GenomeSTRiP CNVDiscoveryPipeline failed
Answered
I am running the CVN pipeline commands on our HPC clusters, got error around lsf library - not sure if this is something I can solve since our clusters use sge and I don't have cluster admin permission. Thank you.
Command:
java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R ${referencepath} \
-I genomestrip.bam.list \
-md output_metadata_directory \
-intervalList chr6 \
-ploidyMapFile software/1000G_phase1/human_g1k_v37_chr.ploidymap.txt \
-runDirectory output_CNVDiscoveryPipeline \
-jobLogDir output_CNVDiscoveryPipeline/logDir \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-run
Error:
java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34)
at org.broadinstitute.gatk.queue.engine.QGraph.org$broadinstitute$gatk$queue$engine$QGraph$$newRunner(QGraph.scala:925)
at org.broadinstitute.gatk.queue.engine.QGraph.startOneJob(QGraph.scala:643)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:507)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:168)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:170)
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.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
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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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You need to specify -jobRunner (typically Drmaa).
Typically you may need -jobNative arguments as well depending on your local cluster configuration.
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HI Bob,
After I added both -jobRunner and -gatkJobrunner Drmaa, it solves the lsf error. However, there are new errors complaining "invalid intervals", though I think those intervals are legitimate. Thank you
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If you are getting the same behavior, it is almost certainly because you are failing to successfully pass the -jobRunner argument. The default job runner, for historical reasons, is LSF 7.
You didn't say what scheduling software you are using on your cluster. Did SVPreprocess run successfully?
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Hi Bob,
I have found out the invalid interval error is caused because in the previous SVPreprocess step I specified only a small region using -L chrXX:start_end, yet CNV -intervalList can only accept unit minimum at chromosome level. After rerun the SVPreprocess step using -L chrXX, CNV pipeline is running now. Is it possible to specify specific region within a chromosome in the CNV commands (I have tried supply with both -intervalList and -L but seems it ignored -L part)? Thank you.
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It is in general not recommended to run SVPreprocess with -L. The job of SVPreprocess is to gather statistics on the overall properties of the sequencing data and these properties are more accurate/robust when run over the whole genome rather than a subset. So you should use -L with care. For example, if you run a single chromosome and there is an aneuploidy or a large CNV, your results for that sample may be thrown off.
The CNV pipeline results will also be affected if you do not run the entire genome. The -intervalList option is specific to the CNV pipeline. It is intended mostly to exclude reference contigs that should not be analyzed (like a mitochondrial contig or unplaced or alt contigs). If you want the safe path, I would run the whole genome. If you run a single chromosome with -intervalList, you should pay attention to the output of stage 5 which assesses samples based on the genome wide rate of CNV calls. If you are doing this, you should probably run to stage 5 (-lastStage 5), inspect the output, manually adjust the list of flagged samples, if appropriate, then continue with the rest of the pipeline. Flagged samples do not generate CNV calls unless there is support from a non-flagged sample. They will still be genotyped however.
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Hi Bob, thanks for the detailed explanation and it makes total sense. Besides these suggestion, could you help troubleshoot - I am stuck (tried multiple times) at stage10 and the error message is unclear to me what causes the failure, plus if I manually execute the command that the error message related instead of qsub the whole original command, it finishes successfully.
ERROR 11:27:49,881 FunctionEdge - Error: 'java' '-Xmx3072m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=.queue/tmp' '-cp' 'svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar' '-cp' 'svtoolkit/lib/SVToolkit.jar:svtoolkit/lib/gatk/GenomeAnalysisTK.jar:svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.main.SVAnnotator' '-vcf' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes.unfiltered.vcf.gz' '-R' 'hg19.fa' '-md' 'output_metadata_directory' '-auxFilePrefix' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes' '-reportDirectory' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/eval' '-genderMapFile' 'output_metadata_directory/sample_gender.report.txt' '-ploidyMapFile' 'human_g1k_v37_chr.ploidymap.txt' -A CNQuality -A ClusterSeparation -A GenotypeFilter '-genotypeFilterFile' 'output_CNVDiscoveryPipeline/gender_gt_filters/gender_gt_filter.txt' '-filterDescriptionFile' 'output_CNVDiscoveryPipeline/gender_gt_filters/gender_gt_filter_descr.txt' '-filterVariants' 'false' '-writeReport' 'true' '-writeSummary' 'true' '-O' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes.base.annotated.vcf.gz'
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You need to provide more information, like what is in the log file, for me to be able to help. The Queue output tells you the location of the log file for each job.
