpUtils.java:827] Range-byte request succeeded ERROR [2016-10-03 05:27:48,067] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:27:48,067] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 05:27:48,067] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 05:27:48,077] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 05:27:48,077] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 05:27:48,077] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 05:27:48,077] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 05:27:48,077] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 05:27:48,077] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 05:27:49,097] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:27:50,561] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 05:27:50,561] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-03 05:27:52,122] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: ZmpylD.w_AR, INFO [2016-10-03 05:27:59,732] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-03 05:28:02,533] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-03 05:28:33,186] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-03 05:28:33,996] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-03 05:28:42,207] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:28:42,207] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 05:28:42,207] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 05:28:42,207] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 05:28:42,207] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 05:28:42,207] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 05:28:42,217] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 05:28:42,217] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 05:28:42,217] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 05:28:42,227] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:28:42,791] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 05:28:42,791] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-03 05:28:43,911] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-03 05:28:46,202] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-03 05:30:15,106] [ShutdownThread.java:51] Shutting down INFO [2016-10-03 05:34:25,721] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-03 05:34:25,721] [Main.java:100] Java 1.8.0_91 INFO [2016-10-03 05:34:25,721] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-03 05:34:25,721] [Main.java:102] OS: Windows 7 INFO [2016-10-03 05:34:27,061] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-03 05:34:46,303] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-03 05:34:47,129] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-03 05:34:47,299] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-03 05:34:47,559] [HttpUtils.java:827] Range-byte request succeeded ERROR [2016-10-03 05:35:23,229] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D08_USR01308480/NGS16011_VLHP1_D08_USR01308480-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:35:23,229] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 05:35:23,239] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 05:35:23,239] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 05:35:23,239] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 05:35:23,239] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 05:35:23,239] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 05:35:23,239] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 05:35:23,249] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 05:35:24,259] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D08_USR01308480/NGS16011_VLHP1_D08_USR01308480-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:35:25,205] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 05:35:25,205] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D08_USR01308480/NGS16011_VLHP1_D08_USR01308480.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-03 05:35:26,885] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D08_USR01308480/NGS16011_VLHP1_D08_USR01308480.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-03 05:35:29,425] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D08_USR01308480/NGS16011_VLHP1_D08_USR01308480-soft_clip.bedgraph ERROR [2016-10-03 05:39:46,487] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:39:46,487] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 05:39:46,487] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 05:39:46,487] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 05:39:46,497] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 05:39:46,497] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 05:39:46,497] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 05:39:46,497] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 05:39:46,497] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 05:39:47,507] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 05:39:48,263] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 05:39:48,263] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-03 05:39:49,823] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-03 05:39:53,683] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-soft_clip.bedgraph INFO [2016-10-03 07:54:02,693] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa INFO [2016-10-03 07:54:03,518] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa ERROR [2016-10-03 07:54:24,787] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:54:24,787] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 07:54:24,787] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 07:54:24,787] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 07:54:24,787] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 07:54:24,797] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 07:54:24,797] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 07:54:24,797] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 07:54:24,797] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 07:54:25,817] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:54:26,538] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 07:54:26,538] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 07:54:27,838] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 07:54:30,158] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-soft_clip.bedgraph ERROR [2016-10-03 07:56:22,729] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:56:22,729] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 07:56:22,729] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 07:56:22,729] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 07:56:22,739] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 07:56:22,739] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 07:56:22,749] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 07:56:22,749] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 07:56:22,749] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 07:56:22,769] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:56:23,505] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 07:56:23,505] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 07:56:24,675] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 07:56:27,295] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-soft_clip.bedgraph ERROR [2016-10-03 07:56:34,484] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:56:34,484] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 07:56:34,484] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 07:56:34,484] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 07:56:34,484] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 07:56:34,494] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 07:56:34,494] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 07:56:34,494] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 07:56:34,494] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 07:56:34,514] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:56:38,190] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 07:56:38,190] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 07:56:38,860] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 07:56:41,240] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-soft_clip.bedgraph ERROR [2016-10-03 07:57:30,636] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:57:30,636] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 07:57:30,636] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 07:57:30,636] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 07:57:30,636] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 07:57:30,646] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 07:57:30,646] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 07:57:30,646] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 07:57:30,646] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 07:57:30,656] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 07:57:31,480] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 07:57:31,480] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 07:57:32,860] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 07:57:34,979] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph ERROR [2016-10-03 08:12:08,208] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 08:12:08,208] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 08:12:08,208] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 08:12:08,208] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 08:12:08,208] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 08:12:08,218] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 08:12:08,218] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 08:12:08,218] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 08:12:08,238] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 08:12:09,238] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 08:12:10,202] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 08:12:10,202] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 08:12:12,602] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 08:12:15,032] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-03 09:04:37,858] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:04:37,858] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:04:37,858] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:04:37,858] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:04:37,858] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:04:37,858] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:04:37,868] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:04:37,868] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:04:37,868] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:04:38,878] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:04:39,630] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:04:39,630] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:04:40,510] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:04:44,830] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-soft_clip.bedgraph ERROR [2016-10-03 09:04:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:04:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:04:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:04:57,749] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:04:57,749] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:04:57,749] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:04:57,749] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:04:57,749] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:04:57,749] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:04:57,759] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:04:58,349] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:04:58,349] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:04:59,239] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:05:01,939] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-soft_clip.bedgraph ERROR [2016-10-03 09:05:13,199] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:05:13,199] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:05:13,199] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:05:13,199] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:05:13,199] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:05:13,199] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:05:13,209] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:05:13,209] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:05:13,209] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:05:13,219] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:05:13,339] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-03 09:05:13,779] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:05:13,779] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:05:14,559] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:05:16,829] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-soft_clip.bedgraph ERROR [2016-10-03 09:05:33,679] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:05:33,679] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:05:33,679] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:05:33,679] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:05:33,679] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:05:33,679] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:05:33,689] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:05:33,689] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:05:33,689] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:05:33,699] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:05:34,249] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:05:34,249] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:05:35,469] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:05:37,769] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A-soft_clip.bedgraph ERROR [2016-10-03 09:05:53,338] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:05:53,338] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:05:53,338] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:05:53,338] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:05:53,338] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:05:53,338] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:05:53,348] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:05:53,348] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:05:53,348] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:05:53,358] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:05:53,888] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:05:53,888] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:05:54,998] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:05:58,048] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-soft_clip.bedgraph ERROR [2016-10-03 09:06:00,798] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:06:00,798] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:06:00,798] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:06:00,798] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:06:00,798] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:06:00,808] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:06:00,808] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:06:00,808] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:06:00,808] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:06:00,818] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:06:01,288] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:06:01,288] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:06:02,078] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:06:04,398] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-soft_clip.bedgraph ERROR [2016-10-03 09:06:32,287] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:06:32,287] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:06:32,287] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:06:32,287] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:06:32,287] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:06:32,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:06:32,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:06:32,297] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:06:32,297] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:06:32,307] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:06:32,757] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:06:32,767] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:06:33,947] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:06:36,147] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-soft_clip.bedgraph ERROR [2016-10-03 09:06:38,047] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:06:38,047] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:06:38,047] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:06:38,047] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:06:38,047] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:06:38,047] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:06:38,057] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:06:38,057] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:06:38,057] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:06:38,067] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:06:38,557] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:06:38,557] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:06:39,287] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:06:41,667] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-soft_clip.bedgraph ERROR [2016-10-03 09:07:14,536] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:07:14,536] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:07:14,536] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:07:14,536] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:07:14,536] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:07:14,536] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:07:14,546] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:07:14,546] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:07:14,546] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:07:14,556] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:07:14,676] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-03 09:07:15,156] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:07:15,156] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:07:16,016] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:07:18,476] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-03 09:07:20,646] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:07:20,646] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:07:20,646] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:07:20,646] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:07:20,646] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:07:20,656] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:07:20,656] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:07:20,666] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:07:20,666] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:07:20,666] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:07:21,186] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:07:21,186] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:07:21,826] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:07:33,085] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:07:36,615] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:07:36,625] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:07:36,625] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:07:37,115] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:07:37,115] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:07:37,845] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:07:49,165] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-03 09:09:04,113] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:09:04,113] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-03 09:09:04,113] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-03 09:09:04,113] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-03 09:09:04,113] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-03 09:09:04,123] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-03 09:09:04,123] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-03 09:09:04,123] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-03 09:09:04,123] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-03 09:09:04,133] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-03 09:09:04,757] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-03 09:09:04,757] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-03 09:09:05,617] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-03 09:09:08,917] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph INFO [2016-10-04 09:27:44,731] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-04 09:27:44,731] [Main.java:100] Java 1.8.0_91 INFO [2016-10-04 09:27:44,731] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-04 09:27:44,731] [Main.java:102] OS: Windows 7 INFO [2016-10-04 09:27:47,172] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-04 09:28:07,329] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa INFO [2016-10-04 09:28:08,209] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa ERROR [2016-10-04 09:28:08,389] [CommandListener.java:124] java.net.BindException: Address already in use: JVM_Bind INFO [2016-10-04 09:28:08,629] [HttpUtils.java:827] Range-byte request succeeded ERROR [2016-10-04 09:28:37,533] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 09:28:37,533] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 09:28:37,533] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 09:28:37,533] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 09:28:37,533] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 09:28:37,543] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 09:28:37,543] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 09:28:37,543] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 09:28:37,543] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 09:28:39,214] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 09:28:39,944] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 09:28:39,944] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 09:28:41,304] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: ZmpylD, INFO [2016-10-04 09:28:44,174] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 09:28:46,925] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654-soft_clip.bedgraph INFO [2016-10-04 09:28:51,365] [ShutdownThread.java:51] Shutting down INFO [2016-10-04 09:28:58,098] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:28:58,789] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:39:08,412] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-04 09:39:09,172] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-04 09:47:57,138] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-04 09:47:57,138] [Main.java:100] Java 1.8.0_91 INFO [2016-10-04 09:47:57,138] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-04 09:47:57,138] [Main.java:102] OS: Windows 7 INFO [2016-10-04 09:47:58,635] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-04 09:48:13,096] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/work/data/ZmpylD.trunc.fa. Trying GET INFO [2016-10-04 09:48:14,282] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/DON2308/work/simulation/for_bioinformatics_meeting/data/WT.fa. Trying GET INFO [2016-10-04 09:48:15,468] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/DON2308/work/simulation/for_bioinformatics_meeting/data/WT.trunc.fa. Trying GET INFO [2016-10-04 09:48:16,669] [HttpUtils.java:283] HEAD request failed for url: http://demeter//project/product_safety_2016/work/ga21/baseclear/my_baseclear_working_dir/baseclear_validation/baseclear_GA21_ref.fa. Trying GET INFO [2016-10-04 09:48:17,870] [HttpUtils.java:283] HEAD request failed for url: http://demeter//project/GED2458/work/data/ZmpylD.trunc.fa. Trying GET INFO [2016-10-04 09:48:19,071] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/DON2308/work/data/references_from_weining/VLHP2.fa. Trying GET INFO [2016-10-04 09:48:20,241] [HttpUtils.java:283] HEAD request failed for url: http://demeter//project/DON2308/work/data/references_from_weining/GW2-2.fa. Trying GET INFO [2016-10-04 09:48:21,442] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/product_safety_2016/work/MiSeq_pipeline/baseclear_GA21_ref_mut1.fa. Trying GET INFO [2016-10-04 09:48:22,644] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/DON2308/delivered/1471973333/MZET154904A003A/GW2-2.fa. Trying GET INFO [2016-10-04 09:48:23,845] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1472658733//baseclear_GA21_ref_mut1.fa. Trying GET INFO [2016-10-04 09:48:25,046] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1472675325/NGS16013_VLHP1_A01_USR01308598/VLHP1.fa. Trying GET INFO [2016-10-04 09:48:26,232] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1473261460/NGS16011_VLHP1_D04_USR01308472/VLHP1_sub-sequence_2214-2587.fa. Trying GET INFO [2016-10-04 09:48:27,433] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1474386940/NGS16013_VLHP2_C07_USR01308688/VLHP2_sub-sequence_2182-2586.fa. Trying GET INFO [2016-10-04 09:48:28,634] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1474386940/NGS16013_VLHP1_A10_USR01308695/VLHP1_sub-sequence_2214-2587.fa. Trying GET INFO [2016-10-04 09:48:29,835] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_D07_USR01308478/VLHP1_sub-sequence_2214-2587.fa. Trying GET INFO [2016-10-04 09:48:31,036] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa. Trying GET INFO [2016-10-04 09:48:32,222] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa. Trying GET INFO [2016-10-04 09:48:33,423] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa. Trying GET INFO [2016-10-04 09:48:34,624] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa. Trying GET INFO [2016-10-04 09:48:35,826] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa. Trying GET INFO [2016-10-04 09:48:37,027] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa. Trying GET INFO [2016-10-04 09:48:38,228] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa. Trying GET INFO [2016-10-04 09:48:39,226] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-04 09:48:40,334] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa.fai. Trying GET ERROR [2016-10-04 09:48:40,599] [IGVCommandBar.java:285] Error initializing genome java.lang.RuntimeException: Error. Unexpected number of tokens parsing: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa.fai at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:97) at org.broad.igv.feature.genome.FastaIndex.(FastaIndex.java:54) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:67) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:297) at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83) at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:308) at javax.swing.JComboBox.fireActionEvent(Unknown Source) at javax.swing.JComboBox.setSelectedItem(Unknown Source) at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:541) at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2517) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGV.startUp(IGV.java:2460) at org.broad.igv.ui.Main.open(Main.java:238) at org.broad.igv.ui.Main.main(Main.java:85) INFO [2016-10-04 09:48:40,802] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-04 09:48:45,778] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:48:47,994] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa.fai. Trying GET INFO [2016-10-04 09:48:49,351] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa. Trying GET ERROR [2016-10-04 09:48:49,694] [IGVCommandBar.java:285] Error initializing genome java.lang.RuntimeException: Error. Unexpected number of tokens parsing: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa.fai at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:97) at org.broad.igv.feature.genome.FastaIndex.(FastaIndex.java:54) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:67) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) ERROR [2016-10-04 09:49:03,282] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 09:49:03,282] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 09:49:03,282] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 09:49:03,282] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 09:49:03,282] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 09:49:03,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 09:49:03,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 09:49:03,297] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 09:49:03,297] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 09:49:04,342] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 09:49:04,561] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.ui.IGV.newSession(IGV.java:1291) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:509) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 09:49:37,181] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:49:39,053] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa.fai. Trying GET ERROR [2016-10-04 09:49:39,302] [IGVCommandBar.java:285] Error initializing genome java.lang.RuntimeException: Error. Unexpected number of tokens parsing: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa.fai at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:97) at org.broad.igv.feature.genome.FastaIndex.(FastaIndex.java:54) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:67) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 09:49:46,868] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa INFO [2016-10-04 09:49:47,991] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa.fai. Trying GET ERROR [2016-10-04 09:49:48,257] [IGVCommandBar.java:285] Error initializing genome java.lang.RuntimeException: Error. Unexpected number of tokens parsing: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa.fai at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:97) at org.broad.igv.feature.genome.FastaIndex.(FastaIndex.java:54) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:67) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 09:50:23,528] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa INFO [2016-10-04 09:50:25,572] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa.fai. Trying GET INFO [2016-10-04 09:50:26,929] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa. Trying GET ERROR [2016-10-04 09:50:27,257] [IGVCommandBar.java:285] Error initializing genome java.lang.RuntimeException: Error. Unexpected number of tokens parsing: http://demeter/project/GED2458/delivered/1475433321/NGS16004_F1_MZET160506A120A/ZmpylD.w_AR.fa.fai at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:97) at org.broad.igv.feature.genome.FastaIndex.(FastaIndex.java:54) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:67) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 09:51:11,516] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:51:13,216] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa.fai. Trying GET INFO [2016-10-04 09:51:14,573] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa. Trying GET ERROR [2016-10-04 09:51:14,916] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.RuntimeException: Error. Unexpected number of tokens parsing: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa.fai at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:97) at org.broad.igv.feature.genome.FastaIndex.(FastaIndex.java:54) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:67) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.ui.IGV.loadGenome(IGV.java:686) at org.broad.igv.ui.IGV.loadGenome(IGV.java:667) at org.broad.igv.ui.action.LoadFromURLMenuAction.actionPerformed(LoadFromURLMenuAction.java:137) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) INFO [2016-10-04 09:53:34,395] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:53:35,222] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 09:53:35,487] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-04 10:23:00,155] [ShutdownThread.java:51] Shutting down INFO [2016-10-04 10:23:19,527] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-04 10:23:19,527] [Main.java:100] Java 1.8.0_91 INFO [2016-10-04 10:23:19,527] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-04 10:23:19,527] [Main.java:102] OS: Windows 7 INFO [2016-10-04 10:23:22,103] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-04 10:23:46,986] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 10:23:48,266] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 10:23:48,437] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-04 10:23:48,827] [HttpUtils.java:827] Range-byte request succeeded ERROR [2016-10-04 10:24:07,160] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A10_USR01308313/NGS16011_VLHP1_A10_USR01308313-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 10:24:07,160] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 10:24:07,160] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 10:24:07,160] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 10:24:07,160] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 10:24:07,176] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 10:24:07,176] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 10:24:07,176] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 10:24:07,176] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 10:24:08,205] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A10_USR01308313/NGS16011_VLHP1_A10_USR01308313-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 10:24:09,095] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 10:24:09,095] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A10_USR01308313/NGS16011_VLHP1_A10_USR01308313.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 10:24:11,123] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A10_USR01308313/NGS16011_VLHP1_A10_USR01308313.