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Input/output error while running combineGVCFs

tungvutungvu VietnamMember

Hi, as the title said, I was trying to combineGVCFs around 120 gvcfs into 1 gvcfs. The initial steps went fine until it reaches chromosome 10 then it prints out the following errors; I've tried multiple times with the same shutdown at chromosome 10.

I was running: ~/toolbox/gatk-4.1.2.0/gatk --java-options "-Xmx28g" CombineGVCFs -R ~/resources/ucsc.hg19.fasta --variant batch1.list -O batch1.g.vcf

Error:
01:16:03.156 INFO ProgressMeter - chr10:23399342 717.5 487779000 679866.7
01:16:15.224 INFO CombineGVCFs - Shutting down engine
[August 7, 2019 1:16:15 AM ICT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 720.20 minutes.
Runtime.totalMemory()=15668871168
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Input/output error
at htsjdk.tribble.readers.SynchronousLineReader.readLine(SynchronousLineReader.java:53)
at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:24)
at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:11)
at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:70)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:373)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:354)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:315)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:394)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:379)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:101)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:117)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:122)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.io.IOException: Input/output error
at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
at sun.nio.ch.IOUtil.read(IOUtil.java:197)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
at java.io.InputStream.read(InputStream.java:101)
at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:132)
at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:84)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at htsjdk.tribble.readers.LongLineBufferedReader.fill(LongLineBufferedReader.java:140)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:300)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:356)
at htsjdk.tribble.readers.SynchronousLineReader.readLine(SynchronousLineReader.java:51)
... 30 more

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Best Answer

  • tungvutungvu Vietnam
    edited August 16 Accepted Answer

    @bshifaw said:
    Hi @tungvu

    Try the following:

    1) Validating your GVCFs using ValidateVariants to make sure nothing is wrong with the format.
    2) Add temp directory to your command --tmp-dir and set it to a directory with ample diskspace.

    Hi, I figured it was something to do with gatk4 so I went with gatk3.7; The error output of gatk3.7 were more informative: org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named variant102.

    Revalidate variant102 on my list came out normal but I ran genotypeGVCFs for variant102 again anyway and combineGVCFs works flawlessly.

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin

    Hi @tungvu

    Try the following:

    1) Validating your GVCFs using ValidateVariants to make sure nothing is wrong with the format.
    2) Add temp directory to your command --tmp-dir and set it to a directory with ample diskspace.

  • tungvutungvu VietnamMember
    edited August 16 Accepted Answer

    @bshifaw said:
    Hi @tungvu

    Try the following:

    1) Validating your GVCFs using ValidateVariants to make sure nothing is wrong with the format.
    2) Add temp directory to your command --tmp-dir and set it to a directory with ample diskspace.

    Hi, I figured it was something to do with gatk4 so I went with gatk3.7; The error output of gatk3.7 were more informative: org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named variant102.

    Revalidate variant102 on my list came out normal but I ran genotypeGVCFs for variant102 again anyway and combineGVCFs works flawlessly.

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