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Invalid sequence number 0 in index file

lucasllucasl Planet EarthMember

Hi, I've been using the RealignerTargetCreator tool with a pair of BAMs representing a tumor/normal pair to do joint indel realignment, and I get the following error message:

ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Invalid sequence number 0 in index file /sc/orga/scratch/xlochol01/liver/sam/SAMEA1324465_1_recal_fix_sorted_rg.bam.bai
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.readReferenceSequence(
at org.broadinstitute.gatk.engine.datasources.reads.BAMSchedule.(
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.advance(
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.populateFilteredIntervalList(
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.createOverMappedReads(
at org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder.shardOverMappedReads(
at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.createShardIteratorOverMappedReads(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getShardStrategy(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.engine.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
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
ERROR MESSAGE: Invalid sequence number 0 in index file /sc/orga/scratch/xlochol01/liver/sam/SAMEA1324465_1_recal_fix_sorted_rg.bam.bai
ERROR ------------------------------------------------------------------------------------------

Any help with this would be appreciated.


  • SheilaSheila Broad InstituteMember, Broadie admin


    This error usually is due to incompatible reference and BAM files. Can you please post your FASTA.dict file and the BAM header? Please also try deleting the BAM index and re-generating it.


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