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Five-dollar-genome workflow failed: HaplotypeCaller4:39:1 exited with return code 1 which has not be

Hi,
I have been trying to run the five dollar genome workflow on my WGS data, but failed after running for more than 24 hours. The error is from HalotypeCaller4 as below. Any idea what I should? Thank you.

message: Job germline_single_sample_workflow.HaplotypeCaller4:39:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:38:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:2:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:33:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:20:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:36:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:32:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:30:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:27:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:22:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:34:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:40:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:46:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
message: Job germline_single_sample_workflow.HaplotypeCaller4:3:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    That particular error message you received indicates that something went wrong in that particular task. What you'll need to do is look at those tasks' error logs.

    If you scroll down, you should see a list of tasks run in your workflow. Click to expand one of the HaplotypeCaller4 tasks that showed an error in the message you posted above. (So, expand HaplotypeCaller4:3, for example.) You should see a stderr.log link, which you can click on to see the error log for that particular task. Copy that error message here and I can help you diagnose it.

  • Thank you @KateN,
    Below is the error message in the stderr.log:

    06:45:10.059 INFO ProgressMeter - chr4:79005627 36.5 232320 6365.6
    06:45:20.060 INFO ProgressMeter - chr4:79416580 36.7 234250 6389.3
    06:45:20.205 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.0690173080000003
    06:45:20.206 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 705.703881255
    06:45:20.206 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 390.75 sec
    06:45:20.206 INFO HaplotypeCaller - Shutting down engine
    [June 17, 2018 6:45:40 AM UTC] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 37.11 minutes.
    Runtime.totalMemory()=6258425856
    htsjdk.samtools.FileTruncatedException: Premature end of file: /c689a628-6a93-4f6c-af36-1cf51881f03c/germline_single_sample_workflow/dc5e5c28-42a8-40fc-b3f1-0747b0575bc6/call-GatherBamFiles/WGS_0001.bam
    at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:530)
    at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
    at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
    at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
    at java.io.DataInputStream.read(DataInputStream.java:149)
    at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:418)
    at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:394)
    at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
    at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:209)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:829)
    at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:981)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:803)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797)
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765)
    at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:1034)
    at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:1024)
    at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:988)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)
    at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)
    at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextRecord(SamReaderQueryingIterator.java:114)
    at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.next(SamReaderQueryingIterator.java:151)
    at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.next(SamReaderQueryingIterator.java:29)
    at org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.next(SAMRecordToReadIterator.java:27)
    at org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.next(SAMRecordToReadIterator.java:13)
    at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42)
    at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14)
    at org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.loadNextRead(ReadFilteringIterator.java:53)
    at org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.next(ReadFilteringIterator.java:47)
    at org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.next(ReadFilteringIterator.java:13)
    at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42)
    at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14)
    at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69)
    at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55)
    at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:49)
    at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.next(ReadsDownsamplingIterator.java:16)
    at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:42)
    at org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.next(ReadCachingIterator.java:17)
    at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71)
    at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
    at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160)
    at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315)
    at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252)
    at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104)
    at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContextToCurrentInterval(IntervalAlignmentContextIterator.java:99)
    at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:69)
    at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.next(IntervalAlignmentContextIterator.java:21)
    at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:143)
    at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135)
    at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:290)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)
    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:159)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:202)
    at org.broadinstitute.hellbender.Main.main(Main.java:288)
    Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -jar /root/gatk.jar HaplotypeCaller -R /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -I gs://fc-e9c7ffbf-a63f-44fc-85b2-7f88f2402954/c689a628-6a93-4f6c-af36-1cf51881f03c/germline_single_sample_workflow/dc5e5c28-42a8-40fc-b3f1-0747b0575bc6/call-GatherBamFiles/WGS_0001.bam -L /cromwell_root/fc-e9c7ffbf-a63f-44fc-85b2-7f88f2402954/c689a628-6a93-4f6c-af36-1cf51881f03c/germline_single_sample_workflow/dc5e5c28-42a8-40fc-b3f1-0747b0575bc6/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/13scattered.interval_list -O WGS_0001.vcf.gz -contamination 0.002771973333333333

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Hm... That's odd because the stderr file should show an error message if FireCloud is complaining the tool errored out. Could you share your workspace in FireCloud with GROUP_FireCloud-[email protected]. (Click the share button on your workspace and enter that email address.)

    Then I will also need you to give the name of the workspace as well as the submission ID for the submission that is giving you these error messages.

  • Hi @KateN, I just shared my workspace with you.
    submission ID is c689a628-6a93-4f6c-af36-1cf51881f03c

    Thank you.

  • Hi @KateN, in other few submissions, they are all failed with message: Job germline_single_sample_workflow.ValidateCram:NA:1 exited with return code 3 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.

    But from‎ ValidateCram-stderr.log, I can't tell what's wrong with it.
    The submission ID is 5d830872-2df3-421e-9a0c-d7e2606d28e5 if you can have a look. Thank you.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Thank you Bingley. I unfortunately still need the name of the workspace where you've seen this issue. As I help a lot of people, I have several hundred workspaces and it's not always easy to figure out which workspace is new.

  • Hi @KateN,
    Sorry, the workspace is fccredits-silver-pumpkin-7172/five-dollar-genome-analysis-pipeline_copy
    Submission ID: c689a628-6a93-4f6c-af36-1cf51881f03c
    And 5d830872-2df3-421e-9a0c-d7e2606d28e5

    Thank you.

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