ERROR running SplitNCigarReads on RNAseq data using Ensembl Mus Musculus referece FASTA file

serineserine MelbourneMember
edited January 2017 in Ask the GATK team

I was trying to run this commands

~/downloads/gatk-3.7 -T SplitNCigarReads -R ~/refFiles/Mus_musculus/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa -I ../cleanRun/preqcBamFiles/H1_sorted_reordered_marked_dups.bam -o H1.intervals -U ALLOW_N_CIGAR_READS
cat ~/downloads/gatk-3.7

#!/bin/bash

jar="$HOME/downloads/GenomeAnalysisTK.jar"

exec java -Xmx3g -jar "$jar" [email protected]

I get this error about an hour into the run

##### ERROR --
##### ERROR stack trace 
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: BUG: requested unknown contig=CHR_MG132_PATCH index=-1
        at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.updateCache(MRUCachingSAMSequenceDictionary.java:178)
        at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.getSequence(MRUCachingSAMSequenceDictionary.java:109)
        at org.broadinstitute.gatk.utils.GenomeLocParser.validateGenomeLoc(GenomeLocParser.java:306)
        at org.broadinstitute.gatk.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:261)
        at org.broadinstitute.gatk.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:471)
        at org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceView.getReferenceContext(ReadReferenceView.java:98)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:140)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:128)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.aggregateMapData(TraverseReadsNano.java:119)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:101)
        at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
        at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:107)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### 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 https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: BUG: requested unknown contig=CHR_MG132_PATCH index=-1
##### ERROR ------------------------------------------------------------------------------------------

Also docs aren't accurate https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_rnaseq_SplitNCigarReads.php

has -U ALLOW_N_CIGARS but it should be -U ALLOW_N_CIGAR_READS according to cmd help and it actually worked the other option didn't

Thanks

Issue · Github
by Sheila

Issue Number
1549
State
closed
Last Updated
Assignee
Array
Closed By
ronlevine

Answers

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