GenomeSTRiP SVPreprocess error
Hello, I ran GenomeSTRiP SVPreprocess in ubuntu 18.04 server, not a cluster, and I met an error.
Command: "java -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 $REF/hg19.fa \
-I $inputDir/input.bam \
-md $outputDir \
-jobLogDir $logDir \
-run
Version of svtoolkit: "SVToolkit version 2.00 (build 1982)"
Here is my std out when SVPreprocess is running. The error messages are presented bold.
INFO 12:48:08,606 QScriptManager - Compiling 2 QScripts
INFO 12:48:12,700 QScriptManager - Compilation complete
INFO 12:48:12,768 HelpFormatter - ----------------------------------------------------------------------
INFO 12:48:12,768 HelpFormatter - Queue v3.7.GS-r1941-0-gb493839, Compiled 2020/08/05 21:22:05
INFO 12:48:12,769 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 12:48:12,769 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:48:12,769 HelpFormatter - Program Args: -S /BiO/Install/svtoolkit/qscript/SVPreprocess.q -S /BiO/Install/svtoolkit/qscript/SVQScript.q -cp /BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar -gatk /BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /BiO/Install/svtoolkit/conf/genstrip_parameters.txt -R /BiO/Reference/hg19.fa -I /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/input/input.bam -md /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output -jobLogDir /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log -run
INFO 12:48:12,770 HelpFormatter - Executing as pmc09@snubh on Linux 4.15.0-169-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_342-8u342-b07-0ubuntu1~18.04-b07.
INFO 12:48:12,771 HelpFormatter - Date/Time: 2022/09/15 12:48:12
INFO 12:48:12,771 HelpFormatter - ----------------------------------------------------------------------
INFO 12:48:12,771 HelpFormatter - ----------------------------------------------------------------------
INFO 12:48:12,775 QCommandLine - Scripting SVPreprocess
INFO 12:48:12,889 QCommandLine - Added 72 functions
INFO 12:48:12,889 QGraph - Generating graph.
INFO 12:48:12,907 QGraph - Running jobs.
INFO 12:48:12,933 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt'
INFO 12:48:12,934 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-1.out
INFO 12:48:16,426 FunctionEdge - Starting: 'java' '-Xmx3072m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-R' '/BiO/Reference/hg19.fa' '-L' 'NONE' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/input/input.bam' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/headers.bam'
INFO 12:48:16,426 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-3.out
INFO 12:48:20,041 QGraph - 70 Pend, 2 Run, 0 Fail, 0 Done
INFO 12:48:42,932 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt'
INFO 12:48:42,933 FunctionEdge - Done: 'java' '-Xmx3072m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-R' '/BiO/Reference/hg19.fa' '-L' 'NONE' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/input/input.bam' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/headers.bam'
INFO 12:48:42,934 QGraph - Writing incremental jobs reports...
INFO 12:48:42,934 QJobsReporter - Writing JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.txt
INFO 12:48:42,950 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.SVToolkitInfo'
INFO 12:48:42,950 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-2.out
INFO 12:48:43,024 FunctionEdge - Starting: samtools index /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/headers.bam
INFO 12:48:43,024 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-4.out
INFO 12:48:43,038 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-R' '/BiO/Reference/hg19.fa' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/genome_sizes.txt'
INFO 12:48:43,038 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-5.out
INFO 12:49:53,386 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-R' '/BiO/Reference/hg19.fa' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-writeReferenceProfile' 'true' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/gcprofile/reference.gcprof.zip'
INFO 12:49:53,386 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-6.out
INFO 12:53:17,585 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/BiO/Reference/hg19.fa' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/input/input.bam' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.hist.bin' '-disableGATKTraversal' 'true' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt' '-chimerismFile' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.chimer.dat' '-createHistogramFile' 'true' -createEmpty
INFO 12:53:17,585 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-7.out
INFO 13:20:49,087 QGraph - 65 Pend, 5 Run, 0 Fail, 2 Done
INFO 13:20:49,089 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.SVToolkitInfo'
INFO 13:20:49,090 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-R' '/BiO/Reference/hg19.fa' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/genome_sizes.txt'
INFO 13:20:49,091 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/BiO/Reference/hg19.fa' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/input/input.bam' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.hist.bin' '-disableGATKTraversal' 'true' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt' '-chimerismFile' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.chimer.dat' '-createHistogramFile' 'true' -createEmpty
INFO 13:20:49,091 FunctionEdge - Done: samtools index /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/headers.bam
ERROR 13:20:49,093 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-R' '/BiO/Reference/hg19.fa' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-writeReferenceProfile' 'true' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/gcprofile/reference.gcprof.zip'
ERROR 13:20:49,095 FunctionEdge - Contents of /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-6.out:
INFO 12:49:56,805 HelpFormatter - ----------------------------------------------------------
INFO 12:49:56,808 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGCProfiles
INFO 12:49:56,811 HelpFormatter - Program Args: -R /BiO/Reference/hg19.fa -md /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output -writeReferenceProfile true -configFile /BiO/Install/svtoolkit/conf/genstrip_parameters.txt -O /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/gcprofile/reference.gcprof.zip
INFO 12:49:56,826 HelpFormatter - Executing as pmc09@snubh on Linux 4.15.0-169-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_342-8u342-b07-0ubuntu1~18.04-b07.
