Re: [svtoolkit-help] About ComputeReadDepthCoverage error

[Bob H. <han...@br...>]

If you are using the pre-computed Homo_sapiens_assembly19 mask, the 
mitochondrial contig is "MT", not "chrM".
> $ grep M Homo_sapiens_assembly19.mask.101.fasta.stats
> SEQUENCE    UNMASKED    MASKED
> MT    15057    1512
The reference sequence you align to has to match the reference used to 
build the genome mask you use exactly, in every respect.

-Bob

On 10/31/12 11:44 AM, Jinlu Cai wrote:
> Dear Team members:
>
> When I run the SVTK with our 6 sample whole genome data, we get the 
> following error in ComputeReadDepthCoverage step :
>
> Standard error contained:
> INFO  03:35:39,889 HelpFormatter - 
> ---------------------------------------------
> --------------------------------------
> INFO  03:35:39,891 HelpFormatter - The Genome Analysis Toolkit (GATK) 
> v1.0-6121-
> g40e3165, Compiled 2011/09/04 20:57:29
> INFO  03:35:39,891 HelpFormatter - Copyright (c) 2010 The Broad Institute
> INFO  03:35:39,891 HelpFormatter - Please view our documentation at 
> http://www.b
> roadinstitute.org/gsa/wiki
> INFO  03:35:39,891 HelpFormatter - For support, please view our 
> support site at
> http://getsatisfaction.com/gsa
> INFO  03:35:39,892 HelpFormatter - Program Args: -T 
> ComputeReadDepthCoverage -R
> /rio1/indexes/ucsc/hg19/fasta/ucsc.hg19.fasta -I 
> /cork/jcai/bernice2/MZH12024_HU
> MzbjR/SVTK_result/merged.bam -O 
> /cork/jcai/bernice2/MZH12024_HUMzbjR/SVTK_result
> /metadata/depth/merged.depth.txt -md 
> /cork/jcai/bernice2/MZH12024_HUMzbjR/SVTK_r
> esult/metadata -genomeMaskFile 
> /cork/jcai/SVTK/mask/Homo_sapiens_assembly19.mask
> .101.fasta -minMapQ 10
> INFO  03:35:39,892 HelpFormatter - Date/Time: 2012/10/31 03:35:39
> INFO  03:35:39,892 HelpFormatter - 
> ---------------------------------------------
> --------------------------------------
> INFO  03:35:39,892 HelpFormatter - 
> ---------------------------------------------
> --------------------------------------
> INFO  03:35:39,897 GenomeAnalysisEngine - Strictness is SILENT
> INFO  03:35:40,866 ComputeReadDepthCoverageWalker - Using genome mask 
> /cork/jcai
> /SVTK/mask/Homo_sapiens_assembly19.mask.101.fasta
> ##### ERROR 
> --------------------------------------------------------------------
> ----------------------
> ##### ERROR stack trace
> java.lang.IllegalArgumentException: Invalid sequence position: chrM:45
> at org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskF
> astaFile.java:80)
> at org.broadinstitute.sv.common.ReadCountAlgorithm.shouldCountRecord(Rea
> dCountAlgorithm.java:260)
> at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.m
> ap(ComputeReadDepthCoverageWalker.java:72)
> at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.m
> ap(ComputeReadDepthCoverageWalker.java:38)
> at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(Trave
> rseReads.java:101)
> at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(Trave
> rseReads.java:49)
> at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
> LinearMicroScheduler.java:70)
> at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnal
> ysisEngine.java:234)
> at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLi
> neExecutable.java:113)
> at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command
> LineProgram.java:221)
> at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.ja
> va:87)
> ##### ERROR 
> --------------------------------------------------------------------
> ----------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165):
> ##### ERROR
> ##### 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 wiki for extensive documentation 
> http://www.broadinstitute
> .org/gsa/wiki
> ##### ERROR Visit our forum to view answers to commonly asked 
> questions http://g
> etsatisfaction.com/gsa
> ##### ERROR
> ##### ERROR MESSAGE: Invalid sequence position: chrM:45
> ##### ERROR 
> --------------------------------------------------------------------
> ----------------------
>
> Thanks.
>
> Jinlu Cai
>
>
> ------------------------------------------------------------------------------
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