Unified Genotyper Error "Expecting 6 columns but got 1"

yvonnesaarayvonnesaara GermanyMember
edited March 2016 in Ask the GATK team

Hi,
I'm trying to make variant calling with GATK and it worked on one server machine, but i had to switch and now it doesn't work anymore. I really hope you can help me. I get the following error message and i've no clue where it's coming from:

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

Post edited by yvonnesaara on

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