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$1 - Done loading BAM index data for next contig INFO 20:22:06,502 ProgressMeter - Chr29:33746 6.91e+05 30.0 s 43.4 s 92.5% 32.4 s 2.4 s INFO 20:22:37,291 ProgressMeter - Chr29:65146 1.34e+06 60.8 s 45.3 s 92.5% 65.7 s 4.9 s INFO 20:23:08,090 ProgressMeter - Chr29:91651 1.95e+06 91.6 s 46.9 s 92.5% 99.0 s 7.5 s INFO 20:23:43,254 ProgressMeter - Chr29:124049 2.64e+06 2.1 m 47.9 s 92.5% 2.3 m 10.3 s INFO 20:23:45,243 GATKRunReport - Uploaded run statistics report to AWS S3
java.lang.IndexOutOfBoundsException: Index: 15, Size: 15 at java.util.LinkedList.entry(LinkedList.java:382) at java.util.LinkedList.get(LinkedList.java:332) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.compressVariantRegion(SlidingWindow.java:597) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:623) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:643) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.closeVariantRegions(SingleSampleCompressor.java:83) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.closeVariantRegionsInAllSamples(MultiSampleCompressor.java:94) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:76) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:387) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:87) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$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)
