Genomestrip 2.0 CNV pipeline

Question

[willgilks]

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

[fire_water]

I'm also experiencing the FunctionEdge error. Did you ever figure out the cause of it?

Answer 1

[willgilks]

I can't for the life of me remember, but the successful, working code can be found here https://zenodo.org/record/159472

[Kevin Blighe]

Hi William, if you have answered your own Question, then you can 'Accept' it as answered, which will help others coming here with the same problem.