Hi,
Can you please help me debug some challenges that i’m having with configuring a local IGV server? As detailed below, I can see reads and variants if I load data via URLs, but not via a custom IGV server, so the problem likely lies in the way i’ve written the XML files.
We use DNAnexus, which for the purposes of accessing data in IGV standalone, you need to generate a secure URL for both the BAM, and BAI file. i.e. BAI url is not just BAM url+”.bai”. I’ve made some scripts to generate an XML representation of a DNAnexus project, creating secure download URLs, and a registry to point to these xml files. Here’s one such project (data is ok to be shared).
* IGV Snapshot is not loading BAM or VCF.gz from URLs. I get empty tracks with no reads.
* tried nesting these Resources into a Category node, but no change.
* removed genome from the Global element, but no change
My best guess is there’s something not quite right in the XML manifest. Do you know what’s going wrong here?
cheers,
Mark
igv.log for 2.3.81 when Load from Server
INFO [2016-09-20 09:13:13,258] [Main.java:133] Startup IGV Version 2.3.81 (127)08/30/2016 02:20 PM
INFO [2016-09-20 09:13:13,258] [Main.java:134] Java 1.8.0_101
INFO [2016-09-20 09:13:13,258] [DirectoryManager.java:72] Fetching user directory...
INFO [2016-09-20 09:13:13,693] [Main.java:135] Default User Directory: /Users/marcow
INFO [2016-09-20 09:13:13,694] [Main.java:136] OS: Mac OS X
INFO [2016-09-20 09:13:18,969] [GenomeManager.java:145] Loading genome: /Users/marcow/igv/genomes/1kg_v37.genome
INFO [2016-09-20 09:13:22,191] [GenomeManager.java:192] Genome loaded. id= 1kg_v37
INFO [2016-09-20 09:13:22,249] [CommandListener.java:106] Listening on port 60151
INFO [2016-09-20 09:13:29,368] [IGV.java:1700] Loading 2 resources.
INFO [2016-09-20 09:13:36,006] [HttpUtils.java:832] Range-byte request succeeded
INFO [2016-09-20 09:13:48,709] [HttpUtils.java:832] Range-byte request succeeded
INFO [2016-09-20 09:14:04,010] [ShutdownThread.java:51] Shutting down
INFO [2016-09-20 09:14:04,016] [ShutdownThread.java:51] Shutting down
ERROR [2016-09-20 09:14:04,018] [DefaultExceptionHandler.java:49] Unhandled exception
java.lang.NullPointerException
at org.broad.igv.sam.AlignmentTrack.dispose(AlignmentTrack.java:1029)
at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:57)
at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)