[svtoolkit-help] About ComputeReadDepthCoverage error

[Jinlu C. <jin...@ei...>]

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