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GenomeAnalysisTK Mutect2 Error "htsjdk.samtools.cram.CRAIIndex$CRAIIndexException: Expecting 6 col"

Dear All,

I used samtools-0.1.19 got the alignment bam file and index, then I am going to use GenomeAnalysisTK/3.5/java.1.7.0_67 to call variations, but it is not working.

If someone can give any advice, I will really appreciate it.

The error informations as follow:

INFO 13:55:57,410 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:55:57,413 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 13:55:57,413 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:55:57,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:55:57,417 HelpFormatter - Program Args: -T MuTect2 --reference_sequence /data/eg02/xhao/reference-genome/mus-musculus/grcm38_68/GRCm38_68.fa -L Y --dbsnp /data/eg02/xhao/reference-genome/mus-musculus/grcm38_mgp/mm10.dbSNP.v138.sorted.vcf --input_file:normal ../processing/4-bwa/f1.gatk.bam --input_file:tumor ../processing/4-bwa/F17.gatk.bam --out ../processing/5-mt2/mm.f1.F17.Y.mt.vcf
INFO 13:55:57,423 HelpFormatter - Executing as [email protected] on Linux 3.10.0-514.6.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_121-mockbuild_2016_11_21_19_08-b00.
INFO 13:55:57,423 HelpFormatter - Date/Time: 2018/03/14 13:55:57
INFO 13:55:57,423 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:55:57,424 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:55:57,564 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:55:57,707 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:55:57,717 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:55:57,860 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
INFO 13:55:58,756 GATKRunReport - Uploaded run statistics report to AWS S3

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

htsjdk.samtools.cram.CRAIIndex$CRAIIndexException: Expecting 6 columns but got 4
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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Expecting 6 columns but got 4
ERROR ------------------------------------------------------------------------------------------

Thank you very much!

Xiaoxiao

Answers

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