Is this likely to be something wrong with my bam.bai file?
INFO 00:33:22,970 HelpFormatter - -------------------------------------------------------------------------------- INFO 00:33:22,975 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 00:33:22,975 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 00:33:22,975 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 00:33:22,980 HelpFormatter - Program Args: -T HaplotypeCaller -R /scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta -I Project_1410AHP-0004_ElenaSchiff_211samples/align/data//61_sorted_unique.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -stand_call_conf 30.0 -stand_emit_conf 10.0 -L 22 --downsample_to_coverage 200 --GVCFGQBands 10 --GVCFGQBands 20 --GVCFGQBands 50 -o Project_1410AHP-0004_ElenaSchiff_211samples/gvcf/data//61_chr22.gvcf.gz INFO 00:33:22,989 HelpFormatter - Executing as rmhanpo@groucho-1-2.local on Linux 2.6.18-371.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18. INFO 00:33:22,989 HelpFormatter - Date/Time: 2014/12/28 00:33:22 INFO 00:33:22,989 HelpFormatter - -------------------------------------------------------------------------------- INFO 00:33:22,989 HelpFormatter - -------------------------------------------------------------------------------- WARN 00:33:23,015 GATKVCFUtils - Creating Tabix index for Project_1410AHP-0004_ElenaSchiff_211samples/gvcf/data/61_chr22.gvcf.gz, ignoring user-specified index type and parameter INFO 00:33:23,649 GenomeAnalysisEngine - Strictness is SILENT INFO 00:33:23,823 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 200 INFO 00:33:23,831 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 00:33:23,854 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 00:33:23,862 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 00:33:23,869 IntervalUtils - Processing 51304566 bp from intervals INFO 00:33:24,114 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 00:33:25,977 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Index: unable to reposition file channel of index file Project_1410AHP-0004_ElenaSchiff_211samples/align/data/61_sorted_unique.bam.bai at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.skipBytes(GATKBAMIndex.java:438) at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.skipToSequence(GATKBAMIndex.java:295) at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.readReferenceSequence(GATKBAMIndex.java:127) at org.broadinstitute.gatk.engine.datasources.reads.BAMSchedule.(BAMSchedule.java:104) at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:295) at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.advance(BAMScheduler.java:184) at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.populateFilteredIntervalList(BAMScheduler.java:104) at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.createOverIntervals(BAMScheduler.java:78) at org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder.shardOverIntervals(IntervalSharder.java:59) at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.createShardIteratorOverIntervals(SAMDataSource.java:1173) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getShardStrategy(GenomeAnalysisEngine.java:623) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: unable to reposition file channel of index file Project_1410AHP-0004_ElenaSchiff_211samples/align/data/61_sorted_unique.bam.bai
ERROR ------------------------------------------------------------------------------------------