Re: [svtoolkit-help] Error message when running SVPreprocess
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Re: [svtoolkit-help] Error message when running SVPreprocess
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From: Wusheng Z. <min...@gm...> - 2018-06-14 15:15:04
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I found that there is such kind of error
INFO 10:53:37,168 HelpFormatter -
-------------------------------------------------------------
INFO 10:53:37,175 HelpFormatter - Program Name:
org.broadinstitute.sv.apps.ComputeDepthProfiles
INFO 10:53:37,180 HelpFormatter - Program Args: -O
/proj/yunligrp/users/minzhi/md_tempdir/profiles_100Kb/profile_seq_chr16_100000.dat.gz
-I md_tempdir/headers.bam -configFile
/proj/yunligrp/users/minzhi/svtoolkit/conf/genstrip_parameters.txt -R
/proj/yunligrp/users/yesu/hs38DH/hs38DH.chr16.fasta/test.fa -L chr16:0-0
-md md_tempdir -profileBinSize 100000 -maximumReferenceGapLength 10000
INFO 10:53:37,192 HelpFormatter - Executing as mi...@b1... on
Linux 3.10.0-693.11.6.el7.x86_64 amd64; OpenJDK 64-Bit Server VM
1.8.0_171-b10.
INFO 10:53:37,192 HelpFormatter - Date/Time: 2018/06/14 10:53:37
INFO 10:53:37,193 HelpFormatter -
-------------------------------------------------------------
INFO 10:53:37,193 HelpFormatter -
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Exception in thread "main"
org.broadinstitute.sv.commandline.ArgumentException: Alignment file does
not exist: md_tempdir/headers.bam
at org.broadinstitute.sv.dataset.SAMLocation.create(SAMLocation.java:99)
at
org.broadinstitute.sv.commandline.CommandLineParser.createSAMLocation(CommandLineParser.java:256)
at
org.broadinstitute.sv.commandline.CommandLineParser.parseSAMLocations(CommandLineParser.java:236)
at
org.broadinstitute.sv.commandline.CommandLineParser.parseSAMLocations(CommandLineParser.java:220)
at
org.broadinstitute.sv.apps.ComputeDepthProfiles.run(ComputeDepthProfiles.java:117)
at
org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at
org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at
org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at
org.broadinstitute.sv.apps.ComputeDepthProfiles.main(ComputeDepthProfiles.java:109)
The "md_tempdir" is the directory of -md flag. My confusion is that the
data in this files should be generated during the running rather than I
prepare at first. Besides, other .out files did not generate such kind of
problem. I used our own reference reference data rather than the data
provided by the genome strip, so will this lead to the error? May I have
your suggestions?
Thank you in advance.
Best regards,
Minzhi
2018-06-14 10:10 GMT-04:00 Wusheng Zhang <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/GenomeAnalysis
> TK.jar::/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/Queue.jar' '-cp'
> '/proj/yunligrp/users/minzhi:/proj/yunligrp/users/minzhi/svt
> oolkit/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
>
>
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