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base recalibration problem

WanboWanbo Member Posts: 8


I am working on bovine exome sequencing datasets. I have 22 animals ( the read length of 11 samples is 90 bp, others are 100 bp) . I merged all of them into a big bam file, and did Indel realignment on it. When I run BaseRecalibrator, my job was aborted on chr12. And I check the region chr12(28982297, 29984297) of my reference file with Samtools, it seems not damaged. Any suggestion?


ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

net.sf.picard.PicardException: Unable to load chr12(28982297, 29984297) from /data/Wanbo/genomes/bosTau6.fasta
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(
at org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(
at org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView.initializeReferenceSequence(
at org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView.(
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.1-13-g1706365):
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
ERROR MESSAGE: Unable to load chr12(28982297, 29984297) from /data/Wanbo/genomes/bosTau6.fasta


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,677 admin

    Hi there,

    Try validating all your input files using the Picard validation tools, that will tell you if there is anything wrong with your files.

    You can also run again using -XL argument to exclude the interval where the program choked the first time, and see if it still errors out. That may help identify whether it's a problem with the file or a problem of not enough computing resources.

    Geraldine Van der Auwera, PhD

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