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 10:24:13,868] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A10_USR01308313/NGS16011_VLHP1_A10_USR01308313-soft_clip.bedgraph INFO [2016-10-04 11:01:37,515] [ShutdownThread.java:51] Shutting down INFO [2016-10-04 11:01:52,251] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-04 11:01:52,251] [Main.java:100] Java 1.8.0_91 INFO [2016-10-04 11:01:52,251] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-04 11:01:52,251] [Main.java:102] OS: Windows 7 INFO [2016-10-04 11:01:53,562] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-04 11:02:07,155] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 11:02:07,202] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 11:02:07,358] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-04 11:02:07,420] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-04 11:15:24,759] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa INFO [2016-10-04 11:15:24,821] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa ERROR [2016-10-04 11:15:33,901] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_E1_MZET160411B044A/NGS16004_E1_MZET160411B044A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:15:33,901] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:15:33,901] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:15:33,901] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:15:33,901] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:15:33,901] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:15:33,917] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:15:33,917] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:15:33,917] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:15:37,411] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_E1_MZET160411B044A/NGS16004_E1_MZET160411B044A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:15:37,754] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:15:37,754] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_E1_MZET160411B044A/NGS16004_E1_MZET160411B044A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:15:37,973] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_E1_MZET160411B044A/NGS16004_E1_MZET160411B044A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:15:38,144] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_E1_MZET160411B044A/NGS16004_E1_MZET160411B044A-soft_clip.bedgraph ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H2_MZET160408A019A/NGS16004_H2_MZET160408A019A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:25:01,104] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:25:01,119] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:25:01,119] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:25:02,149] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H2_MZET160408A019A/NGS16004_H2_MZET160408A019A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:25:02,383] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-04 11:25:02,633] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:25:02,633] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H2_MZET160408A019A/NGS16004_H2_MZET160408A019A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:25:02,695] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H2_MZET160408A019A/NGS16004_H2_MZET160408A019A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:25:02,820] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H2_MZET160408A019A/NGS16004_H2_MZET160408A019A-soft_clip.bedgraph ERROR [2016-10-04 11:27:55,730] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:27:55,730] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:27:55,730] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:27:55,730] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:27:55,730] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:27:55,730] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:27:55,746] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:27:55,746] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:27:55,746] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:27:55,746] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:27:56,198] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:27:56,198] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:27:56,339] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:27:56,682] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A-soft_clip.bedgraph ERROR [2016-10-04 11:28:02,017] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:28:02,017] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:28:02,017] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:28:02,017] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:28:02,017] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:28:02,017] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:28:02,033] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:28:02,033] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:28:02,033] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:28:02,033] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:28:02,126] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-04 11:28:02,438] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:28:02,438] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:28:02,610] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:28:03,047] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_D3_MZET160601B207A/NGS16004_D3_MZET160601B207A-soft_clip.bedgraph ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:29:01,781] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:29:01,781] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:29:01,812] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:29:02,202] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:29:02,202] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:29:02,405] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:29:02,888] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-soft_clip.bedgraph ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:56:57,739] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:56:57,739] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:56:58,784] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:56:59,236] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:56:59,236] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:56:59,845] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:57:00,796] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/NGS16004_C2_MZET160500A132A-soft_clip.bedgraph ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:57:40,092] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:57:40,108] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:57:40,123] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:57:40,576] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:57:40,576] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:57:40,981] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:57:42,401] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_G3_MZET160600A089A/NGS16004_G3_MZET160600A089A-soft_clip.bedgraph ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:58:30,948] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:58:30,948] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:58:30,963] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:58:31,556] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:58:31,572] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:58:32,321] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:58:33,553] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:59:06,921] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:59:06,921] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:59:06,937] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:59:07,249] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:59:07,249] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:59:07,545] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:59:08,902] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-soft_clip.bedgraph ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 11:59:37,949] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 11:59:37,965] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 11:59:37,965] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 11:59:38,542] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 11:59:38,542] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 11:59:39,307] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 11:59:39,525] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:00:19,523] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:00:19,523] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:00:19,539] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:00:19,897] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:00:19,897] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 12:00:20,849] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 12:00:21,099] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C10_MZET160500A050A/NGS16004_C10_MZET160500A050A-soft_clip.bedgraph ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:00:39,694] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:00:39,709] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:00:39,741] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:00:40,131] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:00:40,131] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 12:00:40,677] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 12:00:42,361] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-soft_clip.bedgraph ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:18:09,466] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:18:09,466] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:18:10,511] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:18:12,882] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:18:12,882] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 12:18:13,179] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: ZmpylD, INFO [2016-10-04 12:18:15,519] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 12:18:15,737] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-04 12:18:21,447] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 12:18:21,665] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:18:34,161] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:18:34,161] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:18:34,192] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:18:34,676] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:18:34,738] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 12:18:34,816] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 12:18:34,956] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:20:48,243] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:20:48,258] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:20:49,288] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:20:49,631] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:20:49,631] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 12:20:49,694] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 12:20:49,818] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-soft_clip.bedgraph ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:22:20,281] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:22:20,281] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:22:20,312] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:22:20,905] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:22:20,905] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 12:22:20,983] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 12:22:21,124] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-soft_clip.bedgraph ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:24:33,360] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:24:33,360] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:24:34,389] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:24:37,587] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:24:37,587] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 12:24:37,759] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 12:24:38,164] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-04 12:46:25,351] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa INFO [2016-10-04 12:46:25,585] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa ERROR [2016-10-04 12:46:37,519] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:46:37,519] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:46:37,519] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:46:37,519] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:46:37,519] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:46:37,519] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:46:37,535] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:46:37,535] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:46:37,535] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:46:38,564] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:46:38,876] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:46:38,876] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 12:46:38,923] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 12:46:39,095] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 12:58:03,549] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 12:58:03,580] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 12:58:03,580] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 12:58:04,579] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 12:58:04,735] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-04 12:58:05,078] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 12:58:05,078] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 12:58:05,140] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 12:58:05,249] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H7_Empty/NGS16004_H7_Empty-soft_clip.bedgraph ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 13:06:59,381] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 13:06:59,381] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 13:07:00,411] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 13:07:00,551] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-04 13:07:00,754] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 13:07:00,754] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 13:07:00,801] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 13:07:00,910] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_B12_MZET160500A164A/NGS16004_B12_MZET160500A164A-soft_clip.bedgraph ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 13:12:03,033] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 13:12:03,033] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 13:12:04,063] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 13:12:04,406] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 13:12:04,406] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 13:12:04,453] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 13:12:04,578] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_C7_MZET160500A086A/NGS16004_C7_MZET160500A086A-soft_clip.bedgraph ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 14:47:00,670] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 14:47:00,670] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 14:47:01,731] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:47:02,184] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 14:47:02,199] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 14:47:02,246] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP1,
Genome: ZmpylD, INFO [2016-10-04 14:47:07,266] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 14:47:07,375] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph INFO [2016-10-04 14:47:09,793] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 14:47:09,840] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 14:47:15,893] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 14:47:15,893] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 14:47:15,908] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:47:16,314] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 14:47:16,314] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 14:47:16,376] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 14:47:16,486] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 14:48:41,568] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 14:48:41,568] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 14:48:41,584] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:48:41,927] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 14:48:41,927] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 14:48:41,989] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 14:48:42,098] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-soft_clip.bedgraph ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 14:49:04,297] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 14:49:04,297] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 14:49:04,313] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 14:49:04,750] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 14:49:04,750] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 14:49:04,812] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 14:49:07,979] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-soft_clip.bedgraph ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 15:27:49,544] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 15:27:49,544] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 15:27:50,589] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 15:27:50,948] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 15:27:50,948] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 15:27:50,995] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 15:27:51,119] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_A01_USR01308292/NGS16011_VLHP1_A01_USR01308292-soft_clip.bedgraph ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 15:29:09,962] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 15:29:09,962] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 15:29:09,977] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 15:29:10,321] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 15:29:10,321] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 15:29:10,367] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 15:29:10,477] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-soft_clip.bedgraph ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 15:29:37,745] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 15:29:37,745] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 15:29:37,760] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 15:29:38,119] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 15:29:38,119] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 15:29:38,166] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 15:29:38,291] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_E02_USR01308490/NGS16011_VLHP1_E02_USR01308490-soft_clip.bedgraph ERROR [2016-10-04 16:15:52,235] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:15:52,235] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 16:15:52,235] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 16:15:52,250] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 16:15:52,250] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 16:15:52,250] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 16:15:52,250] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 16:15:52,250] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 16:15:52,250] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 16:15:53,296] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:15:57,367] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 16:15:57,367] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 16:16:01,860] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf ERROR [2016-10-04 16:16:23,372] [TrackLoader.java:256] Unable to parse header with error: connect timed out, for input source: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: connect timed out, for input source: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:231) at htsjdk.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:92) at htsjdk.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:103) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:89) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:92) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:297) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:381) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:217) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) Caused by: java.net.SocketTimeoutException: connect timed out at java.net.TwoStacksPlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) at java.net.AbstractPlainSocketImpl.connect(Unknown Source) at java.net.PlainSocketImpl.connect(Unknown Source) at java.net.SocksSocketImpl.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at sun.net.NetworkClient.doConnect(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.(Unknown Source) at sun.net.www.http.HttpClient.New(Unknown Source) at sun.net.www.http.HttpClient.New(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.HttpURLConnection.getResponseCode(Unknown Source) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:713) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:614) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:220) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:214) at org.broad.igv.util.stream.IGVUrlHelper.openInputStream(IGVUrlHelper.java:71) at htsjdk.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:85) at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:222) ... 21 more ERROR [2016-10-04 16:16:23,372] [IGVSessionReader.java:635] Error loading resource http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf org.broad.igv.exceptions.DataLoadException: Unable to parse header with error: connect timed out, for input source: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 16:16:23,372] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-soft_clip.bedgraph INFO [2016-10-04 16:16:27,288] [MessageUtils.java:74] Errors were encountered loading the session:
http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf
&nbs;p org.broad.igv.exceptions.DataLoadException: Unable to parse header with error: connect timed out, for input source: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf
INFO [2016-10-04 16:17:14,587] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-04 16:17:18,440] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/VLHP1_sub-sequence_2214-2587.fa ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 16:17:23,588] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 16:17:23,588] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 16:17:23,604] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:17:24,353] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 16:17:24,353] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 16:17:28,627] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 16:17:40,982] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_B05_USR01308326/NGS16011_VLHP1_B05_USR01308326-soft_clip.bedgraph ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 16:19:29,168] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 16:19:29,168] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 16:19:29,215] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:19:30,011] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 16:19:30,011] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-04 16:19:31,696] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-04 16:19:41,539] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1475439345/NGS16011_VLHP1_D03_USR01308465/NGS16011_VLHP1_D03_USR01308465-soft_clip.bedgraph ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 16:24:01,607] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 16:24:01,607] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 16:24:02,652] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:24:02,933] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-04 16:24:03,713] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 16:24:03,713] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 16:24:04,352] [MessageUtils.java:74] File: http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam
does not contain any sequence names which match the current genome.

File:      ZmpylD,
Genome: VLHP1, INFO [2016-10-04 16:24:22,745] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 16:24:26,286] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa INFO [2016-10-04 16:24:26,458] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph INFO [2016-10-04 16:24:27,534] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475418626/NGS16004_H3_MZET152401B011A/ZmpylD.w_AR.fa INFO [2016-10-04 16:24:29,156] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa INFO [2016-10-04 16:24:30,217] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475330633/NGS16004_B1_MZET160411A007A/ZmpylD.fa ERROR [2016-10-04 16:24:38,080] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:24:38,080] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-04 16:24:38,080] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-04 16:24:38,080] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-04 16:24:38,080] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-04 16:24:38,095] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-04 16:24:38,095] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-04 16:24:38,095] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-04 16:24:38,095] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-04 16:24:38,111] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-04 16:24:41,777] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-04 16:24:41,777] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-04 16:24:42,775] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-04 16:24:49,109] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475485995/NGS16004_H3_MZET152401B011A/NGS16004_H3_MZET152401B011A-soft_clip.bedgraph INFO [2016-10-05 14:57:45,908] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-05 14:57:45,971] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1475431623/NGS16011_VLHP1_A03_USR01308296/VLHP1_sub-sequence_2214-2587.fa INFO [2016-10-05 14:57:57,546] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474415952/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 14:57:57,842] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 14:57:57,842] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam INFO [2016-10-05 14:57:57,936] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP1_sub-sequence_2214-2587.sort.bam.mod.vcf INFO [2016-10-05 14:57:58,076] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474415952/NGS16011_VLHP1_G06_USR01308654/NGS16011_VLHP1_G06_USR01308654-soft_clip.bedgraph INFO [2016-10-05 15:01:07,615] [GenomeManager.java:145] Loading genome: -1 read1 fastq -2 read2 fastq -r reference fasta -p project ID -s sample ID -d number of trimmed, filtered reads to sample (default=10000 if -1 do not sample) Advanced Options: -f minimum variant frequency (default=25); -a minimum coverage depth (default=40) -b maximum soft-clipping percentage (default=10) -g filter reads minimum percent of bases that must have [-e] quality (default=100) -e trim reads minimum quality score (default=20) -i trim reads minimum length (default=75) -j paired end alignment minimum insert size (default=0) -k paired end alignment maximum insert size (default=700) -l variant calling minimum base quality at a position to count a read (default=10) -m variant calling minimum read depth at a position to make a call (default=1) -n variant calling minimum supporting reads at a position to call variants (default=1) -o ignore soft-clipping occuring N bases from reference termini (default=3) -q alignment info minimum mapping quality of reads used for counting (default=0) -t alignment info minimum base quality at a position to use the read for counting(default=0) -u alignment info maximum percent non-reference base (default=30) -v alignment info maximum percent strand bias (default=90) -w alignment info minimum average reference base quality (default=15) -x anchored coverage minimum mapping quality (default=10) -y output report -z log INFO [2016-10-05 15:01:07,646] [FastaUtils.java:65] Creating index file at C:\Users\rosema1\IGV_2.3.78_jre\-1 read1 fastq -2 read2 fastq -r reference fasta -p project ID -s sample ID -d number of trimmed, filtered reads to sample (default=10000 if -1 do not sample) Advanced Options: -f minimum variant frequency (default=25); -a minimum coverage depth (default=40) -b maximum soft-clipping percentage (default=10) -g filter reads minimum percent of bases that must have [-e] quality (default=100) -e trim reads minimum quality score (default=20) -i trim reads minimum length (default=75) -j paired end alignment minimum insert size (default=0) -k paired end alignment maximum insert size (default=700) -l variant calling minimum base quality at a position to count a read (default=10) -m variant calling minimum read depth at a position to make a call (default=1) -n variant calling minimum supporting reads at a position to call variants (default=1) -o ignore soft-clipping occuring N bases from reference termini (default=3) -q alignment info minimum mapping quality of reads used for counting (default=0) -t alignment info minimum base quality at a position to use the read for counting(default=0) -u alignment info maximum percent non-reference base (default=30) -v alignment info maximum percent strand bias (default=90) -w alignment info minimum average reference base quality (default=15) -x anchored coverage minimum mapping quality (default=10) -y output report -z log.fai INFO [2016-10-05 15:01:07,646] [MessageUtils.java:74] Error loading genome: C:\Users\rosema1\IGV_2.3.78_jre\-1 read1 fastq -2 read2 fastq -r reference fasta -p project ID -s sample ID -d number of trimmed, filtered reads to sample (default=10000 if -1 do not sample) Advanced Options: -f minimum variant frequency (default=25); -a minimum coverage depth (default=40) -b maximum soft-clipping percentage (default=10) -g filter reads minimum percent of bases that must have [-e] quality (default=100) -e trim reads minimum quality score (default=20) -i trim reads minimum length (default=75) -j paired end alignment minimum insert size (default=0) -k paired end alignment maximum insert size (default=700) -l variant calling minimum base quality at a position to count a read (default=10) -m variant calling minimum read depth at a position to make a call (default=1) -n variant calling minimum supporting reads at a position to call variants (default=1) -o ignore soft-clipping occuring N bases from reference termini (default=3) -q alignment info minimum mapping quality of reads used for counting (default=0) -t alignment info minimum base quality at a position to use the read for counting(default=0) -u alignment info maximum percent non-reference base (default=30) -v alignment info maximum percent strand bias (default=90) -w alignment info minimum average reference base quality (default=15) -x anchored coverage minimum mapping quality (default=10) -y output report -z log (The system cannot find the file specified) INFO [2016-10-05 15:01:40,671] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-05 15:01:40,702] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/VLHP2_sub-sequence_2182-2586.fa ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/NGS16013_VLHP2_C02_USR01308599-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:01:45,102] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:01:45,102] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:01:46,162] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/NGS16013_VLHP2_C02_USR01308599-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:01:46,615] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:01:46,615] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/NGS16013_VLHP2_C02_USR01308599.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-05 15:01:46,693] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/NGS16013_VLHP2_C02_USR01308599.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-05 15:01:46,786] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/NGS16013_VLHP2_C02_USR01308599-soft_clip.bedgraph ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1474390324/NGS16013_VLHP2_C09_USR01308693/NGS16013_VLHP2_C09_USR01308693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:02:26,426] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:02:26,426] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:02:26,441] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1474390324/NGS16013_VLHP2_C09_USR01308693/NGS16013_VLHP2_C09_USR01308693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:02:26,894] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:02:26,894] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C09_USR01308693/NGS16013_VLHP2_C09_USR01308693.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-05 15:02:26,941] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C09_USR01308693/NGS16013_VLHP2_C09_USR01308693.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-05 15:02:27,081] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C09_USR01308693/NGS16013_VLHP2_C09_USR01308693-soft_clip.bedgraph ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:03:57,046] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:03:57,046] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:03:57,061] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:03:57,560] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:03:57,560] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-05 15:03:57,592] [MessageUtils.java:74] File: http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP2,
Genome: VLHP2_sub-sequence_2182-2586, INFO [2016-10-05 15:03:59,058] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-05 15:03:59,198] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654-soft_clip.bedgraph INFO [2016-10-05 15:04:31,677] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-05 15:04:31,709] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:04:38,261] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:04:38,261] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:04:38,276] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:04:38,697] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:04:38,697] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-05 15:04:38,760] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-05 15:04:39,197] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/NGS16012_VLHP2_G06_USR01308654-soft_clip.bedgraph ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_H12_WT/NGS16012_VLHP2_H12_WT-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:05:13,610] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:05:13,610] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:05:13,625] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_H12_WT/NGS16012_VLHP2_H12_WT-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:05:14,047] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:05:14,047] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_H12_WT/NGS16012_VLHP2_H12_WT.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-05 15:05:14,109] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_H12_WT/NGS16012_VLHP2_H12_WT.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-05 15:05:14,218] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_H12_WT/NGS16012_VLHP2_H12_WT-soft_clip.bedgraph ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_D12_Empty/NGS16012_VLHP2_D12_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:05:52,329] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:05:52,329] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:05:52,344] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474476719/NGS16012_VLHP2_D12_Empty/NGS16012_VLHP2_D12_Empty-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:05:52,766] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:05:52,766] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_D12_Empty/NGS16012_VLHP2_D12_Empty.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-05 15:05:52,828] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_D12_Empty/NGS16012_VLHP2_D12_Empty.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-05 15:05:52,953] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_D12_Empty/NGS16012_VLHP2_D12_Empty-soft_clip.bedgraph INFO [2016-10-05 15:09:30,649] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa INFO [2016-10-05 15:09:30,696] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2459/delivered/1474408060/NGS16010_GW2-1_D08_USR01308800/NGS16010_GW2-1_D08_USR01308800-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-05 15:09:34,924] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-05 15:09:34,924] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-05 15:09:35,953] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2459/delivered/1474408060/NGS16010_GW2-1_D08_USR01308800/NGS16010_GW2-1_D08_USR01308800-igv_session_file.xml HTTP/1.1 ERROR [2016-10-05 15:09:36,328] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-05 15:09:36,328] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D08_USR01308800/NGS16010_GW2-1_D08_USR01308800.extendedFrags.mod.fastq-vs-GW2-1_sub-sequence_1836-2240.sort.bam INFO [2016-10-05 15:09:36,390] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D08_USR01308800/NGS16010_GW2-1_D08_USR01308800.extendedFrags.mod.fastq-vs-GW2-1_sub-sequence_1836-2240.sort.bam.mod.vcf INFO [2016-10-05 15:09:36,531] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D08_USR01308800/NGS16010_GW2-1_D08_USR01308800-soft_clip.bedgraph INFO [2016-10-09 17:55:14,599] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-09 17:55:14,599] [Main.java:100] Java 1.8.0_91 INFO [2016-10-09 17:55:14,599] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-09 17:55:14,599] [Main.java:102] OS: Windows 7 INFO [2016-10-09 17:55:15,969] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-09 17:55:32,913] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa INFO [2016-10-09 17:55:32,993] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474408060/NGS16010_GW2-1_D02_USR01308759/GW2-1_sub-sequence_1836-2240.fa ERROR [2016-10-09 17:55:33,173] [CommandListener.java:124] java.net.BindException: Address already in use: JVM_Bind INFO [2016-10-09 17:55:33,243] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-09 17:55:38,625] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa INFO [2016-10-09 17:55:38,665] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa INFO [2016-10-09 17:55:47,365] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:55:47,665] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-09 17:55:47,805] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-09 17:55:47,805] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-09 17:55:47,865] [MessageUtils.java:74] File: http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam
does not contain any sequence names which match the current genome.