INFO 12:49:56,827 HelpFormatter - Date/Time: 2022/09/15 12:49:56
INFO 12:49:56,827 HelpFormatter - ----------------------------------------------------------
INFO 12:49:56,827 HelpFormatter - ----------------------------------------------------------
INFO 12:49:56,833 ComputeGCProfiles - Opening reference sequence ...
INFO 12:49:56,833 ComputeGCProfiles - Opened reference sequence.
INFO 12:49:56,834 ComputeGCProfiles - Reading metadata ...
INFO 12:49:56,834 MetaData - Opening metadata ...
INFO 12:49:56,835 MetaData - Adding metadata location /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output ...
INFO 12:49:56,839 MetaData - Opened metadata.
INFO 12:49:56,839 ComputeGCProfiles - Read metadata.
INFO 12:49:56,839 ComputeGCProfiles - Initializing algorithm ...
INFO 12:49:56,841 ComputeGCProfiles - Algorithm initialized.
INFO 12:49:56,841 ComputeGCProfiles - Computing reference GC profile ...
#DBG: Thu Sep 15 12:49:56 KST 2022 computing reference profile for the interval chr1:1-249250621
#DBG: Thu Sep 15 12:50:13 KST 2022 computing reference profile for the interval chr2:1-243199373
#DBG: Thu Sep 15 12:50:29 KST 2022 computing reference profile for the interval chr3:1-198022430
#DBG: Thu Sep 15 12:50:42 KST 2022 computing reference profile for the interval chr4:1-191154276
#DBG: Thu Sep 15 12:50:55 KST 2022 computing reference profile for the interval chr5:1-180915260
#DBG: Thu Sep 15 12:51:07 KST 2022 computing reference profile for the interval chr6:1-171115067
#DBG: Thu Sep 15 12:51:18 KST 2022 computing reference profile for the interval chr7:1-159138663
#DBG: Thu Sep 15 12:51:29 KST 2022 computing reference profile for the interval chr8:1-146364022
#DBG: Thu Sep 15 12:51:39 KST 2022 computing reference profile for the interval chr9:1-141213431
#DBG: Thu Sep 15 12:51:48 KST 2022 computing reference profile for the interval chr10:1-135534747
#DBG: Thu Sep 15 12:51:57 KST 2022 computing reference profile for the interval chr11:1-135006516
#DBG: Thu Sep 15 12:52:06 KST 2022 computing reference profile for the interval chr12:1-133851895
#DBG: Thu Sep 15 12:52:15 KST 2022 computing reference profile for the interval chr13:1-115169878
#DBG: Thu Sep 15 12:52:22 KST 2022 computing reference profile for the interval chr14:1-107349540
#DBG: Thu Sep 15 12:52:28 KST 2022 computing reference profile for the interval chr15:1-102531392
#DBG: Thu Sep 15 12:52:34 KST 2022 computing reference profile for the interval chr16:1-90354753
#DBG: Thu Sep 15 12:52:40 KST 2022 computing reference profile for the interval chr17:1-81195210
#DBG: Thu Sep 15 12:52:45 KST 2022 computing reference profile for the interval chr18:1-78077248
#DBG: Thu Sep 15 12:52:50 KST 2022 computing reference profile for the interval chr19:1-59128983
#DBG: Thu Sep 15 12:52:54 KST 2022 computing reference profile for the interval chr20:1-63025520
#DBG: Thu Sep 15 12:52:58 KST 2022 computing reference profile for the interval chr21:1-48129895
#DBG: Thu Sep 15 12:53:01 KST 2022 computing reference profile for the interval chr22:1-51304566
#DBG: Thu Sep 15 12:53:04 KST 2022 computing reference profile for the interval chrX:1-155270560
#DBG: Thu Sep 15 12:53:14 KST 2022 computing reference profile for the interval chrY:1-59373566
#DBG: Thu Sep 15 12:53:17 KST 2022 computing reference profile for the interval chrM:1-16571
INFO 12:53:17,524 ComputeGCProfiles - Reference GC profile initialized.
