[svtoolkit-help] Genome Strip 2 using wrong bin size

[Wakeling, M. <M.W...@ex...>]

Hi.

I'm trying to run the LCNV detection pipeline from Genome Strip 2 on a set of 237 whole genome samples. I have performed the PreProcess and GenerateDepthProfiles stages, and am trying to run the LCNVDiscoveryPipeline stage. When I run queue, it reports that it has created 19993 jobs, however all the jobs then fail. For instance, the first job is:

INFO  08:31:37,845 FunctionEdge - Starting:    'Rscript'  '/gpfs/ts0/home/mw501/Research_Project-MRC147594/genome_sequencing/genome_strip2/svtoolkit/R/lcnv/lcnv_scan.R'  '--profileFile' 'profiles_10000/profile_seq_1_728.dat.gz'  '--targetSample' 'WG0007'  '--maxDepth' '60'  '--ploidyMapFile' '/gpfs/ts0/home/mw501/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt'  '--genderMapFile' 'output_metadata_directory/sample_gender.report.txt'  '--outputFile' 'lcnv_output/seq_1/1_WG0007.dat'

and this fails because there is no file named profiles_10000/profile_seq_1_728.dat.gz - but there is a file named profiles_10000/profile_seq_1_10000.dat.gz. I'm not sure where it is getting the 728 from.

The arguments for the three stages are:

export SV_DIR=~/Research_Project-MRC147594/genome_sequencing/genome_strip2/svtoolkit
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx4g -cp ${classpath} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -S ${SV_DIR}/qscript/SVPreprocess.q \
     -S ${SV_DIR}/qscript/SVQScript.q \
     -cp ${classpath} \
     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
     -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
     -R ~/Research_Project-MRC147594/resources/grch37/human_g1k_v37.fasta \
     -I bams.list \
     -md output_metadata_directory \
     -bamFilesAreDisjoint true \
     -copyNumberMaskFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gcmask.fasta \
     -genderMaskBedFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gendermask.bed \
     -genomeMaskFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta \
     -ploidyMapFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt \
     -readDepthMaskFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed \
     -jobLogDir logDir \
     -jobRunner ParallelShell \
     -maxConcurrentRun 16 \
     -run

export SV_DIR=~/Research_Project-MRC147594/genome_sequencing/genome_strip2/svtoolkit
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx4g -cp ${classpath} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -S ${SV_DIR}/qscript/profiles/GenerateDepthProfiles.q \
     -S ${SV_DIR}/qscript/SVQScript.q \
     -cp ${classpath} \
     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
     -R ~/Research_Project-MRC147594/resources/grch37/human_g1k_v37.fasta \
     -md output_metadata_directory \
     -profileBinSize 10000 \
     -maximumReferenceGapLength 1000 \
     -runDirectory profiles_10000 \
     -genomeMaskFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta \
     -ploidyMapFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt \
     -jobLogDir profiles_10000/logDir \
     -jobRunner ParallelShell \
     -maxConcurrentRun 16 \
     -run

export SV_DIR=~/Research_Project-MRC147594/genome_sequencing/genome_strip2/svtoolkit
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx4g -cp ${classpath} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -S ${SV_DIR}/qscript/discovery/lcnv/LCNVDiscoveryPipeline.q \
     -S ${SV_DIR}/qscript/SVQScript.q \
     -cp ${classpath} \
     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
     -R ~/Research_Project-MRC147594/resources/grch37/human_g1k_v37.fasta \
     -md output_metadata_directory \
     -profilesDir profiles_10000 \
     -runDirectory lcnv_output \
     -maxDepth 60 \
     -genomeMaskFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta \
     -ploidyMapFile ~/Research_Project-MRC147594/resources/hg19/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt \
     -genderMapFile output_metadata_directory/sample_gender.report.txt \
     -jobLogDir lcnv_output/logDir \
     -jobRunner ParallelShell \
     -maxConcurrentRun 16 \
     -run

Any assistance would be greatly appreciated.

Matthew