File:      ZmpylD,
Genome: GW2-1, INFO [2016-10-09 17:55:53,695] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-09 17:55:53,855] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A-soft_clip.bedgraph INFO [2016-10-09 17:56:24,628] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/ZmpylD.fa INFO [2016-10-09 17:56:24,668] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/ZmpylD.fa ERROR [2016-10-09 17:57:53,781] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:57:53,781] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-09 17:57:53,781] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-09 17:57:53,781] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-09 17:57:53,781] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-09 17:57:53,781] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-09 17:57:53,791] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-09 17:57:53,791] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-09 17:57:53,791] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-09 17:57:53,801] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:57:54,121] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-09 17:57:54,121] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-09 17:57:54,171] [MessageUtils.java:74] File: http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam
does not contain any sequence names which match the current genome.

File:      ZmpylD,
Genome: GW2-1, INFO [2016-10-09 17:58:14,781] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-09 17:58:14,901] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-soft_clip.bedgraph INFO [2016-10-09 17:58:23,333] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa INFO [2016-10-09 17:58:23,373] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa ERROR [2016-10-09 17:58:39,663] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:58:39,663] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-09 17:58:39,663] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-09 17:58:39,663] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-09 17:58:39,663] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-09 17:58:39,663] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-09 17:58:39,673] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-09 17:58:39,673] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-09 17:58:39,673] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-09 17:58:39,683] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:58:40,023] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-09 17:58:40,023] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-09 17:58:40,073] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-09 17:58:40,183] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-soft_clip.bedgraph ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-09 17:59:01,083] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-09 17:59:01,093] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-09 17:59:01,093] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-09 17:59:01,093] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-09 17:59:01,445] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-09 17:59:01,455] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-09 17:59:01,505] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-09 17:59:01,625] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G12_MZET161101A075A/NGS16009_ZmpylD_G12_MZET161101A075A-soft_clip.bedgraph INFO [2016-10-09 17:59:06,247] [ShutdownThread.java:51] Shutting down INFO [2016-10-10 08:29:13,472] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 08:29:13,702] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 08:31:11,015] [ShutdownThread.java:51] Shutting down INFO [2016-10-10 08:35:18,366] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-10 08:35:18,366] [Main.java:100] Java 1.8.0_91 INFO [2016-10-10 08:35:18,366] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-10 08:35:18,366] [Main.java:102] OS: Windows 7 INFO [2016-10-10 08:35:20,352] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-10 08:35:35,710] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 08:35:35,757] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 08:35:35,929] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-10 08:35:35,992] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-10 08:36:18,247] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 08:36:18,294] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/VLHP2_sub-sequence_2182-2586.fa ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 08:36:26,940] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 08:36:26,956] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 08:36:28,004] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:36:28,269] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 08:36:28,269] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 08:36:28,551] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 08:36:28,754] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-soft_clip.bedgraph ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 08:40:01,106] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 08:40:01,106] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 08:40:02,152] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:40:02,480] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 08:40:02,480] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 08:40:02,543] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 08:40:02,652] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A-soft_clip.bedgraph ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 08:45:22,325] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 08:45:22,341] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 08:45:23,370] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:45:23,620] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-10 08:45:23,807] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 08:45:23,807] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 08:45:23,854] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 08:45:23,979] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A-soft_clip.bedgraph ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A4_MZET160602C115A/NGS16007_VLHP2_A4_MZET160602C115A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 08:46:09,560] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 08:46:09,560] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 08:46:09,576] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A4_MZET160602C115A/NGS16007_VLHP2_A4_MZET160602C115A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:46:09,919] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 08:46:09,919] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A4_MZET160602C115A/NGS16007_VLHP2_A4_MZET160602C115A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 08:46:09,966] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A4_MZET160602C115A/NGS16007_VLHP2_A4_MZET160602C115A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 08:46:10,091] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A4_MZET160602C115A/NGS16007_VLHP2_A4_MZET160602C115A-soft_clip.bedgraph ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A5_MZET154903A008A/NGS16007_VLHP2_A5_MZET154903A008A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 08:52:29,951] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 08:52:29,967] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 08:52:30,997] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A5_MZET154903A008A/NGS16007_VLHP2_A5_MZET154903A008A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:52:31,168] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-10 08:52:31,309] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 08:52:31,309] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A5_MZET154903A008A/NGS16007_VLHP2_A5_MZET154903A008A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 08:52:31,355] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A5_MZET154903A008A/NGS16007_VLHP2_A5_MZET154903A008A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 08:52:31,480] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A5_MZET154903A008A/NGS16007_VLHP2_A5_MZET154903A008A-soft_clip.bedgraph ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 08:58:29,370] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 08:58:29,370] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 08:58:30,399] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 08:58:31,008] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 08:58:31,008] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 08:58:31,070] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 08:58:31,179] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-soft_clip.bedgraph ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:04:51,240] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:04:51,255] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:04:51,255] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:04:52,269] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:04:52,566] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:04:52,566] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:04:52,612] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:04:52,737] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-soft_clip.bedgraph ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:05:12,409] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:05:12,409] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:05:12,424] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:05:12,736] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:05:12,736] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:05:12,783] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:05:12,892] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A-soft_clip.bedgraph ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B5_MZET154903A009A/NGS16007_VLHP2_B5_MZET154903A009A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:05:52,095] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:05:52,095] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:05:52,110] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B5_MZET154903A009A/NGS16007_VLHP2_B5_MZET154903A009A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:05:52,500] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:05:52,500] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B5_MZET154903A009A/NGS16007_VLHP2_B5_MZET154903A009A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:05:52,563] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B5_MZET154903A009A/NGS16007_VLHP2_B5_MZET154903A009A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:05:52,688] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B5_MZET154903A009A/NGS16007_VLHP2_B5_MZET154903A009A-soft_clip.bedgraph ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B7_MZET160602B068A/NGS16007_VLHP2_B7_MZET160602B068A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:06:18,942] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:06:18,942] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:06:18,958] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B7_MZET160602B068A/NGS16007_VLHP2_B7_MZET160602B068A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:06:19,317] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:06:19,317] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B7_MZET160602B068A/NGS16007_VLHP2_B7_MZET160602B068A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:06:19,379] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B7_MZET160602B068A/NGS16007_VLHP2_B7_MZET160602B068A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:06:19,535] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B7_MZET160602B068A/NGS16007_VLHP2_B7_MZET160602B068A-soft_clip.bedgraph ERROR [2016-10-10 09:07:24,275] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B10_MZET160605C031A/NGS16007_VLHP2_B10_MZET160605C031A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:07:24,275] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:07:24,290] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:07:24,290] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:07:24,290] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:07:24,290] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:07:24,290] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:07:24,290] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:07:24,290] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:07:24,290] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B10_MZET160605C031A/NGS16007_VLHP2_B10_MZET160605C031A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:07:24,587] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:07:24,587] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B10_MZET160605C031A/NGS16007_VLHP2_B10_MZET160605C031A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:07:24,649] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B10_MZET160605C031A/NGS16007_VLHP2_B10_MZET160605C031A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:07:24,774] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B10_MZET160605C031A/NGS16007_VLHP2_B10_MZET160605C031A-soft_clip.bedgraph ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:08:23,336] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:08:23,352] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:08:23,352] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:08:23,508] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-10 09:08:23,742] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:08:23,742] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:08:23,789] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:08:23,929] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-soft_clip.bedgraph ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:08:31,823] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:08:31,823] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:08:31,870] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:08:32,306] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:08:32,306] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:08:32,369] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:08:32,494] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-soft_clip.bedgraph ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:09:49,822] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:09:49,822] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:09:49,853] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:09:50,399] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:09:50,399] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:09:50,446] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:09:50,602] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-soft_clip.bedgraph ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C12_MZET160605A134A/NGS16007_VLHP2_C12_MZET160605A134A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:13:39,841] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:13:39,841] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:13:40,902] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C12_MZET160605A134A/NGS16007_VLHP2_C12_MZET160605A134A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:13:41,261] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:13:41,261] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C12_MZET160605A134A/NGS16007_VLHP2_C12_MZET160605A134A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:13:41,323] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C12_MZET160605A134A/NGS16007_VLHP2_C12_MZET160605A134A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:13:41,432] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C12_MZET160605A134A/NGS16007_VLHP2_C12_MZET160605A134A-soft_clip.bedgraph ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:18:48,627] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:18:48,627] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:18:49,657] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:18:50,078] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:18:50,078] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:18:50,141] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:18:50,250] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B4_MZET160602A035A/NGS16007_VLHP2_B4_MZET160602A035A-soft_clip.bedgraph ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:23:00,876] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:23:00,876] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:23:01,921] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:23:02,295] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:23:02,295] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:23:02,358] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:23:02,467] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A-soft_clip.bedgraph ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D6_MZET160605A054A/NGS16007_VLHP2_D6_MZET160605A054A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:25:35,831] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:25:35,831] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:25:35,846] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D6_MZET160605A054A/NGS16007_VLHP2_D6_MZET160605A054A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:25:36,423] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:25:36,423] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D6_MZET160605A054A/NGS16007_VLHP2_D6_MZET160605A054A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:25:36,486] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D6_MZET160605A054A/NGS16007_VLHP2_D6_MZET160605A054A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:25:36,595] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D6_MZET160605A054A/NGS16007_VLHP2_D6_MZET160605A054A-soft_clip.bedgraph ERROR [2016-10-10 09:27:23,172] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D11_MZET154903A013A/NGS16007_VLHP2_D11_MZET154903A013A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:27:23,172] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:27:23,172] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:27:23,172] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:27:23,188] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:27:23,188] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:27:23,188] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:27:23,188] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:27:23,188] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:27:23,188] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D11_MZET154903A013A/NGS16007_VLHP2_D11_MZET154903A013A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:27:23,734] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:27:23,734] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D11_MZET154903A013A/NGS16007_VLHP2_D11_MZET154903A013A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:27:23,781] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D11_MZET154903A013A/NGS16007_VLHP2_D11_MZET154903A013A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:27:23,890] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D11_MZET154903A013A/NGS16007_VLHP2_D11_MZET154903A013A-soft_clip.bedgraph ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:28:12,420] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:28:12,451] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:28:12,451] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:28:12,841] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:28:12,841] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 09:28:12,904] [MessageUtils.java:74] File: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam
does not contain any sequence names which match the current genome.

File:      GW2-2,
Genome: VLHP2, INFO [2016-10-10 09:28:15,041] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 09:28:15,166] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-soft_clip.bedgraph INFO [2016-10-10 09:28:46,365] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa INFO [2016-10-10 09:28:46,412] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:28:54,477] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:28:54,477] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:28:54,492] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:28:54,851] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:28:54,851] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 09:28:54,898] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 09:28:55,007] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-soft_clip.bedgraph ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E2_MZET160603B013A/NGS16007_GW2-2_E2_MZET160603B013A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:29:37,485] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:29:37,485] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:29:37,516] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E2_MZET160603B013A/NGS16007_GW2-2_E2_MZET160603B013A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:29:37,812] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:29:37,812] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E2_MZET160603B013A/NGS16007_GW2-2_E2_MZET160603B013A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 09:29:37,875] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E2_MZET160603B013A/NGS16007_GW2-2_E2_MZET160603B013A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 09:29:37,968] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E2_MZET160603B013A/NGS16007_GW2-2_E2_MZET160603B013A-soft_clip.bedgraph ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:29:57,889] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:29:57,889] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:29:57,905] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:29:58,341] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:29:58,341] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 09:29:58,388] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 09:29:58,513] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-soft_clip.bedgraph ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:31:38,351] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:31:38,351] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:31:38,366] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:31:38,678] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:31:38,678] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 09:31:38,725] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 09:31:38,834] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-soft_clip.bedgraph ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:42:32,697] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:42:32,697] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:42:33,742] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:42:34,147] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:42:34,147] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 09:42:34,210] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 09:42:34,319] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-soft_clip.bedgraph INFO [2016-10-10 09:47:31,892] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 09:47:31,923] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/VLHP2_sub-sequence_2182-2586.fa ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:47:40,549] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:47:40,549] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:47:41,595] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:47:42,016] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:47:42,016] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:47:42,063] [MessageUtils.java:74] File: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam
does not contain any sequence names which match the current genome.

File:      VLHP2,
Genome: VLHP2_sub-sequence_2182-2586, INFO [2016-10-10 09:47:43,966] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:47:44,122] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-soft_clip.bedgraph INFO [2016-10-10 09:47:48,536] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 09:47:48,568] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 09:47:55,900] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 09:47:55,900] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 09:47:55,915] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 09:47:56,243] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 09:47:56,243] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 09:47:56,289] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 09:47:56,414] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-soft_clip.bedgraph ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 10:15:35,246] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 10:15:35,246] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 10:15:36,260] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:15:36,479] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-10 10:15:36,713] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 10:15:36,713] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 10:15:36,744] [MessageUtils.java:74] File: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam
does not contain any sequence names which match the current genome.