INFO 12:53:17,524 CommandLineProgram - Program completed.
------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------
INFO 13:20:49,096 QGraph - Writing incremental jobs reports...
INFO 13:20:49,096 QJobsReporter - Writing JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.txt
INFO 13:20:49,104 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.hist.bin' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.hist.bin'
INFO 13:20:49,104 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-8.out
INFO 13:20:53,418 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeChimerismFiles' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.chimer.dat' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/chimerism.dat'
INFO 13:20:53,418 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-11.out
INFO 13:20:56,873 QGraph - 63 Pend, 2 Run, 1 Fail, 6 Done
INFO 13:21:19,104 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeChimerismFiles' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.chimer.dat' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/chimerism.dat'
INFO 13:21:19,105 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd/input.hist.bin' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.hist.bin'
INFO 13:21:19,105 QGraph - Writing incremental jobs reports...
INFO 13:21:19,105 QJobsReporter - Writing JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.txt
INFO 13:21:19,117 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.hist.bin' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.dist.bin'
INFO 13:21:19,118 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-9.out
INFO 13:21:26,662 QGraph - 62 Pend, 1 Run, 1 Fail, 8 Done
INFO 13:21:49,117 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.hist.bin' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.dist.bin'
INFO 13:21:49,117 QGraph - Writing incremental jobs reports...
INFO 13:21:49,117 QJobsReporter - Writing JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.txt
INFO 13:21:49,129 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.dist.bin' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.stats.dat'
INFO 13:21:49,129 FunctionEdge - Output written to /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-10.out
INFO 13:21:52,631 QGraph - 61 Pend, 1 Run, 1 Fail, 9 Done
INFO 13:22:19,129 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.dist.bin' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/isd.stats.dat'
INFO 13:22:19,129 QGraph - Writing incremental jobs reports...
INFO 13:22:19,129 QJobsReporter - Writing JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.txt
INFO 13:22:19,137 QGraph - 61 Pend, 0 Run, 1 Fail, 10 Done
INFO 13:22:19,138 QCommandLine - Writing final jobs report...
INFO 13:22:19,138 QJobsReporter - Writing JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.txt
INFO 13:22:19,142 QJobsReporter - Plotting JobLogging GATKReport to file /BiO/home/pmc09/SVPreprocess.jobreport.pdf
WARN 13:22:20,735 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info.
INFO 13:22:20,737 QCommandLine - Done with errors
INFO 13:22:20,742 QGraph - -------
INFO 13:22:20,743 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/home/pmc09/.queue/tmp' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/Install/svtoolkit/lib/SVToolkit.jar:/BiO/Install/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/Install/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-R' '/BiO/Reference/hg19.fa' '-md' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output' '-writeReferenceProfile' 'true' '-configFile' '/BiO/Install/svtoolkit/conf/genstrip_parameters.txt' '-O' '/BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/output/gcprofile/reference.gcprof.zip'
INFO 13:22:20,743 QGraph - Log: /BiO/home/pmc09/results/20220915_GenomeSTRiP_test_2/log/SVPreprocess-6.out
INFO 13:22:20,744 QCommandLine - Script failed: 61 Pend, 0 Run, 1 Fail, 10 Done
------------------------------------------------------------------------------------------
Done. There were 1 WARN messages, the first 1 are repeated below.
WARN 13:22:20,735 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info.
------------------------------------------------------------------------------------------
The contents of SVPreprocess-6.out is like below:
INFO 10:24:20,496 HelpFormatter - ----------------------------------------------------------
INFO 10:24:20,497 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGCProfiles
INFO 10:24:20,500 HelpFormatter - Program Args: -R /BiO/Reference/hg19.fa -md /BiO/home/pmc09/results/20220915_GenomeSTRiP_test/output -writeReferenceProfile true -configFile /BiO/Install/svtoolkit/conf/genstrip_parameters.txt -O /BiO/home/pmc09/results/20220915_GenomeSTRiP_test/output/gcprofile/reference.gcprof.zip
INFO 10:24:20,515 HelpFormatter - Executing as pmc09@snubh on Linux 4.15.0-169-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_342-8u342-b07-0ubuntu1~18.04-b07.
