Hi,
I was trying to make variant calling with GATK and the problem was
somehow caused due to an invalid header created by samtools (version
1.3) in the .bai file after sorting. With samtools 0.1.19 it's ok and
passes regularly also the ValidateSamFile of Picard and GATK UG has no
problem anymore.. I got the following error message and i've no clue
where it's coming from. I wanted to report it.
INFO 13:58:47,872 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:58:48,095 GenomeAnalysisEngine - Downsampling Settings: Method:
BY_SAMPLE, Target Coverage: 250
INFO 13:58:48,103 SAMDataSource$SAMReaders - Initializing SAMRecords in
serial
INFO 13:58:48,145 SAMDataSource$SAMReaders - Done initializing BAM
readers: total time 0.04
INFO 13:58:49,285 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR
------------------------------------------------------------------------------------------
ERROR stack trace
htsjdk.samtools.cram.CRAIIndex$CRAIIndexException: Expecting 6 columns
but got 1
at htsjdk.samtools.cram.CRAIEntry.(CRAIEntry.java:51)
at htsjdk.samtools.cram.CRAIEntry.fromCraiLine(CRAIEntry.java:45)
at htsjdk.samtools.cram.CRAIIndex.readIndex(CRAIIndex.java:43)
at
htsjdk.samtools.cram.CRAIIndex.openCraiFileAsBaiStream(CRAIIndex.java:128)
at htsjdk.samtools.SamIndexes.asBaiSeekableStreamOrNull(SamIndexes.java:78)
at
org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:314)
at
org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.(GATKBAMIndex.java:97)
at
org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.(SAMDataSource.java:388)
at
org.broadinstitute.gatk.engine.GenomeAnalysisEngine.createReadsDataSource(GenomeAnalysisEngine.java:931)
at
org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:822)
at
org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
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:106)
ERROR
------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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 MESSAGE: Expecting 6 columns but got 1
ERROR
------------------------------------------------------------------------------------------
Many thanks!
Yvonne
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