[svtoolkit-help] Error message when running SVPreprocess

[Wusheng Z. <min...@gm...>]

Dear Genome STRiP users,

I am running SVPreprocess on the cluster with SLURM as the schedule
management software. I started an interactive session with 8 cores, and
then executed the following lines on the terminal:

module purge
module load r/3.5.0
module load samtools/1.8
module load tabix/0.2.6

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/
gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
SV_DIR="/proj/yunligrp/users/minzhi/svtoolkit"
java -Xmx4g -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 /proj/yunligrp/users/yesu/hs38DH/hs38DH.chr16.fasta/test.fa \
     -I /proj/yunligrp/users/minzhi/JHS_30.list \
     -md md_tempdir \
     -ploidyMapFile standard_ploidy.map \
     -bamFilesAreDisjoint true \
     -jobLogDir logs \
     -run

The version of JAVA is here

[minzhi@longleaf-login1 minzhi]$ java -version
openjdk version "1.8.0_171"
OpenJDK Runtime Environment (build 1.8.0_171-b10)
OpenJDK 64-Bit Server VM (build 25.171-b10, mixed mode)

I got NO errors when the first time I executed the above command lines, but
when I run it again, it returns errors shown as below

...
*ERROR* 20:51:55,597 FunctionEdge - Error:  'java'  '-Xmx2048m'
'-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'
'-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/proj/
yunligrp/users/minzhi/.queue/tmp'  '-cp' ':/proj/yunligrp/users/minzhi/
svtoolkit/lib/SVToolkit.jar::/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/
GenomeAnalysisTK.jar::/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/Queue.jar'
'-cp' '/proj/yunligrp/users/minzhi:/proj/yunligrp/users/minzhi/
svtoolkit/lib/SVToolkit.jar:/proj/yunligrp/users/minzhi:/
proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/proj/
yunligrp/users/minzhi:/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/Queue.jar'
'org.broadinstitute.sv.apps.ComputeGCProfiles'  '-O'
'/proj/yunligrp/users/minzhi/md_tempdir/gcprofile/reference.gcprof.zip'
'-R' '/proj/yunligrp/users/yesu/hs38DH/hs38DH.chr16.fasta/test.fa'  '-md'
'md_tempdir'  '-writeReferenceProfile' 'true'  '-configFile'
'/proj/yunligrp/users/minzhi/svtoolkit/conf/genstrip_parameters.txt'
*ERROR* 20:51:55,600 FunctionEdge - Contents of /proj/yunligrp/users/minzhi/
logs/*SVPreprocess-6.out*:
INFO  20:46:16,772 HelpFormatter - ------------------------------
----------------------------
INFO  20:46:16,775 HelpFormatter - Program Name: org.broadinstitute.sv.apps.
ComputeGCProfiles
...
INFO  20:56:10,398 QGraph - 92 Pend, 1 Run, 1 Fail, 67 Done
...
INFO  20:56:35,371 QGraph - 92 Pend, 0 Run, 1 Fail, 68 Done
...
INFO  20:56:38,945 QCommandLine - Done with errors

And then I re-run the svpreprocess with regards to the same .bam files.
However, there are two errors but happened at different indexes
(*SVPreprocess-73.out
and SVPreprocess-80.out*).

I am confused about two parts:

1. Does anyone meet such kind of error before, and may I have your
suggestions about this error? I checked the corresponding log file
such as SVPreprocess-6.out
and the SVPreprocess.jobreport.txt, but there is no error message in those
files.
2. My log file started from index 6 rather than 0 which means that the
first log file is SVPreprocess-6.out but not SVPreprocess-0.out -- does it
mean that I made anything wrong?

Thank you in advance.

Best regards,
Wusheng