INFO 10:24:20,515 HelpFormatter - Date/Time: 2022/09/15 10:24:20
INFO 10:24:20,516 HelpFormatter - ----------------------------------------------------------
INFO 10:24:20,516 HelpFormatter - ----------------------------------------------------------
INFO 10:24:20,521 ComputeGCProfiles - Opening reference sequence ...
INFO 10:24:20,521 ComputeGCProfiles - Opened reference sequence.
INFO 10:24:20,522 ComputeGCProfiles - Reading metadata ...
INFO 10:24:20,522 MetaData - Opening metadata ...
INFO 10:24:20,523 MetaData - Adding metadata location /BiO/home/pmc09/results/20220915_GenomeSTRiP_test/output ...
INFO 10:24:20,527 MetaData - Opened metadata.
INFO 10:24:20,527 ComputeGCProfiles - Read metadata.
INFO 10:24:20,527 ComputeGCProfiles - Initializing algorithm ...
INFO 10:24:20,529 ComputeGCProfiles - Algorithm initialized.
INFO 10:24:20,529 ComputeGCProfiles - Computing reference GC profile ...
#DBG: Thu Sep 15 10:24:20 KST 2022 computing reference profile for the interval chr1:1-249250621
#DBG: Thu Sep 15 10:24:36 KST 2022 computing reference profile for the interval chr2:1-243199373
#DBG: Thu Sep 15 10:24:52 KST 2022 computing reference profile for the interval chr3:1-198022430
#DBG: Thu Sep 15 10:25:05 KST 2022 computing reference profile for the interval chr4:1-191154276
#DBG: Thu Sep 15 10:25:17 KST 2022 computing reference profile for the interval chr5:1-180915260
#DBG: Thu Sep 15 10:25:29 KST 2022 computing reference profile for the interval chr6:1-171115067
#DBG: Thu Sep 15 10:25:41 KST 2022 computing reference profile for the interval chr7:1-159138663
#DBG: Thu Sep 15 10:25:51 KST 2022 computing reference profile for the interval chr8:1-146364022
#DBG: Thu Sep 15 10:26:01 KST 2022 computing reference profile for the interval chr9:1-141213431
#DBG: Thu Sep 15 10:26:09 KST 2022 computing reference profile for the interval chr10:1-135534747
#DBG: Thu Sep 15 10:26:18 KST 2022 computing reference profile for the interval chr11:1-135006516
#DBG: Thu Sep 15 10:26:27 KST 2022 computing reference profile for the interval chr12:1-133851895
#DBG: Thu Sep 15 10:26:36 KST 2022 computing reference profile for the interval chr13:1-115169878
#DBG: Thu Sep 15 10:26:42 KST 2022 computing reference profile for the interval chr14:1-107349540
#DBG: Thu Sep 15 10:26:49 KST 2022 computing reference profile for the interval chr15:1-102531392
#DBG: Thu Sep 15 10:26:55 KST 2022 computing reference profile for the interval chr16:1-90354753
#DBG: Thu Sep 15 10:27:00 KST 2022 computing reference profile for the interval chr17:1-81195210
#DBG: Thu Sep 15 10:27:06 KST 2022 computing reference profile for the interval chr18:1-78077248
#DBG: Thu Sep 15 10:27:11 KST 2022 computing reference profile for the interval chr19:1-59128983
#DBG: Thu Sep 15 10:27:14 KST 2022 computing reference profile for the interval chr20:1-63025520
#DBG: Thu Sep 15 10:27:19 KST 2022 computing reference profile for the interval chr21:1-48129895
#DBG: Thu Sep 15 10:27:21 KST 2022 computing reference profile for the interval chr22:1-51304566
#DBG: Thu Sep 15 10:27:24 KST 2022 computing reference profile for the interval chrX:1-155270560
#DBG: Thu Sep 15 10:27:34 KST 2022 computing reference profile for the interval chrY:1-59373566
#DBG: Thu Sep 15 10:27:37 KST 2022 computing reference profile for the interval chrM:1-16571
INFO 10:27:37,294 ComputeGCProfiles - Reference GC profile initialized.
INFO 10:27:37,294 CommandLineProgram - Program completed.
------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------
I ran 3 times with this script, and then the same error occurs. How can I solve it?
Moreover, I am planning to run GenomeSTRiP in a cluster with PBS scheduler for bam files more than thousands. Is it reasonable to joint-call for those bam files?
I need some advices.
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Thank you for your post. Bob Handsaker has been tagged and will get back to you shortly.
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