How to 'check for known problem'.

I'm new to GATK. Running the ClipReads tool yesterday produced an error. The last log line before the ##### ERROR lines was:

INFO 17:06:18,455 GATKRunReport - Uploaded run statistics report to AWS S3

After the stack trace were these lines:

ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.

How do I identify the problem so I can check to see if it is a known problem?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Generally you can try to search the forum for the error message or the top line of the stack trace. But right now the search function is broken (my bad) so just post your command line and stack trace here and I'll take a look at it.

  • UprLftCstrUprLftCstr SeattleMember
    edited March 2014
    [[email protected] JJseqfiles]$ java -jar -Xmx8g $GATKjar -T ClipReads -I $JJseqs/practice/jclp1/addrg_seq_both_sscs.bam \
    > -o $JJseqs/practice/jclp1/seq_both_sscs_clipped.bam -R $JJseqs/ref/human_g1k_v37.fasta --cyclesToTrim "1-4,80-84" \
    >  --clipRepresentation HARDCLIP_BASES --fix_misencoded_quality_scores
    INFO  17:06:02,307 HelpFormatter - --------------------------------------------------------------------------------
    INFO  17:06:02,309 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.8-1-g932cd3a, Compiled 2013/12/06 16:47:15
    INFO  17:06:02,309 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  17:06:02,309 HelpFormatter - For support and documentation go to
    INFO  17:06:02,313 HelpFormatter - Program Args: -T ClipReads -I /data/dougb/GATKtest/JJseqfiles/practice/jclp1/addrg_seq_both_sscs.bam -o /d                 ata/dougb/GATKtest/JJseqfiles/practice/jclp1/seq_both_sscs_clipped.bam -R /data/dougb/GATKtest/JJseqfiles/ref/human_g1k_v37.fasta --cyclesToT                 rim 1-4,80-84 --clipRepresentation HARDCLIP_BASES --fix_misencoded_quality_scores
    INFO  17:06:02,314 HelpFormatter - Date/Time: 2014/03/26 17:06:02
    INFO  17:06:02,314 HelpFormatter - --------------------------------------------------------------------------------
    INFO  17:06:02,314 HelpFormatter - --------------------------------------------------------------------------------
    INFO  17:06:02,406 GenomeAnalysisEngine - Strictness is SILENT
    INFO  17:06:02,479 GenomeAnalysisEngine - Downsampling Settings: No downsampling
    INFO  17:06:02,487 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO  17:06:02,505 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
    INFO  17:06:02,582 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO  17:06:02,586 GenomeAnalysisEngine - Done preparing for traversal
    INFO  17:06:02,587 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining
    INFO  17:06:02,588 ClipReads - Creating cycle clipper 0-3
    INFO  17:06:02,589 ClipReads - Creating cycle clipper 79-83
    INFO  17:06:02,590 ReadShardBalancer$1 - Loading BAM index data
    INFO  17:06:02,591 ReadShardBalancer$1 - Done loading BAM index data
    INFO  17:06:18,455 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
            at java.util.TimSort.countRunAndMakeAscending(
            at java.util.TimSort.sort(
            at java.util.Arrays.sort(
            at net.sf.samtools.util.SortingCollection.spillToDisk(
            at net.sf.samtools.util.SortingCollection.doneAdding(
            at net.sf.samtools.util.SortingCollection.iterator(
            at net.sf.samtools.util.SortingCollection.iterator(
            at net.sf.samtools.SAMFileWriterImpl.close(
            at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
            at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
            at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
            at org.broadinstitute.sting.commandline.CommandLineProgram.start(
            at org.broadinstitute.sting.commandline.CommandLineProgram.start(
            at org.broadinstitute.sting.gatk.CommandLineGATK.main(  

    Thanks Geraldine.

    Post edited by Geraldine_VdAuwera on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, this looks like a new one. First things to do are to validate your bam file (using Picard ValidateSAMFile) and test whether the error still occurs with the latest version (3.1). If the file is valid and the error reproduces with 3.1, try to narrow down the error to a small snippet of data that we can use for local debugging.

Sign In or Register to comment.