I am attempting to run GenomeSTRiP's CNVDiscoveryPipeline. I have run SVPreprocess successfully and am now running CNVDiscoveryPipeline on a single chromosome. Each command at stage 7 fails with the following stack trace:
Exception in thread "main" java.lang.RuntimeException
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:133)
Caused by: java.lang.NullPointerException
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.computeNextCoordinate(BoundaryRefinementAlgorithm.java:886)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.getRefinedInterval(BoundaryRefinementAlgorithm.java:704)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:612)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:548)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:536)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:232)
at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:204)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
... 5 more
An example command for this stage is:
'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' \
-Djava.io.tmpdir=/exports/eddie/scratch/dparry/bams/.queue/tmp' \
'-cp' '/exports/igmm/eddie/aitman-lab/svtoolkit/lib/SVToolkit.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/Queue.jar' \
'-cp' '/exports/igmm/eddie/aitman-lab/svtoolkit/lib/SVToolkit.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/exports/igmm/eddie/aitman-lab/svtoolkit/lib/gatk/Queue.jar' \
'org.broadinstitute.sv.genotyping.RefineCNVBoundaries' \
'-I' '/exports/eddie/scratch/dparry/sids_bams/per_chrom/cnv_discovery_chr22/cnv_stage6/seq_chr22/seq_chr22.merged_headers.bam' \
'-O' '/exports/eddie/scratch/dparry/sids_bams/per_chrom/cnv_discovery_chr22/cnv_stage7/seq_chr22/P0354/seq_chr22.merged.brig.vcf' \
'-R' '/exports/igmm/software/pkg/el7/apps/bcbio/share2/genomes/Hsapiens/hg38-noalt/seq/hg38-noalt.fa' \
'-md' 'sv_meta_data' \
'-configFile' '/exports/igmm/eddie/aitman-lab/svtoolkit/conf/genstrip_parameters.txt' \
'-P' 'depth.readCountCacheIgnoreGenomeMask:true' \
'-genderMapFile' 'sv_meta_data/sample_gender.report.txt' \
'-ploidyMapFile' '/exports/igmm/eddie/aitman-lab/svtoolkit/Homo_sapiens_assembly38/Homo_sapiens_assembly38.ploidymap.txt' \
'-vcf' 'per_chrom/cnv_discovery_chr22/cnv_stage4/seq_chr22/seq_chr22.merged.genotypes.vcf.gz' \
'-site' 'per_chrom/cnv_discovery_chr22/cnv_stage7/seq_chr22/P0354.sites.list' \
'-boundaryPrecision' '100' \
'-minimumRefinedLength' '500' \
'-maximumReferenceGapLength' '1000'
I have tested this on a different chromosome and get the same error. Any help figuring out what is going wrong would be much appreciated!
Thanks
Dave