Bugs in VQSR step: "Transport endpoint is not connected"

xiaolicbsxiaolicbs Broad InstituteMember

Hi,

I encounter an error when I try to run variant recalibration step over 50 WGS samples. This error message comes up somewhere during the program start to run but everytime it stopped at a different chromosomal location. It was really confusing since same command worked fine for me previously.

Hope to get a clue from you.

Following is the error message.

ERROR stack trace

java.lang.RuntimeException: java.io.IOException: Transport endpoint is not connected
at htsjdk.tribble.readers.LineReaderUtil$2.readLine(LineReaderUtil.java:79)
at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:23)
at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:10)
at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:449)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.next(TribbleIndexedFeatureReader.java:405)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.next(TribbleIndexedFeatureReader.java:373)
at org.broadinstitute.gatk.utils.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:60)
at org.broadinstitute.gatk.utils.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:42)
at org.broadinstitute.gatk.utils.iterators.PushbackIterator.next(PushbackIterator.java:65)
at org.broadinstitute.gatk.utils.iterators.PushbackIterator.element(PushbackIterator.java:51)
at org.broadinstitute.gatk.utils.refdata.SeekableRODIterator.next(SeekableRODIterator.java:223)
at org.broadinstitute.gatk.utils.refdata.SeekableRODIterator.next(SeekableRODIterator.java:66)
at org.broadinstitute.gatk.utils.collections.RODMergingIterator$Element.next(RODMergingIterator.java:72)
at org.broadinstitute.gatk.utils.collections.RODMergingIterator.next(RODMergingIterator.java:111)
at org.broadinstitute.gatk.utils.collections.RODMergingIterator.allElementsLTE(RODMergingIterator.java:145)
at org.broadinstitute.gatk.utils.collections.RODMergingIterator.allElementsLTE(RODMergingIterator.java:129)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.getSpanningTracks(RodLocusView.java:140)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.next(RodLocusView.java:127)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$MapDataIterator.next(TraverseLociNano.java:172)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$MapDataIterator.next(TraverseLociNano.java:153)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:271)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.io.IOException: Transport endpoint is not connected
at java.io.RandomAccessFile.readBytes0(Native Method)
at java.io.RandomAccessFile.readBytes(RandomAccessFile.java:350)
at java.io.RandomAccessFile.read(RandomAccessFile.java:385)
at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:80)
at htsjdk.tribble.TribbleIndexedFeatureReader$BlockStreamWrapper.read(TribbleIndexedFeatureReader.java:539)
at java.io.InputStream.read(InputStream.java:101)
at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:127)
at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:79)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:283)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:325)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:177)
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:298)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:354)
at htsjdk.tribble.readers.LineReaderUtil$2.readLine(LineReaderUtil.java:77)
... 32 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-128-geb484ed):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: java.io.IOException: Transport endpoint is not connected
ERROR ------------------------------------------------------------------------------------------
Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    This is a very unusual error. Are you using multithreading, by any chance? If so, can you please try again without multithreading?

  • xiaolicbsxiaolicbs Broad InstituteMember

    @Geraldine_VdAuwera said:
    Hi there,

    This is a very unusual error. Are you using multithreading, by any chance? If so, can you please try again without multithreading?

    Hi Geraldine,

    I used -nt 1 option on the command line and re-run it. Seemed like the issue still exists. This time the error message I got is slightly different: "Unable to create iterator for rod named input". Do you have an idea what might be going wrong?

    -Xiao

    Whole error message:

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named input
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:248)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:185)
    at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:93)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
    at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.(RodLocusView.java:82)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
    Caused by: java.lang.RuntimeException: java.io.IOException: Transport endpoint is not connected
    at htsjdk.tribble.readers.LineReaderUtil$2.readLine(LineReaderUtil.java:79)
    at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:23)
    at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:10)
    at htsjdk.samtools.util.AbstractIterator.hasNext(AbstractIterator.java:44)
    at htsjdk.tribble.AsciiFeatureCodec.isDone(AsciiFeatureCodec.java:53)
    at htsjdk.tribble.AsciiFeatureCodec.isDone(AsciiFeatureCodec.java:41)
    at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:446)
    at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.(TribbleIndexedFeatureReader.java:389)
    at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:258)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:241)
    ... 13 more
    Caused by: java.io.IOException: Transport endpoint is not connected
    at java.io.RandomAccessFile.readBytes0(Native Method)
    at java.io.RandomAccessFile.readBytes(RandomAccessFile.java:350)
    at java.io.RandomAccessFile.read(RandomAccessFile.java:385)
    at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:80)
    at htsjdk.tribble.TribbleIndexedFeatureReader$BlockStreamWrapper.read(TribbleIndexedFeatureReader.java:539)
    at java.io.InputStream.read(InputStream.java:101)
    at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:127)
    at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:79)
    at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:283)
    at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:325)
    at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:177)
    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:298)
    at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:354)
    at htsjdk.tribble.readers.LineReaderUtil$2.readLine(LineReaderUtil.java:77)
    ... 23 more

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.3-128-geb484ed):
    ERROR
    ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Unable to create iterator for rod named input
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    What version are you using? That doesn't look like one of our precompiled versions. Did you compile from source yourself?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @xiaolicbs
    Hi,

    Can you post the exact command you ran? This looks like an issue with your input resources files. You can try deleting the indices for the resource files and reindexing them. Also, make sure the resource files are not corrupted. You can try using VCF tools Vcf-validator.

    -Sheila

  • xiaolicbsxiaolicbs Broad InstituteMember

    @Geraldine_VdAuwera said:
    What version are you using? That doesn't look like one of our precompiled versions. Did you compile from source yourself?

    Hi Geraldine,

    I am using a version compiled by Laura (from DSDE); but I also used latest version 3.4, the issue still holds. I am now following Sheila's suggestion trying to see if there are any issues with my VCF file.

    -Xiao

  • xiaolicbsxiaolicbs Broad InstituteMember

    @Sheila said:
    xiaolicbs
    Hi,

    Can you post the exact command you ran? This looks like an issue with your input resources files. You can try deleting the indices for the resource files and reindexing them. Also, make sure the resource files are not corrupted. You can try using VCF tools Vcf-validator.

    -Sheila

    Hi Sheila,

    The command I used is:

    java -jar /xchip/gtex/xiaoli/genotype/codes/jointGenotyping/GenomeAnalysisTK.jar -T VariantRecalibrator -input /local/cga-fh/gtex/Genotyping/Individual_Set/jointcalltest/jobs/test50wgs/job.57485708/jointcalltest.raw.wgs.vcf -recalFile /xchip/gtex/xiaoli/genotype/cache/wgs50.output.snps.recal -tranchesFile /xchip/gtex/xiaoli/genotype/cache/wgs50.output.snps.tranches -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /xchip/gtex/resources/VQSR/hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /xchip/gtex/resources/VQSR/1000G_omni2.5.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /xchip/gtex/resources/VQSR/1000G_phase1.snps.high_confidence.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /xchip/gtex/resources/VQSR/dbsnp_138.b37.vcf -nt 1

    I am checking my source file, and will give you an update once I am done checking it.

    -Xiao

  • xiaolicbsxiaolicbs Broad InstituteMember

    @xiaolicbs said:

    Hi Sheila and Geraldine,

    I don't know why but my GATK worked with exact commands I run that report errors. Though I am still curious why I saw this error, the error is gone, we don't need to worry about it for now.

    Thanks so much for your help.

    -Xiao

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That sounds like a transient system glitch; I'm glad to hear it went away! If it happens again, try asking your IT support staff if something may be affecting the server.

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