INFO 01:37:48,780 QGraph - 1566 Pend, 0 Run, 1 Fail, 9 Done INFO 01:37:48,799 QCommandLine - Writing final jobs report... INFO 01:37:48,800 QJobsReporter - Writing JobLogging GATKReport to file /ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/STRiP/SVPreprocess.jobreport.txt INFO 01:37:48,822 QJobsReporter - Plotting JobLogging GATKReport to file /ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/STRiP/SVPreprocess.jobreport.pdf WARN 01:37:51,250 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 01:37:51,254 QCommandLine - Done with errors INFO 01:37:51,306 QGraph - ------- INFO 01:37:51,307 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/STRiP/tmpdir' '-cp' '/ifshk5/PC_HUMAN_PHAR/USER/weikf/bin/software/svtoolkit/lib/SVToolkit.jar:/ifshk5/PC_HUMAN_PHAR/USER/weikf/bin/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/ifshk5/PC_HUMAN_PHAR/USER/weikf/bin/software/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/ifshk5/PC_HUMAN_PHAR/USER/weikf/Lib/hg38/svtoolkit/ftp.broadinstitute.org/pub/svtoolkit/reference_metadata_bundles/Homo_sapiens_assembly38/hg38.fa' '-I' '/ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/process/CHG013302/CHG013302.bqsr.markdup.bam' '-O' '/ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/STRiP/metadata/isd/CHG013302.bqsr.markdup.hist.bin' '-disableGATKTraversal' 'true' '-md' '/ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/STRiP/metadata' '-configFile' '/ifshk5/PC_HUMAN_PHAR/USER/weikf/bin/software/svtoolkit/conf/genstrip_parameters.txt' -createEmpty INFO 01:37:51,307 QGraph - Log: /ifshk5/PC_HUMAN_PHAR/PMO/F16FTSUSAT0323_HUMunsR/results/STRiP/logs/SVPreprocess-7.out INFO 01:37:51,309 QCommandLine - Script failed: 1566 Pend, 0 Run, 1 Fail, 9 Done