File:      GW2-2,
Genome: VLHP2, INFO [2016-10-10 10:15:44,045] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 10:15:44,170] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-soft_clip.bedgraph INFO [2016-10-10 10:15:47,633] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa INFO [2016-10-10 10:15:47,679] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 10:16:21,843] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 10:16:21,843] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 10:16:21,874] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:16:22,296] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 10:16:22,296] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 10:16:22,358] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 10:16:22,483] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-soft_clip.bedgraph ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E7_MZET160603A008A/NGS16007_GW2-2_E7_MZET160603A008A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 10:20:44,323] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 10:20:44,323] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 10:20:45,368] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E7_MZET160603A008A/NGS16007_GW2-2_E7_MZET160603A008A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:20:45,742] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 10:20:45,742] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E7_MZET160603A008A/NGS16007_GW2-2_E7_MZET160603A008A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 10:20:45,789] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E7_MZET160603A008A/NGS16007_GW2-2_E7_MZET160603A008A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 10:20:45,914] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E7_MZET160603A008A/NGS16007_GW2-2_E7_MZET160603A008A-soft_clip.bedgraph INFO [2016-10-10 10:38:25,140] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 10:38:28,198] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1474390324/NGS16013_VLHP2_C02_USR01308599/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 10:38:30,132] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-10 10:38:30,163] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D4_MZET160605A057A/NGS16007_VLHP2_D4_MZET160605A057A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 10:38:47,198] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 10:38:47,198] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 10:38:48,243] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D4_MZET160605A057A/NGS16007_VLHP2_D4_MZET160605A057A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:38:48,602] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 10:38:48,602] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D4_MZET160605A057A/NGS16007_VLHP2_D4_MZET160605A057A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 10:38:48,648] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D4_MZET160605A057A/NGS16007_VLHP2_D4_MZET160605A057A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 10:38:48,789] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D4_MZET160605A057A/NGS16007_VLHP2_D4_MZET160605A057A-soft_clip.bedgraph ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 10:39:17,039] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 10:39:17,039] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 10:39:17,054] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 10:39:17,257] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 10:39:17,257] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-10 10:39:17,320] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-10 10:39:17,429] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A-soft_clip.bedgraph INFO [2016-10-10 12:52:10,186] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa INFO [2016-10-10 12:52:10,233] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 12:52:17,674] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 12:52:17,674] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 12:52:18,735] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 12:52:19,172] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 12:52:19,172] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 12:52:19,250] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 12:52:19,375] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-soft_clip.bedgraph INFO [2016-10-10 13:06:36,651] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/GW2-2_sub-sequence_1909-2304.fa INFO [2016-10-10 13:06:36,697] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/GW2-2_sub-sequence_1909-2304.fa ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 13:06:48,070] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 13:06:48,070] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 13:06:49,099] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 13:06:49,396] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 13:06:49,396] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 13:06:49,474] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 13:06:49,583] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E5_MZET160603B004A/NGS16007_GW2-2_E5_MZET160603B004A-soft_clip.bedgraph ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 13:08:10,328] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 13:08:10,328] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 13:08:10,343] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 13:08:10,546] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-10 13:08:10,811] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 13:08:10,811] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-10 13:08:10,873] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-10 13:08:10,983] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E4_MZET160603B011A/NGS16007_GW2-2_E4_MZET160603B011A-soft_clip.bedgraph INFO [2016-10-10 15:35:29,510] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa INFO [2016-10-10 15:35:29,557] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1475485995/NGS16004_C2_MZET160500A132A/ZmpylD.fa ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-10 15:35:38,199] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-10 15:35:38,199] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-10 15:35:39,244] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-10 15:35:39,447] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-10 15:35:39,447] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-10-10 15:35:39,494] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-10-10 15:35:39,619] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2458/delivered/1475724535/NGS16009_ZmpylD_G7_MZET161501B080A/NGS16009_ZmpylD_G7_MZET161501B080A-soft_clip.bedgraph INFO [2016-10-11 12:07:48,638] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-11 12:07:48,684] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-11 12:07:58,478] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-11 12:07:58,478] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 12:07:59,524] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 12:07:59,946] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-11 12:07:59,946] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam INFO [2016-10-11 12:08:00,024] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam.vcf INFO [2016-10-11 12:08:00,134] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-zero_coverage_gaps.bedgraph INFO [2016-10-11 12:08:00,180] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 12:08:00,212] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-soft_clipping.bedgraph INFO [2016-10-11 12:08:00,243] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-non-ref_freq.bedgraph INFO [2016-10-11 12:08:00,337] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-strand_bias.bedgraph INFO [2016-10-11 12:08:00,415] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-avg-ref-basequality.bedgraph INFO [2016-10-11 12:08:00,493] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-inverse-avg-ref-basequality.bedgraph INFO [2016-10-11 14:10:42,005] [ShutdownThread.java:51] Shutting down INFO [2016-10-11 14:21:15,860] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-11 14:21:15,860] [Main.java:100] Java 1.8.0_91 INFO [2016-10-11 14:21:15,860] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-11 14:21:15,860] [Main.java:102] OS: Windows 7 INFO [2016-10-11 14:21:19,056] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-11 14:21:34,347] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-11 14:21:34,409] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-11 14:21:34,596] [CommandListener.java:106] Listening on port 60151 ERROR [2016-10-11 14:21:38,961] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 14:21:38,961] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-11 14:21:38,961] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-11 14:21:38,961] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-11 14:21:38,961] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-11 14:21:38,961] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-11 14:21:38,977] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-11 14:21:38,977] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-11 14:21:38,977] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 14:21:40,005] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 14:21:40,504] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-11 14:21:40,504] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam INFO [2016-10-11 14:21:40,567] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-11 14:21:40,831] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam.vcf INFO [2016-10-11 14:21:41,330] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-zero_coverage_gaps.bedgraph INFO [2016-10-11 14:21:41,408] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 14:21:41,471] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-soft_clipping.bedgraph INFO [2016-10-11 14:21:41,502] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-non-ref_freq.bedgraph INFO [2016-10-11 14:21:41,595] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-strand_bias.bedgraph INFO [2016-10-11 14:21:41,658] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-avg-ref-basequality.bedgraph INFO [2016-10-11 14:21:41,751] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-inverse-avg-ref-basequality.bedgraph INFO [2016-10-11 14:40:03,869] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733/baseclear_GA21_ref_mut1.fa INFO [2016-10-11 14:40:03,916] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733/baseclear_GA21_ref_mut1.fa ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733/mut1-1476210733-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-11 14:40:13,915] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-11 14:40:13,915] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 14:40:14,960] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733/mut1-1476210733-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 14:40:15,522] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-11 14:40:15,522] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-bowtie2.bam.sort.bam INFO [2016-10-11 14:40:15,584] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-bowtie2.bam.sort.bam.vcf INFO [2016-10-11 14:40:15,756] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-zero_coverage_gaps.bedgraph INFO [2016-10-11 14:40:15,803] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 14:40:15,865] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph ERROR [2016-10-11 14:40:15,881] [HttpUtils.java:312] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:739) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:276) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:291) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:305) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.util.ParsingUtils.estimateLineCount(ParsingUtils.java:262) at org.broad.igv.data.WiggleParser.estArraySize(WiggleParser.java:124) at org.broad.igv.data.WiggleParser.(WiggleParser.java:105) at org.broad.igv.track.TrackLoader.loadWigFile(TrackLoader.java:634) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:179) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) ERROR [2016-10-11 14:40:15,896] [TrackLoader.java:256] java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph java.lang.RuntimeException: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph at org.broad.igv.data.WiggleParser.parseFile(WiggleParser.java:333) at org.broad.igv.data.WiggleParser.parse(WiggleParser.java:143) at org.broad.igv.track.TrackLoader.loadWigFile(TrackLoader.java:634) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:179) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) Caused by: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:739) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:614) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:220) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:214) at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:111) at org.broad.igv.util.ParsingUtils.openAsciiReader(ParsingUtils.java:90) at org.broad.igv.data.WiggleParser.parseFile(WiggleParser.java:159) ... 16 more ERROR [2016-10-11 14:40:15,896] [IGVSessionReader.java:635] Error loading resource http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph org.broad.igv.exceptions.DataLoadException: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 14:40:15,896] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph ERROR [2016-10-11 14:40:15,912] [HttpUtils.java:312] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:739) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:276) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:291) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:305) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.util.ParsingUtils.estimateLineCount(ParsingUtils.java:262) at org.broad.igv.data.WiggleParser.estArraySize(WiggleParser.java:124) at org.broad.igv.data.WiggleParser.(WiggleParser.java:105) at org.broad.igv.track.TrackLoader.loadWigFile(TrackLoader.java:634) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:179) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) ERROR [2016-10-11 14:40:15,928] [TrackLoader.java:256] java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph java.lang.RuntimeException: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph at org.broad.igv.data.WiggleParser.parseFile(WiggleParser.java:333) at org.broad.igv.data.WiggleParser.parse(WiggleParser.java:143) at org.broad.igv.track.TrackLoader.loadWigFile(TrackLoader.java:634) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:179) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) Caused by: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:739) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:614) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:220) at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:214) at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:111) at org.broad.igv.util.ParsingUtils.openAsciiReader(ParsingUtils.java:90) at org.broad.igv.data.WiggleParser.parseFile(WiggleParser.java:159) ... 16 more ERROR [2016-10-11 14:40:15,928] [IGVSessionReader.java:635] Error loading resource http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph org.broad.igv.exceptions.DataLoadException: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258) at org.broad.igv.ui.IGV.load(IGV.java:1808) at org.broad.igv.session.IGVSessionReader$1.run(IGVSessionReader.java:609) at org.broad.igv.session.IGVSessionReader.processResources(IGVSessionReader.java:669) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:527) at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1254) at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:471) at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324) at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473) at org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:563) at org.broad.igv.batch.CommandListener.processGet(CommandListener.java:361) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:201) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 14:40:15,928] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-soft_clipping.bedgraph INFO [2016-10-11 14:40:15,959] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-non-ref_freq.bedgraph INFO [2016-10-11 14:40:16,084] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-strand_bias.bedgraph INFO [2016-10-11 14:40:16,208] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-avg-ref-basequality.bedgraph INFO [2016-10-11 14:40:16,349] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//mut1-1476210733-inverse-avg-ref-basequality.bedgraph INFO [2016-10-11 14:40:16,505] [MessageUtils.java:74] Errors were encountered loading the session:
http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph
&nbs;p org.broad.igv.exceptions.DataLoadException: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-zero_coverage_gaps.bedgraph
http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph
&nbs;p org.broad.igv.exceptions.DataLoadException: java.io.FileNotFoundException: File not found: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476210733//anchored-mut1-1476210733-below_threshold_coverage_gaps.bedgraph
ERROR [2016-10-11 15:00:52,672] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993/mut1-1476211993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 15:00:52,672] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-11 15:00:52,672] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-11 15:00:52,672] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-11 15:00:52,672] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-11 15:00:52,672] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-11 15:00:52,687] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-11 15:00:52,687] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-11 15:00:52,687] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 15:00:52,687] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993/mut1-1476211993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 15:00:53,140] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-11 15:00:53,140] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-bowtie2.bam.sort.bam INFO [2016-10-11 15:00:53,264] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-bowtie2.bam.sort.bam.vcf INFO [2016-10-11 15:00:53,483] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-zero_coverage_gaps.bedgraph INFO [2016-10-11 15:00:53,514] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 15:00:53,576] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//anchored-mut1-1476211993-zero_coverage_gaps.bedgraph INFO [2016-10-11 15:00:53,608] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//anchored-mut1-1476211993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 15:00:53,670] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-soft_clipping.bedgraph INFO [2016-10-11 15:00:53,717] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-non-ref_freq.bedgraph INFO [2016-10-11 15:00:53,842] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-strand_bias.bedgraph INFO [2016-10-11 15:00:53,966] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-avg-ref-basequality.bedgraph INFO [2016-10-11 15:01:03,139] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476211993//mut1-1476211993-inverse-avg-ref-basequality.bedgraph INFO [2016-10-11 15:14:06,004] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-11 15:14:06,051] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980/mir162-1476212980-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-11 15:14:23,445] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-11 15:14:23,445] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-11 15:14:24,490] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980/mir162-1476212980-igv_session_file.xml HTTP/1.1 ERROR [2016-10-11 15:14:24,849] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-11 15:14:24,849] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-bowtie2.bam.sort.bam INFO [2016-10-11 15:14:24,942] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-bowtie2.bam.sort.bam.vcf INFO [2016-10-11 15:14:25,098] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-zero_coverage_gaps.bedgraph INFO [2016-10-11 15:14:25,145] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 15:14:25,192] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//anchored-mir162-1476212980-zero_coverage_gaps.bedgraph INFO [2016-10-11 15:14:25,239] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//anchored-mir162-1476212980-below_threshold_coverage_gaps.bedgraph INFO [2016-10-11 15:14:25,270] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-soft_clipping.bedgraph INFO [2016-10-11 15:14:25,317] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-non-ref_freq.bedgraph INFO [2016-10-11 15:14:25,426] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-strand_bias.bedgraph INFO [2016-10-11 15:14:25,520] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-avg-ref-basequality.bedgraph INFO [2016-10-11 15:14:25,598] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476212980//mir162-1476212980-inverse-avg-ref-basequality.bedgraph INFO [2016-10-11 17:06:45,743] [ShutdownThread.java:51] Shutting down INFO [2016-10-14 13:44:34,359] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-14 13:44:34,360] [Main.java:100] Java 1.8.0_91 INFO [2016-10-14 13:44:34,360] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-14 13:44:34,361] [Main.java:102] OS: Windows 7 INFO [2016-10-14 13:44:37,363] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-14 13:44:54,164] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-14 13:44:54,225] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-14 13:44:54,405] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-14 13:45:02,370] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-14 13:45:02,431] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2459/delivered/1474476719/NGS16012_VLHP2_G06_USR01308654/VLHP2_sub-sequence_2182-2586.fa INFO [2016-10-14 13:45:02,462] [HttpUtils.java:827] Range-byte request succeeded ERROR [2016-10-14 13:45:12,143] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 13:45:12,145] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 13:45:12,148] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 13:45:12,149] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 13:45:12,151] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 13:45:12,152] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 13:45:12,153] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 13:45:12,154] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 13:45:12,156] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 13:45:13,177] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 13:45:13,679] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 13:45:13,681] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 13:45:17,011] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 13:45:19,039] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A1_MZET154903B002A/NGS16007_VLHP2_A1_MZET154903B002A-soft_clip.bedgraph ERROR [2016-10-14 13:45:40,037] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 13:45:40,038] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 13:45:40,040] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 13:45:40,041] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 13:45:40,043] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 13:45:40,044] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 13:45:40,045] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 13:45:40,047] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 13:45:40,049] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 13:45:40,057] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 13:45:40,213] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-14 13:45:40,410] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 13:45:40,411] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 13:45:40,499] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 13:45:40,625] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A2_MZET160602C159A/NGS16007_VLHP2_A2_MZET160602C159A-soft_clip.bedgraph ERROR [2016-10-14 13:46:19,980] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 13:46:19,982] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 13:46:19,983] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 13:46:19,985] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 13:46:19,986] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 13:46:19,987] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 13:46:19,988] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 13:46:19,989] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 13:46:19,990] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 13:46:19,997] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 13:46:20,154] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-14 13:46:20,362] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 13:46:20,363] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 13:46:20,418] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 13:46:20,543] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_A3_MZET160602C140A/NGS16007_VLHP2_A3_MZET160602C140A-soft_clip.bedgraph ERROR [2016-10-14 14:02:56,151] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:02:56,152] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 14:02:56,153] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 14:02:56,154] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 14:02:56,155] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 14:02:56,156] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 14:02:56,156] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 14:02:56,157] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 14:02:56,163] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 14:02:57,182] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:02:57,470] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 14:02:57,470] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 14:02:57,529] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 14:02:57,668] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_B3_MZET160602A045A/NGS16007_VLHP2_B3_MZET160602A045A-soft_clip.bedgraph ERROR [2016-10-14 14:06:39,698] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:06:39,699] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 14:06:39,700] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 14:06:39,702] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 14:06:39,703] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 14:06:39,705] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 14:06:39,706] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 14:06:39,707] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 14:06:39,708] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 14:06:40,723] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:06:41,114] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 14:06:41,114] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 14:06:41,172] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 14:06:41,290] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_C11_MZET160605A139A/NGS16007_VLHP2_C11_MZET160605A139A-soft_clip.bedgraph ERROR [2016-10-14 14:09:14,148] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:09:14,150] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 14:09:14,151] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 14:09:14,153] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 14:09:14,154] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 14:09:14,155] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 14:09:14,156] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 14:09:14,157] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 14:09:14,158] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 14:09:14,176] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:09:14,326] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 14:09:14,326] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 14:09:14,385] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 14:09:17,509] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D2_MZET160605A076A/NGS16007_VLHP2_D2_MZET160605A076A-soft_clip.bedgraph ERROR [2016-10-14 14:17:52,525] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:17:52,526] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 14:17:52,527] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 14:17:52,528] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 14:17:52,529] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 14:17:52,530] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 14:17:52,531] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 14:17:52,532] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 14:17:52,532] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 14:17:53,543] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:17:54,034] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 14:17:54,035] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam INFO [2016-10-14 14:17:54,081] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A.extendedFrags.mod.fastq-vs-VLHP2_sub-sequence_2182-2586.sort.bam.mod.vcf INFO [2016-10-14 14:17:54,179] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_VLHP2_D5_MZET160605A056A/NGS16007_VLHP2_D5_MZET160605A056A-soft_clip.bedgraph ERROR [2016-10-14 14:18:41,166] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:18:41,168] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 14:18:41,169] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 14:18:41,172] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 14:18:41,173] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 14:18:41,174] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 14:18:41,175] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 14:18:41,176] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 14:18:41,177] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 14:18:41,188] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:18:41,766] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 14:18:41,766] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-14 14:18:41,813] [MessageUtils.java:74] File: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam
does not contain any sequence names which match the current genome.

File:      GW2-2,
Genome: VLHP2, INFO [2016-10-14 14:18:46,294] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-14 14:18:46,411] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-soft_clip.bedgraph INFO [2016-10-14 14:18:51,563] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa INFO [2016-10-14 14:18:51,602] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/GW2-2_sub-sequence_1909-2304.fa ERROR [2016-10-14 14:19:00,833] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:19:00,835] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-14 14:19:00,836] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-14 14:19:00,837] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-14 14:19:00,837] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-14 14:19:00,838] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-14 14:19:00,839] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-14 14:19:00,842] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-14 14:19:00,843] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-14 14:19:00,851] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-igv_session_file.xml HTTP/1.1 ERROR [2016-10-14 14:19:01,016] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-14 14:19:01,017] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam INFO [2016-10-14 14:19:01,069] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A.extendedFrags.mod.fastq-vs-GW2-2_sub-sequence_1909-2304.sort.bam.mod.vcf INFO [2016-10-14 14:19:01,179] [TrackLoader.java:118] Loading resource, path http://demeter/project/GED2549_NGS16007/delivered/1476067810/NGS16007_GW2-2_E1_MZET160603C004A/NGS16007_GW2-2_E1_MZET160603C004A-soft_clip.bedgraph INFO [2016-10-17 11:21:48,560] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa INFO [2016-10-17 11:21:53,630] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa.fai. Trying GET INFO [2016-10-17 11:21:53,630] [HttpUtils.java:283] HEAD request failed for url: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/MIR162-A.fa. Trying GET ERROR [2016-10-17 11:21:53,630] [HttpUtils.java:312] Error fetching content length java.net.UnknownHostException: demeter at java.net.AbstractPlainSocketImpl.connect(Unknown Source) at java.net.PlainSocketImpl.connect(Unknown Source) at java.net.SocksSocketImpl.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at sun.net.NetworkClient.doConnect(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.(Unknown Source) at sun.net.www.http.HttpClient.New(Unknown Source) at sun.net.www.http.HttpClient.New(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at java.net.HttpURLConnection.getResponseCode(Unknown Source) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:713) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:287) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:291) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:305) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:57) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-17 11:24:40,250] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-17 11:24:40,250] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-17 11:24:41,346] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 11:24:41,628] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-17 11:24:41,628] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-10-17 11:24:41,660] [MessageUtils.java:74] File: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam
does not contain any sequence names which match the current genome.