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Hi Bob,
Here's the extracted related log file (number 13). I'd appreciate if you can help diagnosis of cause of error. Thank you.
ERROR 11:27:49,881 FunctionEdge - Error: 'java' '-Xmx3072m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/.queue/tmp' '-cp' '/home/software/svtoolkit/lib/SVToolkit.jar:/home/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/software/svtoolkit/lib/SVToolkit.jar:/home/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.main.SVAnnotator' '-vcf' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes.unfiltered.vcf.gz' '-R' '/home/references/hg19/Reference/bwamem/hg19.fa' '-md' 'output_metadata_directory' '-auxFilePrefix' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes' '-reportDirectory' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/eval' '-genderMapFile' 'output_metadata_directory/sample_gender.report.txt' '-ploidyMapFile' '/home/software/1000G_phase1/human_g1k_v37_chr.ploidymap.txt' -A CNQuality -A ClusterSeparation -A GenotypeFilter '-genotypeFilterFile' 'output_CNVDiscoveryPipeline/gender_gt_filters/gender_gt_filter.txt' '-filterDescriptionFile' 'output_CNVDiscoveryPipeline/gender_gt_filters/gender_gt_filter_descr.txt' '-filterVariants' 'false' '-writeReport' 'true' '-writeSummary' 'true' '-O' '/home/output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes.base.annotated.vcf.gz'
ERROR 11:27:49,891 FunctionEdge - Contents of /home/output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/logs/CNVDiscoveryStage10-85.out:
INFO 10:33:30,479 06-Aug-2021 ProgressMeter - Starting 0.0 108.7 m 10780.8 w 100.0% 108.7 m 0.0 s
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INFO 11:27:00,570 06-Aug-2021 ProgressMeter - Starting 0.0 2.7 h 15250.3 w 100.0% 2.7 h 0.0 s
INFO 11:27:49,892 QGraph - Writing incremental jobs reports...
INFO 11:27:49,892 QGraph - 6 Pend, 0 Run, 1 Fail, 84 Done
INFO 11:27:49,894 QCommandLine - Writing final jobs report...
INFO 11:27:49,894 QCommandLine - Done with errors
INFO 11:27:49,896 QGraph - -------
INFO 11:27:49,896 QGraph - Failed: 'java' '-Xmx3072m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/.queue/tmp' '-cp' '/home/software/svtoolkit/lib/SVToolkit.jar:/home/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/software/svtoolkit/lib/SVToolkit.jar:/home/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.main.SVAnnotator' '-vcf' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes.unfiltered.vcf.gz' '-R' '/home/references/hg19/Reference/bwamem/hg19.fa' '-md' 'output_metadata_directory' '-auxFilePrefix' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes' '-reportDirectory' 'output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/eval' '-genderMapFile' 'output_metadata_directory/sample_gender.report.txt' '-ploidyMapFile' '/home/software/1000G_phase1/human_g1k_v37_chr.ploidymap.txt' -A CNQuality -A ClusterSeparation -A GenotypeFilter '-genotypeFilterFile' 'output_CNVDiscoveryPipeline/gender_gt_filters/gender_gt_filter.txt' '-filterDescriptionFile' 'output_CNVDiscoveryPipeline/gender_gt_filters/gender_gt_filter_descr.txt' '-filterVariants' 'false' '-writeReport' 'true' '-writeSummary' 'true' '-O' '/home/output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/seq_chr6.adjacent_merged.genotypes.base.annotated.vcf.gz'
INFO 11:27:49,896 QGraph - Log: /home/output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/logs/CNVDiscoveryStage10-85.out
INFO 11:27:49,897 QCommandLine - Script failed: 6 Pend, 0 Run, 1 Fail, 84 Done
------------------------------------------------------------------------------------------
Done. There were no warn messages.
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The CNV pipeline has nested log files, so it can be a little hard for me to tell which log file I am looking at. Can you zip/tar the log file above and also /home/output_CNVDiscoveryPipeline/cnv_stage10/seq_chr6/logs/CNVDiscoveryStage10-85.out and email them to me directly (rather than cutting/pasting)?
Also, just as something possible to try: you could try rerunning Queue (which should be just retrying the failed job) but increase the memory which I think can be done with "-memLimit 4" or "-memLimit 8" (4G/8G respectively) on the command line or something like that. You should see the -Xmx values in the command line being run change. If you are specifying a -jobNative memory reservation, you may need to turn that up as well.
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Hi Bob, thank you for the suggestion. By increasing the -h_vmem within jobNative parameter the job completes. The ticket can be closed now.
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