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