File:      MIR162-A,
Genome: GW2-2, INFO [2016-10-17 11:24:55,158] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-10-17 11:24:55,299] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-17 11:24:55,346] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 11:24:55,377] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-17 11:24:55,424] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 11:24:55,455] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-soft_clipping.bedgraph INFO [2016-10-17 11:24:55,487] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-non-ref_freq.bedgraph INFO [2016-10-17 11:24:55,549] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-strand_bias.bedgraph INFO [2016-10-17 11:24:55,612] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-avg-ref-basequality.bedgraph INFO [2016-10-17 11:24:55,659] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-inverse-avg-ref-basequality.bedgraph INFO [2016-10-17 11:24:55,784] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-homopolymers.bedgraph INFO [2016-10-17 11:25:30,269] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/MIR162-A.fa INFO [2016-10-17 11:25:30,301] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/MIR162-A.fa ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-17 11:25:55,676] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-17 11:25:55,676] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-17 11:25:55,692] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 11:25:55,974] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-17 11:25:55,974] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-10-17 11:25:56,037] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-10-17 11:25:56,162] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-17 11:25:56,193] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 11:25:56,225] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-17 11:25:56,256] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 11:25:56,287] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-soft_clipping.bedgraph INFO [2016-10-17 11:25:56,319] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-non-ref_freq.bedgraph INFO [2016-10-17 11:25:56,397] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-strand_bias.bedgraph INFO [2016-10-17 11:25:56,460] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-avg-ref-basequality.bedgraph INFO [2016-10-17 11:25:56,522] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-inverse-avg-ref-basequality.bedgraph INFO [2016-10-17 11:25:56,585] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-homopolymers.bedgraph ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-17 12:38:39,799] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-17 12:38:39,814] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-17 12:38:40,891] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 12:38:41,187] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ClassCastException at javax.swing.LayoutComparator.compare(Unknown Source) at javax.swing.LayoutComparator.compare(Unknown Source) at java.util.TimSort.binarySort(Unknown Source) at java.util.TimSort.sort(Unknown Source) at java.util.Arrays.sort(Unknown Source) at java.util.ArrayList.sort(Unknown Source) at java.util.Collections.sort(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(Unknown Source) at javax.swing.SortingFocusTraversalPolicy.getComponentAfter(Unknown Source) at javax.swing.LayoutFocusTraversalPolicy.getComponentAfter(Unknown Source) at java.awt.Component.getNextFocusCandidate(Unknown Source) at java.awt.DefaultKeyboardFocusManager.doRestoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.restoreFocus(Unknown Source) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.SequencedEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) ERROR [2016-10-17 12:38:41,686] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-17 12:38:41,686] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam INFO [2016-10-17 12:38:41,764] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam.vcf INFO [2016-10-17 12:38:41,873] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-zero_coverage_gaps.bedgraph INFO [2016-10-17 12:38:41,951] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 12:38:41,998] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-soft_clipping.bedgraph INFO [2016-10-17 12:38:42,029] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-non-ref_freq.bedgraph INFO [2016-10-17 12:38:42,107] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-strand_bias.bedgraph INFO [2016-10-17 12:38:42,170] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-avg-ref-basequality.bedgraph INFO [2016-10-17 12:38:42,217] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-inverse-avg-ref-basequality.bedgraph ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-17 12:39:49,378] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-17 12:39:49,378] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-17 12:39:49,393] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 12:39:50,064] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-17 12:39:50,064] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-10-17 12:39:50,111] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-10-17 12:39:50,204] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-17 12:39:50,251] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 12:39:50,282] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-17 12:39:50,329] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 12:39:50,360] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-soft_clipping.bedgraph INFO [2016-10-17 12:39:50,392] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-non-ref_freq.bedgraph INFO [2016-10-17 12:39:50,438] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-strand_bias.bedgraph INFO [2016-10-17 12:39:50,516] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-avg-ref-basequality.bedgraph INFO [2016-10-17 12:39:50,579] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-inverse-avg-ref-basequality.bedgraph INFO [2016-10-17 12:39:50,641] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-homopolymers.bedgraph ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-17 12:40:48,287] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-17 12:40:48,287] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-17 12:40:48,303] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094/mir162-1476196094-igv_session_file.xml HTTP/1.1 ERROR [2016-10-17 12:40:48,880] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-17 12:40:48,880] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam INFO [2016-10-17 12:40:48,927] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-bowtie2.bam.sort.bam.vcf INFO [2016-10-17 12:40:49,036] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-zero_coverage_gaps.bedgraph INFO [2016-10-17 12:40:49,067] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-below_threshold_coverage_gaps.bedgraph INFO [2016-10-17 12:40:49,098] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-soft_clipping.bedgraph INFO [2016-10-17 12:40:49,130] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-non-ref_freq.bedgraph INFO [2016-10-17 12:40:49,192] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-strand_bias.bedgraph INFO [2016-10-17 12:40:49,254] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-avg-ref-basequality.bedgraph INFO [2016-10-17 12:40:49,348] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476196094//mir162-1476196094-inverse-avg-ref-basequality.bedgraph INFO [2016-10-18 12:59:42,781] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-18 12:59:42,781] [Main.java:100] Java 1.8.0_91 INFO [2016-10-18 12:59:42,781] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-18 12:59:42,781] [Main.java:102] OS: Windows 7 INFO [2016-10-18 12:59:46,059] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-18 13:00:08,658] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/MIR162-A.fa INFO [2016-10-18 13:00:08,752] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/MIR162-A.fa ERROR [2016-10-18 13:00:08,986] [CommandListener.java:124] java.net.BindException: Address already in use: JVM_Bind INFO [2016-10-19 13:40:39,897] [GenomeManager.java:145] Loading genome: http://demeter/scratch-large/3-monthly/TrEC-SI/test/mut3/1476897632/baseclear_GA21_ref.mut3.5bp_insertion.fa ERROR [2016-10-19 13:40:40,209] [HttpUtils.java:312] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter/scratch-large/3-monthly/TrEC-SI/test/mut3/1476897632/baseclear_GA21_ref.mut3.5bp_insertion.fa at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:739) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:276) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:291) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:305) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:57) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.ui.IGV.loadGenome(IGV.java:686) at org.broad.igv.ui.IGV.loadGenome(IGV.java:667) at org.broad.igv.ui.action.LoadFromURLMenuAction.actionPerformed(LoadFromURLMenuAction.java:137) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) INFO [2016-10-19 13:40:40,240] [MessageUtils.java:74] Error loading genome: File not found: http://demeter/scratch-large/3-monthly/TrEC-SI/test/mut3/1476897632/baseclear_GA21_ref.mut3.5bp_insertion.fa.fai INFO [2016-10-19 13:41:43,699] [GenomeManager.java:145] Loading genome: C:\Users\rosema1\Desktop\DOWNLOAD\product_safety_2016\MiSeq_pipeline\baseclear_GA21_ref.mut3.5bp_insertion.fa INFO [2016-10-19 13:41:43,699] [GenomeManager.java:192] Genome loaded. id= C:\Users\rosema1\Desktop\DOWNLOAD\product_safety_2016\MiSeq_pipeline\baseclear_GA21_ref.mut3.5bp_insertion.fa INFO [2016-10-19 13:42:11,723] [IGV.java:1700] Loading 1 resources. INFO [2016-10-19 13:42:11,723] [TrackLoader.java:118] Loading resource, path C:\Users\rosema1\Desktop\DOWNLOAD\product_safety_2016\MiSeq_pipeline\mut3-1476897632-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-10-19 14:36:22,806] [IGV.java:1700] Loading 1 resources. INFO [2016-10-19 14:36:22,806] [TrackLoader.java:118] Loading resource, path C:\Users\rosema1\Desktop\DOWNLOAD\product_safety_2016\MiSeq_pipeline\mut3-1476899883-bowtie2.bam.sort.bam INFO [2016-10-19 14:36:54,135] [IGV.java:1700] Loading 1 resources. INFO [2016-10-19 14:36:54,135] [TrackLoader.java:118] Loading resource, path C:\Users\rosema1\Desktop\DOWNLOAD\product_safety_2016\MiSeq_pipeline\mut3-1476899883-bowtie2.bam.sort.bam ERROR [2016-10-19 17:48:21,907] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/mut3-1476912925-igv_session_file.xml HTTP/1.1 ERROR [2016-10-19 17:48:21,914] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-19 17:48:21,914] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-19 17:48:21,915] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-19 17:48:21,916] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-19 17:48:21,917] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-19 17:48:21,917] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-19 17:48:21,918] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-19 17:48:21,918] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-19 17:48:22,964] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/mut3-1476912925-igv_session_file.xml HTTP/1.1 ERROR [2016-10-19 17:48:23,752] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-19 17:48:23,753] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam INFO [2016-10-19 17:48:24,213] [MessageUtils.java:74] File: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam
does not contain any sequence names which match the current genome.

File:      baseclear_GA21_ref.mut3.5bp_insertion.uc,
Genome: MIR162-A, INFO [2016-10-19 17:48:26,140] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam.vcf INFO [2016-10-19 17:48:26,286] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-zero_coverage_gaps.bedgraph INFO [2016-10-19 17:48:26,559] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-below_threshold_coverage_gaps.bedgraph INFO [2016-10-19 17:48:27,627] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//anchored-mut3-1476912925-zero_coverage_gaps.bedgraph INFO [2016-10-19 17:48:27,669] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//anchored-mut3-1476912925-below_threshold_coverage_gaps.bedgraph INFO [2016-10-19 17:48:27,723] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-soft_clipping.bedgraph INFO [2016-10-19 17:48:27,761] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-non-ref_freq.bedgraph INFO [2016-10-19 17:48:28,100] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-strand_bias.bedgraph INFO [2016-10-19 17:48:28,403] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-avg-ref-basequality.bedgraph INFO [2016-10-19 17:48:28,771] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-inverse-avg-ref-basequality.bedgraph INFO [2016-10-19 17:48:29,284] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-homopolymers.bedgraph INFO [2016-10-19 17:48:51,522] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/baseclear_GA21_ref.mut3.5bp_insertion.uc.fa INFO [2016-10-19 17:48:51,572] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/baseclear_GA21_ref.mut3.5bp_insertion.uc.fa ERROR [2016-10-19 17:49:00,925] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/mut3-1476912925-igv_session_file.xml HTTP/1.1 ERROR [2016-10-19 17:49:00,926] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-19 17:49:00,927] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-19 17:49:00,927] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-19 17:49:00,928] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-19 17:49:00,928] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-19 17:49:00,929] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-19 17:49:00,929] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-19 17:49:00,930] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-19 17:49:00,941] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/mut3-1476912925-igv_session_file.xml HTTP/1.1 ERROR [2016-10-19 17:49:01,307] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-19 17:49:01,308] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam INFO [2016-10-19 17:49:01,387] [MessageUtils.java:74] File: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam
does not contain any sequence names which match the current genome.

File:      baseclear_GA21_ref.mut3.5bp_insertion.uc,
Genome: MIR162-A, INFO [2016-10-19 17:49:11,829] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam.vcf INFO [2016-10-19 17:49:11,929] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-zero_coverage_gaps.bedgraph INFO [2016-10-19 17:49:11,959] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-below_threshold_coverage_gaps.bedgraph INFO [2016-10-19 17:49:12,018] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//anchored-mut3-1476912925-zero_coverage_gaps.bedgraph INFO [2016-10-19 17:49:12,048] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//anchored-mut3-1476912925-below_threshold_coverage_gaps.bedgraph INFO [2016-10-19 17:49:12,724] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-soft_clipping.bedgraph INFO [2016-10-19 17:49:12,754] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-non-ref_freq.bedgraph INFO [2016-10-19 17:49:14,617] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-strand_bias.bedgraph INFO [2016-10-19 17:49:15,096] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-avg-ref-basequality.bedgraph INFO [2016-10-19 17:49:15,517] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-inverse-avg-ref-basequality.bedgraph INFO [2016-10-19 17:49:16,355] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-homopolymers.bedgraph INFO [2016-10-19 17:49:19,325] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/baseclear_GA21_ref.mut3.5bp_insertion.uc.fa INFO [2016-10-19 17:49:19,358] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/baseclear_GA21_ref.mut3.5bp_insertion.uc.fa INFO [2016-10-19 17:49:29,217] [ShutdownThread.java:51] Shutting down ERROR [2016-10-19 17:49:39,570] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/mut3-1476912925-igv_session_file.xml HTTP/1.1 ERROR [2016-10-19 17:49:39,570] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-19 17:49:39,571] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-19 17:49:39,571] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-19 17:49:39,572] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-19 17:49:39,572] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-19 17:49:39,573] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-19 17:49:39,573] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-19 17:49:39,573] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-19 17:49:39,578] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925/mut3-1476912925-igv_session_file.xml HTTP/1.1 ERROR [2016-10-19 17:49:39,924] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-19 17:49:39,925] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam INFO [2016-10-19 17:49:39,991] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-bowtie2.bam.sort.bam.vcf INFO [2016-10-19 17:49:40,093] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-zero_coverage_gaps.bedgraph INFO [2016-10-19 17:49:40,129] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-below_threshold_coverage_gaps.bedgraph INFO [2016-10-19 17:49:40,205] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//anchored-mut3-1476912925-zero_coverage_gaps.bedgraph INFO [2016-10-19 17:49:40,238] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//anchored-mut3-1476912925-below_threshold_coverage_gaps.bedgraph INFO [2016-10-19 17:49:40,288] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-soft_clipping.bedgraph INFO [2016-10-19 17:49:40,318] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-non-ref_freq.bedgraph INFO [2016-10-19 17:49:40,691] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-strand_bias.bedgraph INFO [2016-10-19 17:49:41,106] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-avg-ref-basequality.bedgraph INFO [2016-10-19 17:49:41,512] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-inverse-avg-ref-basequality.bedgraph INFO [2016-10-19 17:49:41,866] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476912925//mut3-1476912925-homopolymers.bedgraph INFO [2016-10-20 13:15:42,507] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133/baseclear_GA21_ref_mut1.fa INFO [2016-10-20 13:15:42,663] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133/baseclear_GA21_ref_mut1.fa ERROR [2016-10-20 13:15:53,958] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133/mut1-1476983133-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:15:53,959] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 13:15:53,959] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 13:15:53,959] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 13:15:53,960] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 13:15:53,960] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 13:15:53,960] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 13:15:53,961] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 13:15:53,961] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 13:15:54,979] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133/mut1-1476983133-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:15:55,266] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 13:15:55,267] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-bowtie2.bam.sort.bam INFO [2016-10-20 13:15:55,338] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 13:15:55,454] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:15:55,791] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:15:55,844] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//anchored-mut1-1476983133-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:15:55,877] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//anchored-mut1-1476983133-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:15:55,924] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-soft_clipping.bedgraph INFO [2016-10-20 13:15:55,953] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-non-ref_freq.bedgraph INFO [2016-10-20 13:15:56,088] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-strand_bias.bedgraph INFO [2016-10-20 13:15:56,219] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-avg-ref-basequality.bedgraph INFO [2016-10-20 13:15:56,352] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983133//mut1-1476983133-inverse-avg-ref-basequality.bedgraph ERROR [2016-10-20 13:20:50,563] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494/mut1-1476983494-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:20:50,564] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 13:20:50,565] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 13:20:50,565] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 13:20:50,566] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 13:20:50,566] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 13:20:50,566] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 13:20:50,567] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 13:20:50,567] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 13:20:51,575] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494/mut1-1476983494-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:20:52,108] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 13:20:52,109] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-bowtie2.bam.sort.bam INFO [2016-10-20 13:20:52,169] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 13:20:52,280] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:20:52,313] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:20:52,356] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//anchored-mut1-1476983494-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:20:55,398] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//anchored-mut1-1476983494-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:20:58,442] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-soft_clipping.bedgraph INFO [2016-10-20 13:21:01,473] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-non-ref_freq.bedgraph INFO [2016-10-20 13:21:01,594] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-strand_bias.bedgraph INFO [2016-10-20 13:21:01,720] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-avg-ref-basequality.bedgraph INFO [2016-10-20 13:21:04,866] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983494//mut1-1476983494-inverse-avg-ref-basequality.bedgraph ERROR [2016-10-20 13:30:58,354] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799/mut1-1476983799-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:30:58,355] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 13:30:58,355] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 13:30:58,355] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 13:30:58,356] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 13:30:58,356] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 13:30:58,356] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 13:30:58,357] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 13:30:58,357] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 13:30:59,354] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799/mut1-1476983799-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:31:00,053] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 13:31:00,054] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-bowtie2.bam.sort.bam INFO [2016-10-20 13:31:00,120] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 13:31:03,240] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:31:03,276] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:31:03,341] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//anchored-mut1-1476983799-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:31:03,381] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//anchored-mut1-1476983799-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:31:03,434] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-soft_clipping.bedgraph INFO [2016-10-20 13:31:12,468] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-non-ref_freq.bedgraph INFO [2016-10-20 13:31:12,591] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-strand_bias.bedgraph INFO [2016-10-20 13:31:12,764] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-avg-ref-basequality.bedgraph INFO [2016-10-20 13:31:12,905] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 13:31:13,331] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut1/1476983799//mut1-1476983799-homopolymers.bedgraph INFO [2016-10-20 13:44:29,551] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901/baseclear_GA21_ref.mut3.5bp_insertion.fa INFO [2016-10-20 13:44:29,629] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901/baseclear_GA21_ref.mut3.5bp_insertion.fa ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901/mut3-1476984901-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 13:44:42,455] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 13:44:42,455] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 13:44:43,516] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901/mut3-1476984901-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 13:44:43,968] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 13:44:43,984] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-bowtie2.bam.sort.bam INFO [2016-10-20 13:44:44,062] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 13:44:50,520] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:44:53,562] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:44:53,640] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//anchored-mut3-1476984901-zero_coverage_gaps.bedgraph INFO [2016-10-20 13:44:53,671] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//anchored-mut3-1476984901-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 13:44:53,734] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-soft_clipping.bedgraph INFO [2016-10-20 13:44:54,077] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-non-ref_freq.bedgraph INFO [2016-10-20 13:44:57,244] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-strand_bias.bedgraph INFO [2016-10-20 13:44:57,384] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-avg-ref-basequality.bedgraph INFO [2016-10-20 13:44:57,540] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 13:44:57,696] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476984901//mut3-1476984901-homopolymers.bedgraph ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841/mut3-1476989841-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 15:10:37,169] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 15:10:37,169] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 15:10:38,230] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841/mut3-1476989841-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 15:10:38,948] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 15:10:38,948] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-bowtie2.bam.sort.bam INFO [2016-10-20 15:10:39,088] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 15:10:42,270] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-zero_coverage_gaps.bedgraph INFO [2016-10-20 15:10:42,333] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 15:10:42,395] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//anchored-mut3-1476989841-zero_coverage_gaps.bedgraph INFO [2016-10-20 15:10:42,442] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//anchored-mut3-1476989841-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 15:10:42,520] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-soft_clipping.bedgraph INFO [2016-10-20 15:10:42,551] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-non-ref_freq.bedgraph INFO [2016-10-20 15:10:45,952] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-strand_bias.bedgraph INFO [2016-10-20 15:10:46,529] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-avg-ref-basequality.bedgraph INFO [2016-10-20 15:10:46,669] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 15:10:47,730] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476989841//mut3-1476989841-homopolymers.bedgraph ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547/mut3-1476991547-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 15:35:15,042] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 15:35:15,042] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 15:35:16,087] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547/mut3-1476991547-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 15:35:16,602] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 15:35:16,602] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-bowtie2.bam.sort.bam INFO [2016-10-20 15:35:16,680] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 