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SVDiscovery error with X chromosome

tfarauttfaraut Toulouse, FranceMember

Dear GenomSTRIP team,

I am using GenomSTRIP to detect deletions in goat.
I could successfully run the pipeline (SVpreprocess, SVdiscovery, and SVgenotyping) on all autosomes but the SVdiscovery script failed on the X chromosome with an error of the R script compute_depth_pvalue.R :

ERROR MESSAGE: Error running script ...../svtoolkit/R/discovery/compute_depth_pvalue.R: Error in chisq.test(m) :
ERROR all entries of 'x' must be nonnegative and finite
ERROR Calls: main -> cat -> sprintf -> depth.chisq.1
ERROR Execution halted

My command is

java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVDiscovery.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-jobProject Capri \
-jobRunner Drmaa \
-gatkJobRunner Drmaa \
-jobQueue workq \
-jobNative '-l mem=16G -l h_vmem=16G' \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R ${reference_prefix}.fasta \
-genderMaskBedFile ${reference_prefix}.gendermask.bed \
-genomeMaskFile ${reference_prefix}.svmask.fasta \
-ploidyMapFile ${reference_prefix}.ploidymap.txt \
-genderMapFile gender.map \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-jobLogDir ${runDir}/logs \
-L $chrom \
-minimumSize 100 \
-maximumSize 1000000 \
-suppressVCFCommandLines \
-I ${inputFile} \
-O ${sites} \
-run

It seems to be same problem as in
http://gatkforums.broadinstitute.org/gatk/discussion/comment/26118#Comment_26118

but I have created a reference metadata bundle for my genome.

My ploidy map is

chrX 8000000 121952644 F 2
chrX 8000000 121952644 M 1

        • 2

Thank you for your help,
Thomas Faraut

UMR 1388 INRA-INPT GenPhySE
Toulouse, France
http://genphyse.toulouse.inra.fr

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