igvtools on cluster

[Dario]

Hello,

I'm trying to execute igvtools (version 1.5.10, java version 1.6.0_35) on a our cluster (lustre file system) via lsf/bsub and I'm getting the exceptions below. My understanding is that igvtools requires libraries for the graphical interface, which I don't need and I don't have on the cluster.

Is there an easy workaround to avoid igvtools to avoid requiring the graphical displays?

Many thanks!
Dario

Here's the command I submitted and the exceptions:
# --------------------------------

bsub "igvtools count -e 300 myfile.bam myfile.tdf hg18"

# -------------------------------
# LSF log:
# -------------------------------

Sender: LSF System <lsfadmin@crinode19>
Subject: Job 854213: <tdf> Exited

Job <tdf> was submitted from host <uk-cri-lcst01> by user <berald01> in cluster <uk-cri-cluster01>.
Job was executed on host(s) <crinode19>, in queue <cluster>, as user <berald01> in cluster <uk-cri-cluster01>.
</home/berald01> was used as the home directory.
</lustre/sblab/berald01/repository/bam_clean> was used as the working directory.
Started at Tue Nov 13 10:18:34 2012
Results reported at Tue Nov 13 10:18:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
igvtools count -e 300 el016_hf2_9.bwa.hg18.clean.bam el016_hf2_9.bwa.hg18.clean.tdf hg18
------------------------------------------------------------

Exited with exit code 1.

Resource usage summary:

    CPU time   :      0.53 sec.
    Max Memory :         2 MB
    Max Swap   :        27 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

Computing coverage.  File = el016_hf2_9.bwa.hg18.clean.bam
Max zoom = 7
Window size = 25
Window functions: mean
Ext factor = 300
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159)
    at java.awt.Window.<init>(Window.java:433)
    at java.awt.Frame.<init>(Frame.java:403)
    at java.awt.Frame.<init>(Frame.java:368)
    at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(SwingUtilities.java:1733)
    at javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1810)
    at javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1673)
    at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:846)
    at javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:779)
    at javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:741)
    at javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:702)
    at org.broad.igv.ui.UIConstants.getIgvDirectory(UIConstants.java:190)
    at org.broad.igv.ui.UIConstants.getGenomeCacheDirectory(UIConstants.java:250)
    at org.broad.igv.feature.GenomeManager.<init>(GenomeManager.java:83)
    at org.broad.igv.feature.GenomeManager.getInstance(GenomeManager.java:93)
    at org.broad.igv.tools.IgvTools.loadGenome(IgvTools.java:425)
    at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:304)
    at org.broad.igv.tools.IgvTools.main(IgvTools.java:197)

[Jacob Silterra]

I would suggest using the latest version of IGVTools, available on the download page. A graphical environment should not be required. Errors like this can be misleading, a different error may be occurring which attempts to bring up a dialog, which then causes another error in a headless environment. The latest version is much less susceptible to this issue.

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Jacob Silterra
Software Engineer
Broad Institute