15:35:16,820] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-zero_coverage_gaps.bedgraph INFO [2016-10-20 15:35:16,867] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 15:35:16,914] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//anchored-mut3-1476991547-zero_coverage_gaps.bedgraph INFO [2016-10-20 15:35:16,961] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//anchored-mut3-1476991547-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 15:35:17,023] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-soft_clipping.bedgraph INFO [2016-10-20 15:35:20,081] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-non-ref_freq.bedgraph INFO [2016-10-20 15:35:20,268] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-strand_bias.bedgraph INFO [2016-10-20 15:35:20,424] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-avg-ref-basequality.bedgraph INFO [2016-10-20 15:35:20,876] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 15:35:24,062] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476991547//mut3-1476991547-homopolymers.bedgraph ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166/mut3-1476994166-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 16:19:35,919] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 16:19:35,919] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 16:19:36,980] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166/mut3-1476994166-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 16:19:37,588] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 16:19:37,588] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-bowtie2.bam.sort.bam INFO [2016-10-20 16:19:37,651] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 16:19:37,776] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-zero_coverage_gaps.bedgraph INFO [2016-10-20 16:19:37,822] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 16:19:37,885] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//anchored-mut3-1476994166-zero_coverage_gaps.bedgraph INFO [2016-10-20 16:19:37,932] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//anchored-mut3-1476994166-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 16:19:37,994] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-soft_clipping.bedgraph INFO [2016-10-20 16:19:38,041] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-non-ref_freq.bedgraph INFO [2016-10-20 16:19:38,415] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-strand_bias.bedgraph INFO [2016-10-20 16:19:38,540] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-avg-ref-basequality.bedgraph INFO [2016-10-20 16:19:38,727] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 16:19:39,304] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476994166//mut3-1476994166-homopolymers.bedgraph ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/mut3-1476996993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 17:15:52,295] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 17:15:52,295] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 17:15:53,309] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/mut3-1476996993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 17:15:53,808] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 17:15:53,808] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-bowtie2.bam.sort.bam INFO [2016-10-20 17:15:53,886] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 17:15:54,323] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-zero_coverage_gaps.bedgraph INFO [2016-10-20 17:15:54,354] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 17:15:54,728] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//anchored-mut3-1476996993-zero_coverage_gaps.bedgraph INFO [2016-10-20 17:15:57,755] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//anchored-mut3-1476996993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 17:15:57,817] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-soft_clipping.bedgraph INFO [2016-10-20 17:15:57,848] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-non-ref_freq.bedgraph INFO [2016-10-20 17:15:58,020] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-strand_bias.bedgraph INFO [2016-10-20 17:15:58,160] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-avg-ref-basequality.bedgraph INFO [2016-10-20 17:15:58,301] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 17:15:58,441] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-homopolymers.bedgraph INFO [2016-10-20 18:57:17,384] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/baseclear_GA21_ref.mut3.5bp_insertion.fa INFO [2016-10-20 18:57:18,744] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/baseclear_GA21_ref.mut3.5bp_insertion.fa ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/mut3-1476996993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 18:57:29,891] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 18:57:29,891] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 18:57:30,936] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/mut3-1476996993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 18:57:31,841] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 18:57:31,841] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-bowtie2.bam.sort.bam INFO [2016-10-20 18:57:37,067] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 18:57:40,873] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-zero_coverage_gaps.bedgraph INFO [2016-10-20 18:57:42,027] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 18:57:42,979] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//anchored-mut3-1476996993-zero_coverage_gaps.bedgraph INFO [2016-10-20 18:57:44,211] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//anchored-mut3-1476996993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 18:57:44,975] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-soft_clipping.bedgraph INFO [2016-10-20 18:57:45,615] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-non-ref_freq.bedgraph INFO [2016-10-20 18:57:47,549] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-strand_bias.bedgraph INFO [2016-10-20 18:57:49,925] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-avg-ref-basequality.bedgraph INFO [2016-10-20 18:57:51,438] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 18:57:53,403] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-homopolymers.bedgraph ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 19:06:31,655] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 19:06:31,655] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 19:06:32,669] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693/mir162-1476714693-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 19:06:33,839] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 19:06:33,839] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-10-20 19:06:35,243] [MessageUtils.java:74] File: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam
does not contain any sequence names which match the current genome.

File:      MIR162-A,
Genome: baseclear_GA21_ref.mut3.5bp_insertion, INFO [2016-10-20 19:06:40,611] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-10-20 19:06:43,825] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-20 19:06:47,683] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 19:06:48,510] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-zero_coverage_gaps.bedgraph INFO [2016-10-20 19:06:52,534] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//anchored-mir162-1476714693-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 19:06:53,314] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-soft_clipping.bedgraph INFO [2016-10-20 19:06:54,734] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-non-ref_freq.bedgraph INFO [2016-10-20 19:06:56,637] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-strand_bias.bedgraph INFO [2016-10-20 19:06:57,932] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-avg-ref-basequality.bedgraph INFO [2016-10-20 19:07:02,346] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 19:07:06,750] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir162/1476714693//mir162-1476714693-homopolymers.bedgraph INFO [2016-10-20 19:08:29,498] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/baseclear_GA21_ref.mut3.5bp_insertion.fa INFO [2016-10-20 19:08:33,180] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/baseclear_GA21_ref.mut3.5bp_insertion.fa ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/mut3-1476996993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 19:08:45,020] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 19:08:45,020] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 19:08:45,035] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993/mut3-1476996993-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 19:08:46,221] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 19:08:46,221] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-bowtie2.bam.sort.bam INFO [2016-10-20 19:08:46,925] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 19:08:49,926] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-zero_coverage_gaps.bedgraph INFO [2016-10-20 19:08:50,940] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 19:08:54,639] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//anchored-mut3-1476996993-zero_coverage_gaps.bedgraph INFO [2016-10-20 19:08:55,250] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//anchored-mut3-1476996993-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 19:08:56,654] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-soft_clipping.bedgraph INFO [2016-10-20 19:08:57,262] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-non-ref_freq.bedgraph INFO [2016-10-20 19:09:00,993] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-strand_bias.bedgraph INFO [2016-10-20 19:09:03,130] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-avg-ref-basequality.bedgraph INFO [2016-10-20 19:09:04,893] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 19:09:06,718] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1476996993//mut3-1476996993-homopolymers.bedgraph ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659/mut3-1477005659-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 19:32:15,139] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 19:32:15,139] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 19:32:16,200] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659/mut3-1477005659-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 19:32:20,177] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 19:32:20,177] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-bowtie2.bam.sort.bam INFO [2016-10-20 19:32:21,956] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 19:32:24,904] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-zero_coverage_gaps.bedgraph INFO [2016-10-20 19:32:25,918] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 19:32:26,979] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//anchored-mut3-1477005659-zero_coverage_gaps.bedgraph INFO [2016-10-20 19:32:27,852] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//anchored-mut3-1477005659-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 19:32:28,929] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-soft_clipping.bedgraph INFO [2016-10-20 19:32:29,755] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-non-ref_freq.bedgraph INFO [2016-10-20 19:32:31,692] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-strand_bias.bedgraph INFO [2016-10-20 19:32:36,858] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-avg-ref-basequality.bedgraph INFO [2016-10-20 19:32:39,167] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 19:32:41,740] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut3/1477005659//mut3-1477005659-homopolymers.bedgraph INFO [2016-10-20 20:29:06,377] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/baseclear_GA21_ref.mut2.mod.fa INFO [2016-10-20 20:29:12,197] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/baseclear_GA21_ref.mut2.mod.fa ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/mut2-1477008989-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 20:29:22,469] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 20:29:22,485] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 20:29:23,519] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/mut2-1477008989-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 20:29:24,627] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 20:29:24,627] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-bowtie2.bam.sort.bam INFO [2016-10-20 20:29:35,722] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 20:29:43,447] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-zero_coverage_gaps.bedgraph INFO [2016-10-20 20:29:48,867] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 20:29:51,966] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//anchored-mut2-1477008989-zero_coverage_gaps.bedgraph INFO [2016-10-20 20:29:54,100] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//anchored-mut2-1477008989-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 20:29:57,584] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-soft_clipping.bedgraph INFO [2016-10-20 20:29:59,862] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-non-ref_freq.bedgraph INFO [2016-10-20 20:30:06,968] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-strand_bias.bedgraph INFO [2016-10-20 20:30:12,163] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-avg-ref-basequality.bedgraph INFO [2016-10-20 20:30:16,535] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 20:30:21,282] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-homopolymers.bedgraph ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/mut2-1477008989-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 20:34:05,269] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 20:34:05,269] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 20:34:06,317] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/mut2-1477008989-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 20:34:07,554] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 20:34:07,554] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-bowtie2.bam.sort.bam INFO [2016-10-20 20:34:09,862] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 20:34:16,426] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-zero_coverage_gaps.bedgraph INFO [2016-10-20 20:34:19,765] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 20:34:28,248] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//anchored-mut2-1477008989-zero_coverage_gaps.bedgraph INFO [2016-10-20 20:34:30,530] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//anchored-mut2-1477008989-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 20:34:32,464] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-soft_clipping.bedgraph INFO [2016-10-20 20:34:37,222] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-non-ref_freq.bedgraph INFO [2016-10-20 20:34:42,499] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-strand_bias.bedgraph INFO [2016-10-20 20:34:48,236] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-avg-ref-basequality.bedgraph INFO [2016-10-20 20:34:51,022] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 20:34:53,752] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-homopolymers.bedgraph INFO [2016-10-20 20:38:37,466] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/baseclear_GA21_ref.mut2.mod.fa INFO [2016-10-20 20:38:42,195] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/baseclear_GA21_ref.mut2.mod.fa ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/mut2-1477008989-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-20 20:39:04,402] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-20 20:39:04,402] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-20 20:39:05,447] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/mut2-1477008989-igv_session_file.xml HTTP/1.1 ERROR [2016-10-20 20:39:06,477] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-20 20:39:06,477] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-bowtie2.bam.sort.bam INFO [2016-10-20 20:39:08,357] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-bowtie2.bam.sort.bam.vcf INFO [2016-10-20 20:39:18,504] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-zero_coverage_gaps.bedgraph INFO [2016-10-20 20:39:20,100] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 20:39:22,446] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//anchored-mut2-1477008989-zero_coverage_gaps.bedgraph INFO [2016-10-20 20:39:24,167] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//anchored-mut2-1477008989-below_threshold_coverage_gaps.bedgraph INFO [2016-10-20 20:39:26,600] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-soft_clipping.bedgraph INFO [2016-10-20 20:39:31,239] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-non-ref_freq.bedgraph INFO [2016-10-20 20:39:33,448] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-strand_bias.bedgraph INFO [2016-10-20 20:39:35,882] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-avg-ref-basequality.bedgraph INFO [2016-10-20 20:39:38,363] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-inverse-avg-ref-basequality.bedgraph INFO [2016-10-20 20:39:40,991] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-homopolymers.bedgraph INFO [2016-10-20 20:40:01,000] [HttpUtils.java:283] HEAD request failed for url: http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989//mut2-1477008989-homopolymers.bedgraph. Trying GET INFO [2016-10-20 20:42:07,527] [ShutdownThread.java:51] Shutting down INFO [2016-10-25 17:03:35,669] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-25 17:03:35,669] [Main.java:100] Java 1.8.0_91 INFO [2016-10-25 17:03:35,669] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-25 17:03:35,669] [Main.java:102] OS: Windows 7 INFO [2016-10-25 17:03:37,619] [Main.java:150] A later version of IGV is available (2.3.79) INFO [2016-10-25 17:03:59,920] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/baseclear_GA21_ref.mut2.mod.fa INFO [2016-10-25 17:04:00,630] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mut2/1477008989/baseclear_GA21_ref.mut2.mod.fa INFO [2016-10-25 17:04:00,820] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-25 17:04:08,982] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073/MIR604-ISFS1.d2u.fa INFO [2016-10-25 17:04:09,762] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073/MIR604-ISFS1.d2u.fa ERROR [2016-10-25 17:04:15,982] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073/mir604-1477429073-igv_session_file.xml HTTP/1.1 ERROR [2016-10-25 17:04:15,982] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-25 17:04:15,982] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-25 17:04:15,992] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-25 17:04:15,992] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-25 17:04:15,992] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-25 17:04:15,992] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-25 17:04:15,992] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-25 17:04:15,992] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-25 17:04:17,022] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073/mir604-1477429073-igv_session_file.xml HTTP/1.1 ERROR [2016-10-25 17:04:17,592] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-25 17:04:17,592] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-bowtie2.bam.sort.bam INFO [2016-10-25 17:04:18,142] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-25 17:04:19,655] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-bowtie2.bam.sort.bam.vcf INFO [2016-10-25 17:04:21,925] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-zero_coverage_gaps.bedgraph INFO [2016-10-25 17:04:22,605] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-below_threshold_coverage_gaps.bedgraph INFO [2016-10-25 17:04:23,285] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//anchored-mir604-1477429073-zero_coverage_gaps.bedgraph INFO [2016-10-25 17:04:23,925] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//anchored-mir604-1477429073-below_threshold_coverage_gaps.bedgraph INFO [2016-10-25 17:04:24,585] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-soft_clipping.bedgraph INFO [2016-10-25 17:04:25,375] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-non-ref_freq.bedgraph INFO [2016-10-25 17:04:26,515] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-strand_bias.bedgraph INFO [2016-10-25 17:04:27,705] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-avg-ref-basequality.bedgraph INFO [2016-10-25 17:04:28,865] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-inverse-avg-ref-basequality.bedgraph INFO [2016-10-25 17:04:30,015] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073//mir604-1477429073-homopolymers.bedgraph ERROR [2016-10-26 05:42:23,147] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033/mir604-1477474033-igv_session_file.xml HTTP/1.1 ERROR [2016-10-26 05:42:23,157] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-26 05:42:23,157] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-26 05:42:23,157] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-26 05:42:23,157] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-26 05:42:23,157] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-26 05:42:23,157] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-26 05:42:23,167] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-26 05:42:23,167] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-26 05:42:24,187] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033/mir604-1477474033-igv_session_file.xml HTTP/1.1 ERROR [2016-10-26 05:42:25,115] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-26 05:42:25,115] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-bowtie2.bam.sort.bam INFO [2016-10-26 05:42:28,395] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-bowtie2.bam.sort.bam.vcf INFO [2016-10-26 05:42:30,585] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-zero_coverage_gaps.bedgraph INFO [2016-10-26 05:42:31,245] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-below_threshold_coverage_gaps.bedgraph INFO [2016-10-26 05:42:32,015] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//anchored-mir604-1477474033-zero_coverage_gaps.bedgraph INFO [2016-10-26 05:42:32,645] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//anchored-mir604-1477474033-below_threshold_coverage_gaps.bedgraph INFO [2016-10-26 05:42:33,265] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-soft_clipping.bedgraph INFO [2016-10-26 05:42:36,955] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-non-ref_freq.bedgraph INFO [2016-10-26 05:42:38,055] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-strand_bias.bedgraph INFO [2016-10-26 05:42:39,045] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-avg-ref-basequality.bedgraph INFO [2016-10-26 05:42:40,215] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-inverse-avg-ref-basequality.bedgraph INFO [2016-10-26 05:42:41,514] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477474033//mir604-1477474033-homopolymers.bedgraph INFO [2016-10-26 09:07:19,800] [ShutdownThread.java:51] Shutting down INFO [2016-10-31 10:17:38,869] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-10-31 10:17:38,869] [Main.java:100] Java 1.8.0_91 INFO [2016-10-31 10:17:38,869] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-10-31 10:17:38,869] [Main.java:102] OS: Windows 7 INFO [2016-10-31 10:17:41,590] [Main.java:150] A later version of IGV is available (2.3.84) INFO [2016-10-31 10:17:56,230] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073/MIR604-ISFS1.d2u.fa INFO [2016-10-31 10:17:56,310] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604/1477429073/MIR604-ISFS1.d2u.fa INFO [2016-10-31 10:17:56,490] [CommandListener.java:106] Listening on port 60151 INFO [2016-10-31 10:18:26,611] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373/MIR604-ISFS1_20-5886.fa INFO [2016-10-31 10:18:26,641] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373/MIR604-ISFS1_20-5886.fa ERROR [2016-10-31 10:18:36,885] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373/mir604-2005886-1477920373-igv_session_file.xml HTTP/1.1 ERROR [2016-10-31 10:18:36,885] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-10-31 10:18:36,885] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-10-31 10:18:36,895] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-10-31 10:18:36,895] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-10-31 10:18:36,895] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-10-31 10:18:36,895] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-10-31 10:18:36,895] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-10-31 10:18:36,905] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-10-31 10:18:37,925] [CommandListener.java:167] GET /load?file=http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373/mir604-2005886-1477920373-igv_session_file.xml HTTP/1.1 ERROR [2016-10-31 10:18:38,279] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-10-31 10:18:38,279] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-bowtie2.bam.sort.bam INFO [2016-10-31 10:18:38,339] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-10-31 10:18:38,559] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-bowtie2.bam.sort.bam.vcf INFO [2016-10-31 10:18:38,739] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-zero_coverage_gaps.bedgraph INFO [2016-10-31 10:18:38,799] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-below_threshold_coverage_gaps.bedgraph INFO [2016-10-31 10:18:38,829] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//anchored-mir604-2005886-1477920373-zero_coverage_gaps.bedgraph INFO [2016-10-31 10:18:38,869] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//anchored-mir604-2005886-1477920373-below_threshold_coverage_gaps.bedgraph INFO [2016-10-31 10:18:38,899] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-soft_clipping.bedgraph INFO [2016-10-31 10:18:38,959] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-non-ref_freq.bedgraph INFO [2016-10-31 10:18:39,069] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-strand_bias.bedgraph INFO [2016-10-31 10:18:39,239] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-avg-ref-basequality.bedgraph INFO [2016-10-31 10:18:39,319] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-inverse-avg-ref-basequality.bedgraph INFO [2016-10-31 10:18:39,409] [TrackLoader.java:118] Loading resource, path http://demeter//project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373//mir604-2005886-1477920373-homopolymers.bedgraph INFO [2016-11-04 12:06:01,194] [ShutdownThread.java:51] Shutting down INFO [2016-11-07 14:05:15,619] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-11-07 14:05:15,619] [Main.java:100] Java 1.8.0_91 INFO [2016-11-07 14:05:15,619] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-07 14:05:15,619] [Main.java:102] OS: Windows 7 INFO [2016-11-07 14:05:21,717] [Main.java:150] A later version of IGV is available (2.3.84) INFO [2016-11-07 14:05:36,931] [GenomeManager.java:145] Loading genome: http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373/MIR604-ISFS1_20-5886.fa INFO [2016-11-07 14:05:36,983] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/product_safety_2016/work/delivery_dir_for_test/test/mir604-2005886/1477920373/MIR604-ISFS1_20-5886.fa INFO [2016-11-07 14:05:37,183] [CommandListener.java:106] Listening on port 60151 ERROR [2016-11-07 14:05:50,569] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/mut1-1478544789-igv_session_file.xml HTTP/1.1 ERROR [2016-11-07 14:05:50,569] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-07 14:05:50,569] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-07 14:05:50,579] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-07 14:05:50,579] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-07 14:05:50,579] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-07 14:05:50,589] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-07 14:05:50,589] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-07 14:05:50,589] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-07 14:05:51,601] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/mut1-1478544789-igv_session_file.xml HTTP/1.1 ERROR [2016-11-07 14:05:52,199] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-11-07 14:05:52,199] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-bowtie2.bam.sort.bam INFO [2016-11-07 14:05:52,289] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-11-07 14:05:52,439] [MessageUtils.java:74] File: http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-bowtie2.bam.sort.bam
does not contain any sequence names which match the current genome.

