The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

ReduceReads Error

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 Cambridge, MAMember, Administrator, Broadie

    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

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

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

  • ebanksebanks Broad InstituteMember, Broadie, Dev

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

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

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

Sign In or Register to comment.