ReduceReads Error
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Comments (9)

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 ------------------------------------------------------------------------------------------

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