java.net.SocketTimeoutException: connect timed out

[Lakshmanan Iyer]

Hi

I am running igv seesion using xvfb-run. I am uploading a local copy of the genome:

INFO [2018-08-06 09:37:58,171]  [GenomeManager.java:186] [pool-2-thread-1]  Loading genome: /home/clcapp/igv/genomes/hg19.genome

However, on start up igv giving me this timeout error

java.net.SocketTimeoutException: connect timed out 

However, everything works fine and I get my results. I was wondering how I can either suppress this warning or avoid this connecting.

-Lax

more details...

xvfb-run --auto-servernum --server-num=1 --server-args='-screen 0, 1024x768x24' java -Dhttp.proxyHost=corpgate.labcorp.com -Dhttp.proxyPort=8080 -Xmx10000m -jar /NGS/NGSAPPS/IGV/2.4.10/igv.jar -b /NGS/QA/NGS_DATA/CLC/MYELOID/PROCESSED/2018-08/000000000-BKTLF/1812399045800_451953/igvsnapshot_images/IGV_snapshots.bat --preferences /NGS/NGSAPPS/igvsnapshot/1.0.0/prefs.properties

 

 

Current time is:

2018-08-06 09:37:26.806645

 

 

Running the IGV command...

WARN [2018-08-06 09:37:34,367]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled

INFO [2018-08-06 09:37:34,765]  [DirectoryManager.java:171] [AWT-EventQueue-0]  IGV Directory: /home/clcapp/igv

INFO [2018-08-06 09:37:34,765] [DirectoryManager.java:171]  IGV Directory: /home/clcapp/igv

INFO [2018-08-06 09:37:34,768]  [Main.java:154] [AWT-EventQueue-0]  Startup  IGV Version 2.4.10 03/20/2018 10:50 PM

INFO [2018-08-06 09:37:34,776]  [Main.java:155] [AWT-EventQueue-0]  Java 1.8.0_92

INFO [2018-08-06 09:37:34,776]  [DirectoryManager.java:76] [AWT-EventQueue-0]  Fetching user directory...

INFO [2018-08-06 09:37:34,889]  [Main.java:156] [AWT-EventQueue-0]  Default User Directory: /home/clcapp

INFO [2018-08-06 09:37:34,890]  [Main.java:157] [AWT-EventQueue-0]  OS: Linux

 

 

Aug 06, 2018 9:37:35 AM java.util.prefs.FileSystemPreferences$6 run

WARNING: Prefs file removed in background /home/clcapp/.java/.userPrefs/prefs.xml

java.net.SocketTimeoutException: connect timed out

                at java.net.PlainSocketImpl.socketConnect(Native Method)

                at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)

                at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)

                at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)

                at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)

                at java.net.Socket.connect(Socket.java:589)

                at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:668)

                at sun.net.NetworkClient.doConnect(NetworkClient.java:175)

                at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)

                at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)

                at sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:264)

                at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)

                at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)

                at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105)

                at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999)

                at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)

                at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1513)

                at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441)

                at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)

                at sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:338)

                at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:734)

                at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:611)

                at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:607)

                at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:148)

                at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:141)

                at org.broad.igv.ga4gh.OAuthUtils.fetchOauthProperties(OAuthUtils.java:135)

                at org.broad.igv.ga4gh.OAuthUtils.<init>(OAuthUtils.java:123)

                at org.broad.igv.ga4gh.OAuthUtils.<clinit>(OAuthUtils.java:104)

                at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:628)

                at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:611)

                at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:607)

                at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:148)

                at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:141)

                at org.broad.igv.ui.Main.lambda$checkVersion$0(Main.java:189)

                at java.lang.Thread.run(Thread.java:745)

INFO [2018-08-06 09:37:58,171]  [GenomeManager.java:186] [pool-2-thread-1]  Loading genome: /home/clcapp/igv/genomes/hg19.genome

INFO [2018-08-06 09:38:04,276]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box

INFO [2018-08-06 09:38:04,286]  [GenomeManager.java:275] [pool-2-thread-1]  Genome loaded.  id= hg19