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Timeout Error while using CNNScoreVariants

Hi all,
I had a question. While running CNNScoreVariants I'm getting this message:
Timeout waiting for background stream write to complete
The message pops out always in the same position at the log, but I can't say exactly what causes it since I have no output file.
The command line I use is:

/gatk  --java-options "-Xmx4g" \
  CNNScoreVariants \
  --output output.vcf  \
  -R hg19.fa \
  --tensor-type read_tensor \
  --read-validation-stringency SILENT \
  --lenient \
  --variant input.vcf
--input sample1.bam \
--input sample2.bam \
--input sample3.bam 

The 3 samples provided as bam files are the same in the VCF file and they have matching names.
The last position reported in the progress meter is always the same. See below the full error.
Any help would be appreciated! Thanks!

Riccardo

The exact error I get is:

02:35:15.244 INFO  ProgressMeter -       chr1:121369795            610.9                620000           1014.9
02:36:10.389 INFO  ProgressMeter -       chr1:121385379            611.8                621000           1015.0
02:37:31.393 INFO  ProgressMeter -       chr1:121404184            613.2                622000           1014.4
02:38:30.521 INFO  ProgressMeter -       chr1:121434185            614.2                623000           1014.4
02:39:30.832 INFO  ProgressMeter -       chr1:121468162            615.2                624000           1014.3
02:41:30.623 INFO  ProgressMeter -       chr1:142538024            617.2                625000           1012.7
02:43:37.629 INFO  CNNScoreVariants - Shutting down engine
[June 21, 2018 2:43:37 AM CEST] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 619.34 minutes.
Runtime.totalMemory()=3863478272
org.broadinstitute.hellbender.exceptions.GATKException: Timeout waiting for background stream write to complete
    at org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriterService.waitForPreviousBatchCompletion(AsynchronousStreamWriterService.java:96)
    at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.sendBatchIfReady(CNNScoreVariants.java:319)
    at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.apply(CNNScoreVariants.java:297)
    at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:109)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    at java.util.Iterator.forEachRemaining(Iterator.java:116)
    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:107)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:994)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

Best Answer

  • samwellsamwell Cambridge, MA ✭✭
    Accepted Answer

    @berutti The timeouts have been removed in the latest version of the tool. If you clone the latest GATK code from the github repository this issue should be resolved. We will cut a release shortly that includes this fix as well. Sorry for the inconvenience.

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