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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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IGV 2.7.2 does not start - can someone give me hint? #718

Closed AKWB closed 4 years ago

AKWB commented 5 years ago

Hi,

I searched the repository, but I did not really find a solution for my issue.

I start IGV 2.7.2 with the following command: java --module-path=lib -Xmx4g @igv.args --module=org.igv/org.broad.igv.ui.Main

I am not a java-person...I tried to set the proxy in /etc/java-11-openjdk/net.properties, but this did not change. Maybe someone can help? Or give me a hint?

I get this error message: WARNING: package com.sun.java.swing.plaf.windows not in java.desktop WARNING: package sun.awt.windows not in java.desktop WARN [2019-10-24T12:51:54,108] [Globals.java:139] [main] Development mode is enabled INFO [2019-10-24T12:51:54,124] [DirectoryManager.java:179] [main] IGV Directory: /home/sem_awie/igv ERROR [2019-10-24T12:52:14,240] [OAuthUtils.java:95] [main] java.net.SocketTimeoutException: connect timed out INFO [2019-10-24T12:52:14,568] [Main.java:156] [AWT-EventQueue-0] Startup IGV Version 2.7.2 10/21/2019 11:01 PM INFO [2019-10-24T12:52:14,578] [Main.java:157] [AWT-EventQueue-0] Java 11.0.4 (build 11.0.4+11-post-Ubuntu-1ubuntu218.04.3) 2019-07-16 INFO [2019-10-24T12:52:14,578] [Main.java:160] [AWT-EventQueue-0] Java Vendor: Ubuntu https://ubuntu.com/ INFO [2019-10-24T12:52:14,579] [Main.java:162] [AWT-EventQueue-0] JVM: OpenJDK 64-Bit Server VM
INFO [2019-10-24T12:52:14,579] [DirectoryManager.java:84] [AWT-EventQueue-0] Fetching user directory... INFO [2019-10-24T12:52:14,621] [Main.java:165] [AWT-EventQueue-0] Default User Directory: /home/sem_awie INFO [2019-10-24T12:52:14,622] [Main.java:166] [AWT-EventQueue-0] OS: Linux 4.15.0-65-generic amd64 ERROR [2019-10-24T12:52:15,122] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception java.lang.NullPointerException: null at org.broad.igv.ui.IGVMenuBar.createGoogleMenu(IGVMenuBar.java:1050) ~[igv.jar:?] at org.broad.igv.ui.IGVMenuBar.createMenus(IGVMenuBar.java:186) ~[igv.jar:?] at org.broad.igv.ui.IGVMenuBar.(IGVMenuBar.java:152) ~[igv.jar:?] at org.broad.igv.ui.IGVMenuBar.lambda$createInstance$1(IGVMenuBar.java:139) ~[igv.jar:?] at org.broad.igv.ui.util.UIUtilities.invokeAndWaitOnEventThread(UIUtilities.java:166) ~[igv.jar:?] at org.broad.igv.ui.IGVMenuBar.createInstance(IGVMenuBar.java:139) ~[igv.jar:?] at org.broad.igv.ui.IGV.(IGV.java:243) ~[igv.jar:?] at org.broad.igv.ui.IGV.createInstance(IGV.java:144) ~[igv.jar:?] at org.broad.igv.ui.Main.open(Main.java:294) ~[igv.jar:?] at org.broad.igv.ui.Main.lambda$main$0(Main.java:112) ~[igv.jar:?] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) ~[?:?] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) ~[?:?] at java.awt.EventQueue$4.run(EventQueue.java:721) ~[?:?] at java.awt.EventQueue$4.run(EventQueue.java:715) ~[?:?] at java.security.AccessController.doPrivileged(Native Method) ~[?:?] at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) ~[?:?] at java.awt.EventQueue.dispatchEvent(EventQueue.java:740) ~[?:?] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) [?:?] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) [?:?] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) [?:?] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?] at java.awt.EventDispatchThread.run(EventDispatchThread.java:90) [?:?] ERROR [2019-10-24T12:52:34,666] [Main.java:221] [Thread-2] Error checking version java.net.SocketTimeoutException: connect timed out at java.net.PlainSocketImpl.socketConnect(Native Method) ~[?:?] at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399) ~[?:?] at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242) ~[?:?] at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224) ~[?:?] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403) ~[?:?] at java.net.Socket.connect(Socket.java:591) ~[?:?] at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:285) ~[?:?] at sun.net.NetworkClient.doConnect(NetworkClient.java:177) ~[?:?] at sun.net.www.http.HttpClient.openServer(HttpClient.java:474) ~[?:?] at sun.net.www.http.HttpClient.openServer(HttpClient.java:569) ~[?:?] at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:265) ~[?:?] at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:372) ~[?:?] at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191) ~[?:?] at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1187) ~[?:?] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1081) ~[?:?] at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177) ~[?:?] at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1587) ~[?:?] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1515) ~[?:?] at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527) ~[?:?] at sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:334) ~[?:?] at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:816) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:698) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:694) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:202) ~[igv.jar:?] at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:194) ~[igv.jar:?] at org.broad.igv.ui.Main.lambda$checkVersion$1(Main.java:199) [igv.jar:?] at java.lang.Thread.run(Thread.java:834) [?:?]

jrobinso commented 5 years ago

Apologies for this, it looks like a proxy issue as you suggest. We occasionally see this on Linux systems but haven't been able to reproduce it locally. It appears that java is not picking up the proxy information. IGV has a UI for setting proxy but of course if you can't start it you can't use it.

Try this as a workaround. Look in the directory "igv" in you home directory, if it doesn't exist create it. In that directory look for a file called "prefs.properties", again if it doesn't exist create it. Add the following lines to the file, substituting your proxy and port, save and restart IGV.

PROXY.USE=true PROXY.HOST={your host} PROXY.PORT={port number}

AKWB commented 5 years ago

thanks for your suggestion!! I have this pref.properties file and as I used an old version of IGV (2.4.14). The proxy information is already in there. If I start the old IGV (of course with Java 8) I also get the second part of the error message (Error checking version), but IGC starts anyway and I can work with it.

What about the first part of the error message? --> ERROR [2019-10-24T12:52:15,122] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception java.lang.NullPointerException: null at org.broad.igv.ui.IGVMenuBar.createGoogleMenu(IGVMenuBar.java:1050) ~[igv.jar:?]

or do I need to delete the igv-folder from my "old" IGV-version?

jrobinso commented 5 years ago

Are you trying to use IGV offline?

jrobinso commented 5 years ago

If you are getting those errors with the proxy information set, perhaps that proxy information is not correct. You could try removing it.

Also, could you try the "snapshot" build? I just pushed a change to protect against the specific error that stopping the startup, but you might encounter another one downstream if there is no network connection. You can download the snapshot from https://software.broadinstitute.org/software/igv/download_snapshot

AKWB commented 5 years ago

No, my PC is online... But, if the old IGV-version can use the proxy info, it should be correct, or? ok, so I will the snapshot version ;-). And come back to you. Thanks!!

AKWB commented 5 years ago

the snapshot works...I get this (Error checking version), but it does not harm IGV from working... I can also download genomes from a server. Thus, I guess everything should work?

Thanks a lot!!

jrobinso commented 5 years ago

OK, that's for confirming it. If you're able to download genomes your proxy is working. The version check is not used anymore, I will just remove that.