Entering edit mode
8.7 years ago
willgilks
▴
360
Hi,
I'm running Genomestrip/2.0 on a Linux SGE, 222 individuals, 160Mb genome size. My deletion genotyping pipeline is working fine but the CNV errors-out with:
ERROR 15:25:44,924 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/tmpdir' '-cp' '/cm/shared/apps/svtoolkit/2.0.1602//lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602//lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602//lib/gatk/Queue.jar' '-cp' '/cm/shared/apps/svtoolkit/2.0.1602/lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/lhm_RG_bams.list' '-O' '/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/lhm_rg_gstrip_small/bam_headers/merged_headers.bam' '-L' 'NONE'
ERROR 15:25:44,932 FunctionEdge - Contents of /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/lhm_rg_gstrip_small/logs/CNVDiscoveryPipeline-1.out:
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sv/apps/ExtractBAMSubset : Unsupported major.minor version 51.0
It looks as though the problem might be caused by not finding the ExtractBAMSubset function. Does anyone know how I can fix this? My inputs are below.
Sincerely,
William Gilks
module load sge
module load genomestrip/2.0
module load jre/1.7.0_25
SV_TMPDIR=./tmpdir
SV_DIR=/cm/shared/apps/svtoolkit/2.0.1602/
runDir=lhm_rg_gstrip_small
bams=lhm_RG_bams.list
ref_seq=local_ref/dm6.fa
my_config=adjuvants/genstrip_test3_parameters.txt
genome_mask=ref_metadata/dm6.svmask.fasta
depth_mask=ref_metadata/dm6.rdmask.bed
ploidy=adjuvants/ploidy_dm6.map
gender_map=adjuvants/gstrip_lhm_rg_gender.map
out_pf=lhm_rg_gstrip_CNV_small
which java > /dev/null || exit 1
which Rscript > /dev/null || exit 1
which samtools > /dev/null || exit 1
export PATH=${SV_DIR}/bwa:${PATH}
export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
mx="-Xmx4g" classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar
## (preprocessing already done)
java -cp ${classpath} ${mx} org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-jobRunner Drmaa \
-gatkJobRunner Drmaa \
-jobNative '-v SV_DIR' \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${my_config} \
-R ${ref_seq} \
-I ${bams} \
-genderMapFile ${gender_map} \
-md ${runDir}/metadata \
-runDirectory ${runDir} \
-jobLogDir ${runDir}/logs \
-genomeMaskFile ${genome_mask} \
-readDepthMaskFile ${depth_mask} \
-ploidyMapFile ${ploidy} \
-tempDir ${SV_TMPDIR} \
-disableGATKTraversal \
-L chr2L
-maximumSize 10000 \
-minimumSize 200 \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-debug true \
-run \
|| exit 1
I'm also experiencing the FunctionEdge error. Did you ever figure out the cause of it?