ReduceReads Error

aeonsimaeonsim Posts: 64Member ✭✭

The BAM files are generated with a non BWA aligner and have been processed following the GATK pipeline Indel realignment, BQSR.

java -jar GenomeAnalysisTK-2.3-5-g49ed93c/GenomeAnalysisTK.jar -R /data/seq/indexed-genomes/bos_taurus/umd31MT/umd31MT.fa -T ReduceReads -I /data/seq/chhar0/phd/GATK/Chr29-realigned-recal.bam -o Chr29-GATK-reduced.bam

INFO 20:21:36,082 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:21:36,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-5-g49ed93c, Compiled 2013/01/06 20:58:13 INFO 20:21:36,084 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 20:21:36,084 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 20:21:36,088 HelpFormatter - Program Args: -R /data/seq/indexed-genomes/bos_taurus/umd31MT/umd31MT.fa -T ReduceReads -I /data/seq/chhar0/phd/GATK/Chr29-realigned-recal.bam -o Chr29-GATK-reduced.bam INFO 20:21:36,089 HelpFormatter - Date/Time: 2013/01/07 20:21:36 INFO 20:21:36,089 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:21:36,089 HelpFormatter - -------------------------------------------------------------------------------- INFO 20:21:36,160 GenomeAnalysisEngine - Strictness is SILENT INFO 20:21:36,248 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 20:21:36,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 20:21:36,449 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.19 INFO 20:21:36,499 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 20:21:36,499 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 20:21:36,671 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 20:21:36,674 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 20:22:06,502 ProgressMeter - Chr29:33746 6.91e+05 30.0 s 43.4 s 92.5% 32.4 s 2.4 s INFO 20:22:37,291 ProgressMeter - Chr29:65146 1.34e+06 60.8 s 45.3 s 92.5% 65.7 s 4.9 s INFO 20:23:08,090 ProgressMeter - Chr29:91651 1.95e+06 91.6 s 46.9 s 92.5% 99.0 s 7.5 s INFO 20:23:43,254 ProgressMeter - Chr29:124049 2.64e+06 2.1 m 47.9 s 92.5% 2.3 m 10.3 s INFO 20:23:45,243 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IndexOutOfBoundsException: Index: 15, Size: 15 at java.util.LinkedList.entry(LinkedList.java:382) at java.util.LinkedList.get(LinkedList.java:332) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.compressVariantRegion(SlidingWindow.java:597) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:623) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:643) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.closeVariantRegions(SingleSampleCompressor.java:83) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.closeVariantRegionsInAllSamples(MultiSampleCompressor.java:94) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:76) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:387) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:87) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:226) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:215) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:254) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-5-g49ed93c):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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: Index: 15, Size: 15
ERROR ------------------------------------------------------------------------------------------
Tagged:

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,815Administrator, GATK Developer admin

    Hi there, could you please upload a snippet of your bam file for testing?

    Detailed instructions here: http://www.broadinstitute.org/gatk/guide/article?id=1894

    Geraldine Van der Auwera, PhD

  • annatannat Posts: 21Member

    Hi, I reheadered so that I now have 16 unique sample names, but am still having problems.

    java -jar /software/additional/GenomeAnalysisTK-2.3-5-g49ed93c/GenomeAnalysisTK.jar -T ReduceReads 
    -I bamForReduceReads.list -R data/abH97.fa --nwayout -o reduced.bam
    INFO  11:23:10,296 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  11:23:10,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-5-g49ed93c, Compiled 2013/01/06 20:58:13 
    INFO  11:23:10,300 HelpFormatter - Copyright (c) 2010 The Broad Institute 
    INFO  11:23:10,300 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
    INFO  11:23:10,305 HelpFormatter - Program Args: -T ReduceReads -I bamForReduceReads.list -R data/abH97.fa --nwayout -o reduced.bam 
    INFO  11:23:10,306 HelpFormatter - Date/Time: 2013/01/11 11:23:10 
    INFO  11:23:10,306 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  11:23:10,306 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  11:23:10,448 GenomeAnalysisEngine - Strictness is SILENT 
    INFO  11:23:10,705 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
    INFO  11:23:10,717 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
    INFO  11:23:10,864 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14 
    INFO  11:23:10,932 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
    INFO  11:23:10,933 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
    INFO  11:23:11,131 ReadShardBalancer$1 - Loading BAM index data for next contig 
    INFO  11:23:11,139 ReadShardBalancer$1 - Done loading BAM index data for next contig 
    INFO  11:23:17,182 GATKRunReport - Uploaded run statistics report to AWS S3 
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace 
    java.lang.NullPointerException
        at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.closeVariantRegions(SingleSampleCompressor.java:83)
        at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.closeVariantRegionsInAllSamples(MultiSampleCompressor.java:94)
        at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:76)
        at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67)
        at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:387)
        at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:87)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:226)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:215)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:254)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-5-g49ed93c):
    ##### ERROR
    ##### ERROR Please visit the wiki to see if this is a known problem
    ##### ERROR If not, please post the error, 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: Code exception (see stack trace for error itself)
    ##### ERROR ------------------------------------------------------------------------------------------
    
  • aeonsimaeonsim Posts: 64Member ✭✭

    Sample bam and Ref uploaded: reduce-reads-issue.tar.bz2

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,815Administrator, GATK Developer admin

    Thanks @aeonsim, we'll have a look at these and get back to you asap.

    Geraldine Van der Auwera, PhD

  • ebanksebanks Posts: 684GATK Developer mod

    @annat: your error should be fixed in version 2.3-8, which will be coming out later.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • annatannat Posts: 21Member

    sorry - I wrote the above comment on the wrong question. Could you remove above post please.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,815Administrator, GATK Developer admin

    That's fine, don't worry about it.

    Geraldine Van der Auwera, PhD

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