File:      baseclear_GA21_ref_mut1,
Genome: MIR604-ISFS1_20-5886, INFO [2016-11-07 14:05:54,494] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-bowtie2.bam.sort.bam.vcf INFO [2016-11-07 14:05:54,739] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-zero_coverage_gaps.bedgraph INFO [2016-11-07 14:05:54,829] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-below_threshold_coverage_gaps.bedgraph INFO [2016-11-07 14:05:54,879] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//anchored-mut1-1478544789-zero_coverage_gaps.bedgraph INFO [2016-11-07 14:05:54,909] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//anchored-mut1-1478544789-below_threshold_coverage_gaps.bedgraph INFO [2016-11-07 14:05:54,959] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-soft_clipping.bedgraph INFO [2016-11-07 14:05:54,999] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-non-ref_freq.bedgraph INFO [2016-11-07 14:05:55,109] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-strand_bias.bedgraph INFO [2016-11-07 14:05:55,209] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-homopolymers.bedgraph INFO [2016-11-07 14:06:57,220] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/dataset_10776.dat INFO [2016-11-07 14:06:57,575] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/dataset_10776.dat ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/mut1-1478544789-igv_session_file.xml HTTP/1.1 ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-07 14:07:06,680] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-07 14:07:06,680] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-07 14:07:06,680] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/mut1-1478544789-igv_session_file.xml HTTP/1.1 ERROR [2016-11-07 14:07:06,880] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-11-07 14:07:06,880] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-bowtie2.bam.sort.bam INFO [2016-11-07 14:07:07,110] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-bowtie2.bam.sort.bam.vcf INFO [2016-11-07 14:07:07,220] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-zero_coverage_gaps.bedgraph INFO [2016-11-07 14:07:07,260] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-below_threshold_coverage_gaps.bedgraph INFO [2016-11-07 14:07:07,310] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//anchored-mut1-1478544789-zero_coverage_gaps.bedgraph INFO [2016-11-07 14:07:07,340] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//anchored-mut1-1478544789-below_threshold_coverage_gaps.bedgraph INFO [2016-11-07 14:07:07,380] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-soft_clipping.bedgraph INFO [2016-11-07 14:07:07,410] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-non-ref_freq.bedgraph INFO [2016-11-07 14:07:07,512] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-strand_bias.bedgraph INFO [2016-11-07 14:07:07,622] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478544789//mut1-1478544789-homopolymers.bedgraph INFO [2016-11-07 14:11:09,796] [ShutdownThread.java:51] Shutting down INFO [2016-11-08 08:28:46,076] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-11-08 08:28:46,077] [Main.java:100] Java 1.8.0_91 INFO [2016-11-08 08:28:46,077] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-08 08:28:46,078] [Main.java:102] OS: Windows 7 INFO [2016-11-08 08:28:48,290] [Main.java:150] A later version of IGV is available (2.3.84) INFO [2016-11-08 08:29:03,509] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/dataset_10776.dat INFO [2016-11-08 08:29:03,558] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478544789/dataset_10776.dat INFO [2016-11-08 08:29:03,758] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-08 08:29:33,890] [GenomeManager.java:145] Loading genome: C:\Users\rosema1\Desktop\DOWNLOAD\batch_detection\VLHP1_sub-sequence_2214-2587.fa INFO [2016-11-08 08:29:33,899] [GenomeManager.java:192] Genome loaded. id= C:\Users\rosema1\Desktop\DOWNLOAD\batch_detection\VLHP1_sub-sequence_2214-2587.fa INFO [2016-11-08 08:29:57,255] [IGV.java:1700] Loading 1 resources. INFO [2016-11-08 08:29:57,257] [TrackLoader.java:118] Loading resource, path C:\Users\rosema1\Desktop\DOWNLOAD\batch_detection\NGS16011_VLHP1_H12_WT.extendedFrags.fastq-vs-VLHP1_sub-sequence_2214-2587.fa.sort.bam INFO [2016-11-11 09:58:56,090] [ShutdownThread.java:51] Shutting down INFO [2016-11-11 10:16:20,511] [Main.java:99] Startup IGV Version 2.3.78 (117)06/28/2016 12:08 PM INFO [2016-11-11 10:16:20,511] [Main.java:100] Java 1.8.0_91 INFO [2016-11-11 10:16:20,511] [Main.java:101] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-11 10:16:20,511] [Main.java:102] OS: Windows 7 INFO [2016-11-11 10:16:22,856] [Main.java:150] A later version of IGV is available (2.3.84) INFO [2016-11-11 10:16:43,121] [GenomeManager.java:145] Loading genome: C:\Users\rosema1\Desktop\DOWNLOAD\batch_detection\VLHP1_sub-sequence_2214-2587.fa INFO [2016-11-11 10:16:43,152] [GenomeManager.java:192] Genome loaded. id= C:\Users\rosema1\Desktop\DOWNLOAD\batch_detection\VLHP1_sub-sequence_2214-2587.fa INFO [2016-11-11 10:16:43,389] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-11 10:17:28,928] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478827359/baseclear_GA21_ref_mut1.fa INFO [2016-11-11 10:17:28,959] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478827359/baseclear_GA21_ref_mut1.fa ERROR [2016-11-11 10:17:35,714] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478827359/mut1-1478827359-igv_session_file.xml HTTP/1.1 ERROR [2016-11-11 10:17:35,714] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-11 10:17:35,714] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-11 10:17:35,714] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-11 10:17:35,714] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-11 10:17:35,730] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-11 10:17:35,730] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-11 10:17:35,730] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-11 10:17:35,730] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-11 10:17:36,791] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/DEV/testgalaxy/mut1/1478827359/mut1-1478827359-igv_session_file.xml HTTP/1.1 ERROR [2016-11-11 10:17:37,243] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-11-11 10:17:37,243] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//mut1-1478827359-bowtie2.bam.sort.bam INFO [2016-11-11 10:17:37,305] [HttpUtils.java:827] Range-byte request succeeded INFO [2016-11-11 10:17:37,773] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//mut1-1478827359-bowtie2.bam.sort.bam.vcf INFO [2016-11-11 10:17:38,101] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//mut1-1478827359-zero_coverage_gaps.bedgraph INFO [2016-11-11 10:17:38,273] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//mut1-1478827359-below_threshold_coverage_gaps.bedgraph INFO [2016-11-11 10:17:38,397] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//anchored-mut1-1478827359-zero_coverage_gaps.bedgraph INFO [2016-11-11 10:17:38,444] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//anchored-mut1-1478827359-below_threshold_coverage_gaps.bedgraph INFO [2016-11-11 10:17:38,553] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//baseclear_GA21_ref_mut1.fa-1478827359-soft_clipping.bedgraph INFO [2016-11-11 10:17:38,600] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//baseclear_GA21_ref_mut1.fa-1478827359-non-ref_freq.bedgraph INFO [2016-11-11 10:17:38,897] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//baseclear_GA21_ref_mut1.fa-1478827359-strand_bias.bedgraph INFO [2016-11-11 10:17:39,115] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/DEV/testgalaxy/mut1/1478827359//baseclear_GA21_ref_mut1.fa-1478827359-homopolymers.bedgraph ERROR [2016-11-11 11:28:38,177] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257/GA21_mut1-1478881257-igv_session_file.xml HTTP/1.1 ERROR [2016-11-11 11:28:38,177] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-11 11:28:38,179] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-11 11:28:38,179] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-11 11:28:38,182] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-11 11:28:38,182] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-11 11:28:38,182] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-11 11:28:38,184] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-11 11:28:38,187] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-11 11:28:39,217] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257/GA21_mut1-1478881257-igv_session_file.xml HTTP/1.1 ERROR [2016-11-11 11:28:39,584] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-11-11 11:28:39,584] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//GA21_mut1-1478881257-bowtie2.bam.sort.bam INFO [2016-11-11 11:28:39,662] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//GA21_mut1-1478881257-bowtie2.bam.sort.bam.vcf INFO [2016-11-11 11:28:39,784] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//GA21_mut1-1478881257-zero_coverage_gaps.bedgraph INFO [2016-11-11 11:28:39,827] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//GA21_mut1-1478881257-below_threshold_coverage_gaps.bedgraph INFO [2016-11-11 11:28:39,904] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//anchored-GA21_mut1-1478881257-zero_coverage_gaps.bedgraph INFO [2016-11-11 11:28:39,947] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//anchored-GA21_mut1-1478881257-below_threshold_coverage_gaps.bedgraph INFO [2016-11-11 11:28:40,009] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//baseclear_GA21_ref_mut1.fa-1478881257-soft_clipping.bedgraph INFO [2016-11-11 11:28:40,044] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//baseclear_GA21_ref_mut1.fa-1478881257-non-ref_freq.bedgraph INFO [2016-11-11 11:28:40,209] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//baseclear_GA21_ref_mut1.fa-1478881257-strand_bias.bedgraph INFO [2016-11-11 11:28:40,394] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/GA21_mut1/1478881257//baseclear_GA21_ref_mut1.fa-1478881257-homopolymers.bedgraph INFO [2016-11-14 11:06:09,204] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/MIR604-ISFS1_20-5886.fa INFO [2016-11-14 11:06:09,261] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/MIR604-ISFS1_20-5886.fa ERROR [2016-11-14 11:06:17,793] [CommandExecutor.java:199] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/mir604-1479138733-igv_session_file.xml HTTP/1.1 ERROR [2016-11-14 11:06:17,795] [CommandExecutor.java:199] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-14 11:06:17,796] [CommandExecutor.java:199] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-14 11:06:17,801] [CommandExecutor.java:199] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-14 11:06:17,801] [CommandExecutor.java:199] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-14 11:06:17,803] [CommandExecutor.java:199] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-14 11:06:17,803] [CommandExecutor.java:199] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-14 11:06:17,805] [CommandExecutor.java:199] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-14 11:06:17,806] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-14 11:06:18,861] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/mir604-1479138733-igv_session_file.xml HTTP/1.1 ERROR [2016-11-14 11:06:19,182] [IGVSessionReader.java:367] Non integer version number in session file: null INFO [2016-11-14 11:06:19,184] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-14 11:06:19,251] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-14 11:06:19,409] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-zero_coverage_gaps.bedgraph INFO [2016-11-14 11:06:19,448] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-below_threshold_coverage_gaps.bedgraph INFO [2016-11-14 11:06:19,493] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//anchored-mir604-1479138733-zero_coverage_gaps.bedgraph INFO [2016-11-14 11:06:19,530] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//anchored-mir604-1479138733-below_threshold_coverage_gaps.bedgraph INFO [2016-11-14 11:06:19,570] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-soft_clipping.bedgraph INFO [2016-11-14 11:06:19,605] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-non-ref_freq.bedgraph INFO [2016-11-14 11:06:19,733] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-strand_bias.bedgraph INFO [2016-11-14 11:06:19,835] [TrackLoader.java:118] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-homopolymers.bedgraph INFO [2016-11-14 11:55:51,066] [ShutdownThread.java:51] Shutting down INFO [2016-11-14 11:58:20,182] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-14 11:58:20,182] [Main.java:135] Java 1.8.0_101 INFO [2016-11-14 11:58:20,182] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-14 11:58:20,182] [Main.java:137] OS: Windows 7 INFO [2016-11-14 11:58:45,229] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/MIR604-ISFS1_20-5886.fa INFO [2016-11-14 11:58:45,276] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/MIR604-ISFS1_20-5886.fa INFO [2016-11-14 11:58:45,454] [CommandListener.java:106] Listening on port 60151 ERROR [2016-11-14 11:58:59,076] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/mir604-1479138733-igv_session_file.xml HTTP/1.1 ERROR [2016-11-14 11:58:59,079] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-14 11:58:59,079] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-14 11:58:59,081] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-14 11:58:59,081] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-14 11:58:59,084] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-14 11:58:59,084] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-14 11:58:59,086] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-14 11:58:59,091] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(SocketInputStream.java:209) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-14 11:59:00,129] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/testgalaxy/mir604/1479138733/mir604-1479138733-igv_session_file.xml HTTP/1.1 ERROR [2016-11-14 11:59:00,650] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-14 11:59:00,655] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-14 11:59:00,708] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-14 11:59:00,985] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-14 11:59:01,148] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-zero_coverage_gaps.bedgraph INFO [2016-11-14 11:59:01,195] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//mir604-1479138733-below_threshold_coverage_gaps.bedgraph INFO [2016-11-14 11:59:01,230] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//anchored-mir604-1479138733-zero_coverage_gaps.bedgraph INFO [2016-11-14 11:59:01,263] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//anchored-mir604-1479138733-below_threshold_coverage_gaps.bedgraph INFO [2016-11-14 11:59:01,300] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-soft_clipping.bedgraph INFO [2016-11-14 11:59:01,370] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-non-ref_freq.bedgraph INFO [2016-11-14 11:59:01,490] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-strand_bias.bedgraph INFO [2016-11-14 11:59:01,613] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/testgalaxy/mir604/1479138733//MIR604-ISFS1_20-5886.fa-1479138733-homopolymers.bedgraph ERROR [2016-11-15 15:18:21,072] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:18:21,077] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:18:21,077] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:18:21,077] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:18:21,077] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:18:21,079] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:18:21,079] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:18:21,079] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:18:21,104] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(SocketInputStream.java:209) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:18:22,162] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:18:22,924] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:18:22,924] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:18:22,971] [MessageUtils.java:74] File: http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam
does not contain any sequence names which match the current genome.

