SVPreprocess error following ReduceInsertSizeHistograms

Hi,

When I try to run SVPreprocess, I am getting the following error multiple times, each for different sample files:

ERROR 13:56:09,433 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/u/scratch/t/traceyc' '-cp' '/u/project/zarlab/traceyc/svtoolkit/lib/SVToolkit.jar:/u/project/zarlab/traceyc/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/u/project/zarlab/traceyc/svtoolkit/lib/gatk/Queue.jar' '-cp' '/u/project/zarlab/traceyc/svtoolkit/lib/SVToolkit.jar:/u/project/zarlab/traceyc/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/u/project/zarlab/traceyc/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/u/project/zarlab/traceyc/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.hist.bin' '-O' '/u/project/zarlab/traceyc/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.dist.bin' ERROR 13:56:09,433 FunctionEdge - Contents of /u/project/zarlab/traceyc/svtoolkit/first/30mappedbams/logs/SVPreprocess-37.out: INFO 13:45:46,621 HelpFormatter - ------------------------------------------------------------------- INFO 13:45:46,623 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 13:45:46,628 HelpFormatter - Program Args: -I /u/project/zarlab/traceyc/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.hist.bin -O /u/project/zarlab/traceyc/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.dist.bin INFO 13:45:46,634 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_05_14_07_23-b00. INFO 13:45:46,635 HelpFormatter - Date/Time: 2015/10/27 13:45:46 INFO 13:45:46,635 HelpFormatter - ------------------------------------------------------------------- INFO 13:45:46,635 HelpFormatter - ------------------------------------------------------------------- Processing HG00097/IWG_IND-TG.HG00097-4_1pA/null ... INFO 13:45:54,155 CommandLineProgram - Program completed.

As suggested in previous discussions (http://gatkforums.broadinstitute.org/discussion/4906/genome-strip-script-failed-with-error), I tried to run ReduceInsertSizeHistograms directly with

java -Xmx4g -cp ${classpath} \ org.broadinstitute.sv.apps.ReduceInsertSizeHistograms \ -I /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.hist.bin \ -O /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.dist.bin

and get the result:
SVToolkit version 2.00 (build 1602) Build date: 2015/07/21 09:43:14 Web site: http://www.broadinstitute.org/software/genomestrip INFO 16:54:12,380 HelpFormatter - ------------------------------------------------------------------- INFO 16:54:12,383 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 16:54:12,390 HelpFormatter - Program Args: -I /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.hist.bin -O /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.dist.bin INFO 16:54:12,402 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_05_14_07_23-b00. INFO 16:54:12,402 HelpFormatter - Date/Time: 2015/10/27 16:54:12 INFO 16:54:12,403 HelpFormatter - ------------------------------------------------------------------- INFO 16:54:12,403 HelpFormatter - ------------------------------------------------------------------- Processing HG00097/IWG_IND-TG.HG00097-4_1pA/null ... INFO 16:54:27,635 CommandLineProgram - Program completed.

Does this output suggest that ReduceInsertSizeHistograms was successful for this run and that I have a problem in my environment? I am not sure how to "figure out why there is a non-zero exit status being returned" by running the command explicitly or in a shell script wrapper. What are possible problems in the environment and what would you suggest to do to solve such problems?

Thanks,
Tracey

Comments

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    Does this output suggest that ReduceInsertSizeHistograms was successful for this run and that I have a problem in my environment?

    Yes. Queue is seeing a non-zero exit status from running the job, even though it looks like the job was successful. It is hard to say why without being able to run some tests in your environment, such as trying the java command at the command line, trying to submit the java command through your workflow manager, etc.

    When you run the above java command, you should check the exit status after you run the command, e.g. with echo $?. And you need to also see if this is different when you execute the job through your workflow manager.

  • traceyctraceyc Member

    Hi Bob,

    Thanks for the suggestions - I tried running ReduceInsertSizeHistograms in three ways:
    1) When I try the java command at the command line, I get the error "Could not find or load main class org.broadinstitute.sv.apps.ReduceInsertSizeHistograms" and a nonzero exit status.

    [[email protected] first]$ mx="-Xmx4g" [[email protected] first]$ echo $SV_DIR /u/home/t/tracey/project-zarlab/svtoolkit [[email protected] first]$ classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar" [[email protected] first]$ java -Xmx4g -cp ${classpath} \ org.broadinstitute.sv.apps.ReduceInsertSizeHistograms \ -I /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.hist.bin \ -O /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.dist.bin Error: Could not find or load main class org.broadinstitute.sv.apps.ReduceInsertSizeHistograms [[email protected] first]$ echo $? 1

    2) When I run a simple script with the same java command, I get a zero exit status.

    [[email protected] first]$ ./test_RISH.sh SVToolkit version 2.00 (build 1602) Build date: 2015/07/21 09:43:14 Web site: http://www.broadinstitute.org/software/genomestrip INFO 09:55:09,228 HelpFormatter - ------------------------------------------------------------------- INFO 09:55:09,232 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 09:55:09,238 HelpFormatter - Program Args: -I /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.hist.bin -O /u/home/t/traceyc/project-zarlab/svtoolkit/first/30mappedbams/metadata/isd/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.dist.bin INFO 09:55:09,250 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.23.4.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_05_14_07_23-b00. INFO 09:55:09,250 HelpFormatter - Date/Time: 2015/10/28 09:55:09 INFO 09:55:09,251 HelpFormatter - ------------------------------------------------------------------- INFO 09:55:09,251 HelpFormatter - ------------------------------------------------------------------- Processing HG00097/IWG_IND-TG.HG00097-4_1pA/null ... INFO 09:55:23,656 CommandLineProgram - Program completed. [[email protected] first]$ echo $? 0

    3) When I submit the job (same script as in #2) through my workflow manager, I get a nonzero exit status.

    So it appears that the exit status does change depending on how the command is executed. What would you suggest as further steps to figure out what is going wrong?

    Thanks,
    Tracey

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