'sort base' command through port failed

[Xin Gong]

HI,

I have a java code to take the igv snapshot of variants. The following commands in java code through port are used

new
load
maxPanelHeight 5000
snapshotDirectory
goto
sort position
sort base
snapshot
..........

periodically "sort base" failed, it will be fine if I rerun it. here is the error message from igv.log file:

ERROR [2015-07-1 10:33:38,455] [DefaultExceptionHandler.java:42]  Unhandled exception
java.lang.NullPointerException
at org.broad.igv.feature.genome.SequenceWrapper.getBase(SequenceWrapper.java:50)
at org.broad.igv.feature.genome.Genome.getReference(Genome.java:430)
at org.broad.igv.sam.AlignmentInterval.getReference(AlignmentInterval.java:90)
at org.broad.igv.sam.Row.calculateScore(Row.java:65)
at org.broad.igv.sam.Row.updateScore(Row.java:40)
at org.broad.igv.sam.AlignmentDataManager.sortRows(AlignmentDataManager.java:173)
at org.broad.igv.sam.AlignmentTrack.sortRows(AlignmentTrack.java:445)
at org.broad.igv.ui.IGV.sortAlignmentTracks(IGV.java:1889)
at org.broad.igv.batch.CommandExecutor.sort(CommandExecutor.java:797)
at org.broad.igv.batch.CommandExecutor.execute(CommandExecutor.java:137)
at org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:204)

Thank you,

Xin

[Jim Robinson]

Hi,

What version if IGV is this?

Jim

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[Xin Gong]

Hi Jim,

It is 2.3.59. I had the same problem with 2.3.23.

Thanks,

Xin

[Jim Robinson]

The line numbers in the stack trace are not from 2.3.59,  that's why I asked, I'm trying to determine what line the failure is at.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/0e9a2c71-0090-4de3-acc1-33189d7e99e9%40googlegroups.com.

[Xin Gong]

Hi Jim,

Sorry about that, it was 2.3.57.

Xin

[Xin Gong]

Hi Jim,

Did you get chance to look into this issue?

Thanks,

Xin

[James Robinson]

Hi,

No progress yet, it is difficult to reproduce.    

Jim

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[Xin Gong]

Hi Jim,

I think I am able to reproduce the issue without using port command on one computer. I start igv 2.3.53, them load a bam file, then paste the position, for example, chr13:28608226-28608326, then click "go". Then I right click the reads, click "sort alignments by " -> base, then I see the following error:
ERROR [2015-09-17 16:45:24,242]  [DefaultExceptionHandler.java:42] [AWT-EventQueue-0]  Unhandled exception

java.lang.NullPointerException
    at org.broad.igv.feature.genome.SequenceWrapper.getBase(SequenceWrapper.java:50)
    at org.broad.igv.feature.genome.Genome.getReference(Genome.java:430)
    at org.broad.igv.sam.AlignmentInterval.getReference(AlignmentInterval.java:90)
    at org.broad.igv.sam.Row.calculateScore(Row.java:65)
    at org.broad.igv.sam.Row.updateScore(Row.java:40)
    at org.broad.igv.sam.AlignmentDataManager.sortRows(AlignmentDataManager.java:173)
    at org.broad.igv.sam.AlignmentTrack.sortRows(AlignmentTrack.java:445)
    at org.broad.igv.ui.IGV.sortAlignmentTracks(IGV.java:1889)

    at org.broad.igv.ui.IGV.sortAlignmentTracks(IGV.java:1879)
    at org.broad.igv.sam.AlignmentTrack.sortAlignmentTracks(AlignmentTrack.java:1221)
    at org.broad.igv.sam.AlignmentTrack$PopupMenu$8.actionPerformed(AlignmentTrack.java:1489)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$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 javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
    at java.awt.Component.processMouseEvent(Component.java:6535)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
    at java.awt.Component.processEvent(Component.java:6300)
    at java.awt.Container.processEvent(Container.java:2236)
    at java.awt.Component.dispatchEventImpl(Component.java:4891)
    at java.awt.Container.dispatchEventImpl(Container.java:2294)
    at java.awt.Component.dispatchEvent(Component.java:4713)
    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:2750)
    at java.awt.Component.dispatchEvent(Component.java:4713)
    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)

the igv is running on CentOS6.7. I got the same result using different jre, Sun 1.6, 1.7 and 1.8, I have tried the same IGV on another Linux box, CentOS 6.6, it is just fine. Please let me know if you need other information.

Xin

[Jim Robinson]

Hi,

I can't reproduce this,  the root cause is the same as when issued via the command.   However, there is enough info in the stack trace to do a check and prevent the error, which I have pushed to the snapshot build.   My concern is you should never see this (null sequence),  and the root cause is something else.

Could you try the snapshot build and see if you get the error?   You can access it at http://www.broadinstitute.org/software/igv/download_snapshot. 

Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/53d2c20e-5831-407a-9029-2fef9186ffeb%40googlegroups.com.

[Xin Gong]

Hi Jim,

Thank you very much for the quick reply.  I didn't get the nullpoint exception error with the the snapshot build. I can do the "sort base" without problem. I got one error when I paste the position and press "GO", probably it is not related.

INFO [2015-09-19 22:31:03,594]  [HttpUtils.java:829] [AWT-EventQueue-0]  Range-byte test failed -- Server does not support range-byte requests or problem with client network environment.

When are you going to roll out the snapshot build? 

Thank you!

Xin 

[Jim Robinson]

Hi,

That is not an error but is a warning that warrants investigation.   It indicates that the server, which should be listed in the preceding line,  does not support requests with the "range-byte" header.  Many file types depend on this, including sequence (fasta) and bam.   There is an inefficient workaround that IGV employs if the resources are accessible from our server, but ideally you should contact the admin of the server and see if this can be corrected.

The snapshot build will be released in the next few weeks.

Jim

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[Xin Gong]

Thank you very much, Jim

Xin

[Jim Robinson]

Hi Xin, I should mention this "range-byte" problem can also be caused if there is a proxy between your computer and the server it is trying to reach that removes the header from the request.  The "Squid" proxy for example does this with certain settings.   This is also something you network admin can address.  

Jim

[Xin Gong]

Hi Jim,

Thank you very much for your very helpful information.

Best,

Xin

[Xin Gong]

Hi Jim,

Is this fix included in the new release 2.3.61?

Thank you!

Xin

On Friday, August 14, 2015 at 11:05:35 AM UTC-4, Xin Gong wrote:

[Jim Robinson]

Hi,

Since I was not able to reproduce it I can't be sure it is fixed.    I did add some code to check for a "null" sequence before sorting,  however if the condition occurs it is unlikely to be sorted correctly.   This is a condition that should never occur,  and I don't know the root cause.

Jim

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