File:      ZmpylD,
Genome: MIR604-ISFS1_20-5886, INFO [2016-11-15 15:18:24,736] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:18:24,901] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-soft_clip.bedgraph INFO [2016-11-15 15:19:05,430] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/ZmpylD.fa ERROR [2016-11-15 15:19:05,457] [HttpUtils.java:317] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/ZmpylD.fa at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:744) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:623) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:281) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:296) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:310) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:57) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.ui.IGV.loadGenome(IGV.java:687) at org.broad.igv.ui.IGV.loadGenome(IGV.java:668) at org.broad.igv.ui.action.LoadFromURLMenuAction.actionPerformed(LoadFromURLMenuAction.java:146) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2016-11-15 15:19:05,475] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/ZmpylD.fa ERROR [2016-11-15 15:19:43,681] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:19:43,681] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:19:43,684] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:19:43,684] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:19:43,686] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:19:43,686] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:19:43,689] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:19:43,689] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:19:43,691] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:19:43,696] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:19:44,114] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:19:44,116] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:19:44,172] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:19:44,302] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-soft_clip.bedgraph ERROR [2016-11-15 15:21:26,830] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D06_GVG00625769/NGS16013_ZmpylD_D06_GVG00625769-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:21:26,833] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:21:26,835] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:21:26,838] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:21:26,838] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:21:26,840] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:21:26,840] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:21:26,843] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:21:26,850] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(SocketInputStream.java:209) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:21:26,858] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D06_GVG00625769/NGS16013_ZmpylD_D06_GVG00625769-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:21:27,317] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:21:27,317] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D06_GVG00625769/NGS16013_ZmpylD_D06_GVG00625769.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:21:27,367] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D06_GVG00625769/NGS16013_ZmpylD_D06_GVG00625769.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:21:27,509] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D06_GVG00625769/NGS16013_ZmpylD_D06_GVG00625769-soft_clip.bedgraph ERROR [2016-11-15 15:23:45,941] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:23:45,941] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:23:45,944] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:23:45,944] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:23:45,944] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:23:45,944] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:23:45,949] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:23:45,949] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:23:45,949] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:23:45,954] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:23:46,422] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:23:46,422] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:23:46,474] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:23:46,619] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-soft_clip.bedgraph ERROR [2016-11-15 15:27:45,407] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:27:45,409] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:27:45,409] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:27:45,412] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:27:45,412] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:27:45,414] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:27:45,417] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:27:45,417] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:27:45,419] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:27:46,442] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:27:47,140] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:27:47,140] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:27:47,192] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:27:50,335] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-soft_clip.bedgraph INFO [2016-11-15 15:30:53,973] [ShutdownThread.java:51] Shutting down INFO [2016-11-15 15:31:06,928] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-15 15:31:06,928] [Main.java:135] Java 1.8.0_101 INFO [2016-11-15 15:31:06,928] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-15 15:31:06,928] [Main.java:137] OS: Windows 7 INFO [2016-11-15 15:31:26,135] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/ZmpylD.fa ERROR [2016-11-15 15:31:26,160] [HttpUtils.java:317] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/ZmpylD.fa at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:744) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:623) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:281) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:296) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:310) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:57) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:297) at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83) at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:308) at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258) at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586) at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:541) at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2516) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGV.startUp(IGV.java:2459) at org.broad.igv.ui.Main.open(Main.java:273) at org.broad.igv.ui.Main.main(Main.java:94) INFO [2016-11-15 15:31:26,190] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1479240651/NGS16013_ZmpylD_D11_GVG00625871/ZmpylD.fa INFO [2016-11-15 15:31:26,385] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-15 15:31:42,941] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/ZmpylD.fa ERROR [2016-11-15 15:31:42,973] [HttpUtils.java:317] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/ZmpylD.fa at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:744) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:623) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:281) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:296) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:310) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:57) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.ui.IGV.loadGenome(IGV.java:687) at org.broad.igv.ui.IGV.loadGenome(IGV.java:668) at org.broad.igv.ui.action.LoadFromURLMenuAction.actionPerformed(LoadFromURLMenuAction.java:146) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395) at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2016-11-15 15:31:42,991] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/ZmpylD.fa ERROR [2016-11-15 15:31:50,558] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:31:50,561] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:31:50,561] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:31:50,563] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:31:50,566] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:31:50,568] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:31:50,568] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:31:50,571] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:31:50,573] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:31:51,588] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:31:51,903] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:31:51,903] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:31:51,963] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-15 15:31:52,201] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:31:52,411] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-soft_clip.bedgraph ERROR [2016-11-15 15:34:30,619] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:34:30,619] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:34:30,621] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:34:30,621] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:34:30,624] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:34:30,624] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:34:30,624] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:34:30,626] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:34:30,626] [CommandListener.java:225] Error processing client session java.net.SocketException: Connection reset at java.net.SocketInputStream.read(SocketInputStream.java:209) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:34:30,649] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:34:31,175] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:34:31,177] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:34:31,232] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:34:31,355] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/NGS16013_ZmpylD_D10_GVG00625773-soft_clip.bedgraph ERROR [2016-11-15 15:37:39,597] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter//project/GED2458/delivered/1479241561/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:37:39,597] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-15 15:37:39,600] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-15 15:37:39,600] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-15 15:37:39,602] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-15 15:37:39,602] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-15 15:37:39,605] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-15 15:37:39,605] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-15 15:37:39,607] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-15 15:37:40,645] [CommandListener.java:167] GET /load?file=http://demeter//project/GED2458/delivered/1479241561/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-igv_session_file.xml HTTP/1.1 ERROR [2016-11-15 15:37:41,029] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-15 15:37:41,029] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479241561/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam INFO [2016-11-15 15:37:41,089] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479241561/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871.extendedFrags.mod.fastq-vs-ZmpylD.sort.bam.mod.vcf INFO [2016-11-15 15:37:41,216] [TrackLoader.java:122] Loading resource, path http://demeter/project/GED2458/delivered/1479241561/NGS16013_ZmpylD_D11_GVG00625871/NGS16013_ZmpylD_D11_GVG00625871-soft_clip.bedgraph INFO [2016-11-15 15:45:34,370] [ShutdownThread.java:51] Shutting down INFO [2016-11-16 16:13:52,196] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-16 16:13:52,196] [Main.java:135] Java 1.8.0_101 INFO [2016-11-16 16:13:52,196] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-16 16:13:52,196] [Main.java:137] OS: Windows 7 INFO [2016-11-16 16:14:10,656] [GenomeManager.java:145] Loading genome: http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/ZmpylD.fa ERROR [2016-11-16 16:14:10,688] [HttpUtils.java:317] Error fetching content length java.io.FileNotFoundException: File not found: http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/ZmpylD.fa at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:744) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:623) at org.broad.igv.util.HttpUtils.openConnectionHeadOrGet(HttpUtils.java:281) at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:296) at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:310) at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:236) at org.broad.igv.feature.genome.FastaIndexedSequence.(FastaIndexedSequence.java:57) at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:300) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167) at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129) at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:297) at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83) at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:308) at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258) at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586) at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:541) at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2516) at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57) at org.broad.igv.ui.IGV.startUp(IGV.java:2459) at org.broad.igv.ui.Main.open(Main.java:273) at org.broad.igv.ui.Main.main(Main.java:94) INFO [2016-11-16 16:14:10,719] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/GED2458/delivered/1479240295/NGS16013_ZmpylD_D10_GVG00625773/ZmpylD.fa INFO [2016-11-16 16:14:10,906] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-16 16:14:19,023] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-16 16:14:19,054] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa ERROR [2016-11-16 16:14:27,355] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:14:27,355] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-16 16:14:27,355] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-16 16:14:27,355] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-16 16:14:27,355] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-16 16:14:27,371] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-16 16:14:27,371] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-16 16:14:27,371] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-16 16:14:27,371] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-16 16:14:28,416] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:14:28,806] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-16 16:14:28,806] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-16 16:14:28,868] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-16 16:14:29,102] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-16 16:14:29,305] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:14:29,430] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:14:29,539] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:14:29,586] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:14:29,664] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-soft_clipping.bedgraph INFO [2016-11-16 16:14:29,711] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-non-ref_freq.bedgraph INFO [2016-11-16 16:14:29,914] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-strand_bias.bedgraph INFO [2016-11-16 16:14:30,054] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-homopolymers.bedgraph ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479328911/ga21_mut1-1479328911-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-16 16:17:40,861] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-16 16:17:40,861] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-16 16:17:41,922] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479328911/ga21_mut1-1479328911-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:17:42,499] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-16 16:17:42,515] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//ga21_mut1-1479328911-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-16 16:17:42,593] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//ga21_mut1-1479328911-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-16 16:17:42,702] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//ga21_mut1-1479328911-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:17:42,749] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//ga21_mut1-1479328911-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:17:42,842] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//anchored-ga21_mut1-1479328911-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:17:42,889] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//anchored-ga21_mut1-1479328911-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:17:42,967] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//baseclear_GA21_ref_mut1.fa-1479328911-soft_clipping.bedgraph INFO [2016-11-16 16:17:43,014] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//baseclear_GA21_ref_mut1.fa-1479328911-non-ref_freq.bedgraph INFO [2016-11-16 16:17:43,185] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//baseclear_GA21_ref_mut1.fa-1479328911-strand_bias.bedgraph INFO [2016-11-16 16:17:43,341] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479328911//baseclear_GA21_ref_mut1.fa-1479328911-homopolymers.bedgraph INFO [2016-11-16 16:20:07,129] [ShutdownThread.java:51] Shutting down INFO [2016-11-16 16:21:59,150] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-16 16:21:59,150] [Main.java:135] Java 1.8.0_101 INFO [2016-11-16 16:21:59,150] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-16 16:21:59,150] [Main.java:137] OS: Windows 7 INFO [2016-11-16 16:22:16,039] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-16 16:22:16,106] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-16 16:22:16,278] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-16 16:24:52,606] [ShutdownThread.java:51] Shutting down INFO [2016-11-16 16:27:49,590] [Main.java:134] Startup IGV Version 2.3.86 (137)11/01/2016 05:27 PM INFO [2016-11-16 16:27:49,590] [Main.java:135] Java 1.8.0_60 INFO [2016-11-16 16:27:49,590] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-16 16:27:49,605] [Main.java:137] OS: Windows 7 INFO [2016-11-16 16:28:12,351] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-16 16:28:12,398] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-16 16:28:12,632] [CommandListener.java:106] Listening on port 60151 ERROR [2016-11-16 16:30:36,145] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:30:36,145] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-16 16:30:36,145] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-16 16:30:36,161] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-16 16:30:36,176] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-16 16:30:36,176] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-16 16:30:36,176] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-16 16:30:36,176] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-16 16:30:36,176] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-16 16:30:37,206] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:30:37,487] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-16 16:30:37,502] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-16 16:30:37,549] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-16 16:30:37,799] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-16 16:30:37,955] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:30:38,017] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:30:38,095] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:30:38,158] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:30:38,204] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-soft_clipping.bedgraph INFO [2016-11-16 16:30:38,236] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-non-ref_freq.bedgraph INFO [2016-11-16 16:30:38,797] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-strand_bias.bedgraph INFO [2016-11-16 16:30:38,969] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-homopolymers.bedgraph INFO [2016-11-16 16:34:08,756] [IGV.java:1701] Loading 1 resources. INFO [2016-11-16 16:34:08,756] [TrackLoader.java:122] Loading resource, path http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam ERROR [2016-11-16 16:44:11,134] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:44:11,134] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-16 16:44:11,134] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-16 16:44:11,165] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-16 16:44:11,165] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-16 16:44:11,165] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-16 16:44:11,165] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-16 16:44:11,165] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-16 16:44:11,165] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at java.net.SocketInputStream.read(Unknown Source) at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) at sun.nio.cs.StreamDecoder.implRead(Unknown Source) at sun.nio.cs.StreamDecoder.read(Unknown Source) at java.io.InputStreamReader.read(Unknown Source) at java.io.BufferedReader.fill(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Unknown Source) INFO [2016-11-16 16:44:12,179] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-16 16:44:12,522] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-16 16:44:12,522] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-16 16:44:12,569] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-16 16:44:12,678] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:44:12,709] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:44:12,772] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-16 16:44:12,803] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-16 16:44:12,850] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-soft_clipping.bedgraph INFO [2016-11-16 16:44:12,881] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-non-ref_freq.bedgraph INFO [2016-11-16 16:44:13,021] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-strand_bias.bedgraph INFO [2016-11-16 16:44:13,131] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-homopolymers.bedgraph INFO [2016-11-17 07:04:10,458] [ShutdownThread.java:51] Shutting down INFO [2016-11-17 07:07:29,188] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-17 07:07:29,204] [Main.java:135] Java 1.8.0_101 INFO [2016-11-17 07:07:29,204] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-17 07:07:29,204] [Main.java:137] OS: Windows 7 INFO [2016-11-17 07:08:12,981] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 07:08:13,902] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 07:08:14,112] [CommandListener.java:106] Listening on port 60151 ERROR [2016-11-17 07:08:45,165] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-17 07:08:45,165] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-17 07:08:45,165] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-17 07:08:45,165] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-17 07:08:45,165] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-17 07:08:45,180] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-17 07:08:45,180] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-17 07:08:45,180] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-17 07:08:45,180] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-17 07:08:46,210] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-17 07:08:47,115] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-17 07:08:47,115] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-17 07:08:47,599] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-17 07:08:48,926] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-17 07:08:51,646] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-17 07:08:52,456] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-17 07:08:53,912] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-17 07:08:54,567] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-17 07:08:55,473] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-soft_clipping.bedgraph INFO [2016-11-17 07:08:56,144] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-non-ref_freq.bedgraph INFO [2016-11-17 07:08:57,759] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-strand_bias.bedgraph INFO [2016-11-17 07:08:59,868] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-homopolymers.bedgraph INFO [2016-11-17 07:13:08,442] [ShutdownThread.java:51] Shutting down INFO [2016-11-17 07:25:24,248] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-17 07:25:24,248] [Main.java:135] Java 1.8.0_101 INFO [2016-11-17 07:25:24,248] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-17 07:25:24,248] [Main.java:137] OS: Windows 7 INFO [2016-11-17 07:25:59,404] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 07:26:00,265] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 07:26:00,499] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-17 07:26:53,338] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 07:26:54,024] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa ERROR [2016-11-17 07:27:09,621] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-17 07:27:09,621] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-17 07:27:09,621] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-17 07:27:09,621] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-17 07:27:09,621] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-17 07:27:09,637] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-17 07:27:09,637] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-17 07:27:09,637] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-17 07:27:09,637] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-17 07:27:10,672] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/ga21_mut1-1479329518-igv_session_file.xml HTTP/1.1 ERROR [2016-11-17 07:27:11,327] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-17 07:27:11,327] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-17 07:27:11,951] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-17 07:27:13,105] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-17 07:27:19,025] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-17 07:27:20,559] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-17 07:27:21,781] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-zero_coverage_gaps.bedgraph INFO [2016-11-17 07:27:22,608] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//anchored-ga21_mut1-1479329518-below_threshold_coverage_gaps.bedgraph INFO [2016-11-17 07:27:23,762] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-soft_clipping.bedgraph INFO [2016-11-17 07:27:24,620] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-non-ref_freq.bedgraph INFO [2016-11-17 07:27:26,040] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-strand_bias.bedgraph INFO [2016-11-17 07:27:27,496] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//baseclear_GA21_ref_mut1.fa-1479329518-homopolymers.bedgraph INFO [2016-11-17 07:32:48,314] [IGV.java:1701] Loading 1 resources. INFO [2016-11-17 07:32:48,314] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-17 07:38:00,808] [IGV.java:1701] Loading 1 resources. INFO [2016-11-17 07:38:00,808] [TrackLoader.java:122] Loading resource, path C:\Users\rosema1\Desktop\DOWNLOAD\LEE2705\ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-17 07:51:11,874] [IGV.java:1701] Loading 1 resources. INFO [2016-11-17 07:51:11,874] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/training_session/ga21_mut1/1479329518//ga21_mut1-1479329518-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-17 10:40:50,821] [ShutdownThread.java:51] Shutting down INFO [2016-11-17 12:47:06,968] [Main.java:134] Startup IGV Version 2.3.88 (140)11/07/2016 05:47 AM INFO [2016-11-17 12:47:06,968] [Main.java:135] Java 1.8.0_101 INFO [2016-11-17 12:47:06,968] [Main.java:136] Default User Directory: \\USREPFIL01\rosema1$\Documents INFO [2016-11-17 12:47:06,968] [Main.java:137] OS: Windows 7 INFO [2016-11-17 12:47:47,231] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 12:47:48,074] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/training_session/ga21_mut1/1479329518/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 12:47:48,339] [CommandListener.java:106] Listening on port 60151 INFO [2016-11-17 12:48:02,462] [GenomeManager.java:145] Loading genome: http://demeter/project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051/baseclear_GA21_ref_mut1.fa INFO [2016-11-17 12:48:03,429] [GenomeManager.java:192] Genome loaded. id= http://demeter/project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051/baseclear_GA21_ref_mut1.fa ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: HEAD /load?file=http://demeter/project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051/ga21-1479404051-igv_session_file.xml HTTP/1.1 ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: Connection: Keep-Alive ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: Authorization: Bearer ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: User-Agent: Microsoft Office Excel 2013 (15.0.4771) Windows NT 6.1 ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: X-MS-CookieUri-Requested: t ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: X-FeatureVersion: 1 ERROR [2016-11-17 12:48:29,512] [CommandExecutor.java:208] UNKOWN COMMAND: X-IDCRL_ACCEPTED: t ERROR [2016-11-17 12:48:29,528] [CommandExecutor.java:208] UNKOWN COMMAND: Host: localhost:60151 ERROR [2016-11-17 12:48:29,528] [CommandListener.java:225] Error processing client session java.net.SocketException: Software caused connection abort: recv failed at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) at java.net.SocketInputStream.read(SocketInputStream.java:170) at java.net.SocketInputStream.read(SocketInputStream.java:141) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:151) at org.broad.igv.batch.CommandListener.run(CommandListener.java:111) at java.lang.Thread.run(Thread.java:745) INFO [2016-11-17 12:48:30,589] [CommandListener.java:167] GET /load?file=http://demeter/project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051/ga21-1479404051-igv_session_file.xml HTTP/1.1 ERROR [2016-11-17 12:48:31,213] [IGVSessionReader.java:368] Non integer version number in session file: null INFO [2016-11-17 12:48:31,228] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//ga21-1479404051-bowtie2.bam.sort.rmdup.bam.sort.bam INFO [2016-11-17 12:48:31,842] [HttpUtils.java:833] Range-byte request succeeded INFO [2016-11-17 12:48:37,177] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//ga21-1479404051-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf INFO [2016-11-17 12:48:39,813] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//ga21-1479404051-zero_coverage_gaps.bedgraph INFO [2016-11-17 12:48:40,718] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//ga21-1479404051-below_threshold_coverage_gaps.bedgraph INFO [2016-11-17 12:48:42,029] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//anchored-ga21-1479404051-zero_coverage_gaps.bedgraph INFO [2016-11-17 12:48:43,230] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//anchored-ga21-1479404051-below_threshold_coverage_gaps.bedgraph INFO [2016-11-17 12:48:44,025] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//baseclear_GA21_ref_mut1.fa-1479404051-soft_clipping.bedgraph INFO [2016-11-17 12:48:47,738] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//baseclear_GA21_ref_mut1.fa-1479404051-non-ref_freq.bedgraph INFO [2016-11-17 12:48:49,751] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//baseclear_GA21_ref_mut1.fa-1479404051-strand_bias.bedgraph INFO [2016-11-17 12:48:51,716] [TrackLoader.java:122] Loading resource, path http://demeter//project/LEE2705/TEST/TrEC-SI_training/ga21/1479404051//baseclear_GA21_ref_mut1.fa-1479404051-homopolymers.bedgraph