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.