Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
Hello GATK team, I am working on CNV calling using Genome STRiP pipelines for human WGS data. Here I obtained a error in SVPreprocess step. Bug information is listed as follows:
INFO 23:24:12,696 FunctionEdge - Output written to /public/home/hpc202501006/ACGCanalysis/SV/genome
strip/script/logDir/SVPreprocess-18.out
INFO 23:41:05,749 QGraph - 920 Pend, 4 Run, 1 Fail, 10 Done
ERROR 23:41:05,751 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:Paralle
lGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/public/home/hpc202
501006/ACGCanalysis/SV/genomestrip/script/.queue/tmp' '-cp' '/public/home/hpc202501006/tools/svtool
kit/lib/SVToolkit.jar:/public/home/hpc202501006/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/publi
c/home/hpc202501006/tools/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T
' 'ComputeReadDepthCoverageWalker' '-R' '/public/home/hpc202501006/reflib/hg38/genome/hg38.fa' '-I
' '/public/home/hpc202501006/ACGCanalysis/realn_bam/ASDcs0036_realn.bam' '-O' '/public/home/hpc2025
01006/ACGCanalysis/SV/genomestrip/SVpreprocess/depth/ASDcs0036_realn.depth.txt' '-disableGATKTraver
sal' 'true' '-md' '/public/home/hpc202501006/ACGCanalysis/SV/genomestrip/SVpreprocess' '-configF
ile' '/public/home/hpc202501006/tools/svtoolkit/conf/genstrip_parameters.txt' '-minMapQ' '10' '-in
sertSizeRadius' '10.0'
ERROR 23:41:05,752 FunctionEdge - Contents of /public/home/hpc202501006/ACGCanalysis/SV/genomestrip/
script/logDir/SVPreprocess-12.out:
##### ERROR --
##### ERROR stack trace
org.broadinstitute.gatk.utils.commandline.MissingArgumentException:
Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing.
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:300)
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:280)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.jav
a:225)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.jav
a:158)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:95)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:66)
##### ERROR ----------------------------------------------------------------------------------------
--
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1941-0-gb493839):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known prob
lem.
##### 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: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing.
##### ERROR ----------------------------------------------------------------------------------------
--
Before this, I have red the post named ''Genomestrip cannot find --ploidyMapFile" released by Swanthana Rekulapally (https://gatk.broadinstitute.org/hc/en-us/community/posts/360068166052-Genomestrip-cannot-find-ploidyMapFile).
I do use the hg38 reference with alt contigs and I can not find the ploidyMap file before I run SVPreprocess step.
Thank you very much if you can give some advice !
-
Bob Handsaker could you take a look at this post?
-
You should consult the documentation here:
https://software.broadinstitute.org/software/genomestrip/index.html
and especially here
https://software.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html
You need to download the appropriate reference metadata bundle and use the files contained therein. If this doesn't match the reference you aligned to, then you may have difficulty.
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