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Variant Discovery in High-Throughput Sequencing Data

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GenomeSTRiP CNVDiscoveryPipeline failed

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11 comments

  • Avatar
    Bob Handsaker

    You need to specify -jobRunner (typically Drmaa).

    See here: http://software.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_QCommandLine.html 

    Typically you may need -jobNative arguments as well depending on your local cluster configuration.

     

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    Jenny Xu

    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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    Genevieve Brandt (she/her)

    Thank you for your post. Bob Handsaker has been tagged and will get back to you shortly.

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    Bob Handsaker

    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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    Jenny Xu

    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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    Bob Handsaker

    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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    Jenny Xu

    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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    Bob Handsaker

    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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    Jenny Xu

    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
    INFO 10:34:10,479 06-Aug-2021 ProgressMeter - Starting 0.0 109.3 m 10847.0 w 100.0% 109.3 m 0.0 s
    INFO 10:34:40,480 06-Aug-2021 ProgressMeter - Starting 0.0 109.8 m 10896.6 w 100.0% 109.8 m 0.0 s
    INFO 10:35:10,481 06-Aug-2021 ProgressMeter - Starting 0.0 110.3 m 10946.2 w 100.0% 110.3 m 0.0 s
    INFO 10:35:40,482 06-Aug-2021 ProgressMeter - Starting 0.0 110.8 m 10995.8 w 100.0% 110.8 m 0.0 s
    INFO 10:36:10,484 06-Aug-2021 ProgressMeter - Starting 0.0 111.3 m 11045.4 w 100.0% 111.3 m 0.0 s
    INFO 10:36:40,484 06-Aug-2021 ProgressMeter - Starting 0.0 111.8 m 11095.0 w 100.0% 111.8 m 0.0 s
    INFO 10:37:10,486 06-Aug-2021 ProgressMeter - Starting 0.0 112.3 m 11144.6 w 100.0% 112.3 m 0.0 s
    INFO 10:37:40,486 06-Aug-2021 ProgressMeter - Starting 0.0 112.8 m 11194.2 w 100.0% 112.8 m 0.0 s
    INFO 10:38:10,487 06-Aug-2021 ProgressMeter - Starting 0.0 113.3 m 11243.8 w 100.0% 113.3 m 0.0 s
    INFO 10:38:40,489 06-Aug-2021 ProgressMeter - Starting 0.0 113.8 m 11293.4 w 100.0% 113.8 m 0.0 s
    INFO 10:39:10,490 06-Aug-2021 ProgressMeter - Starting 0.0 114.3 m 11343.0 w 100.0% 114.3 m 0.0 s
    INFO 10:39:40,491 06-Aug-2021 ProgressMeter - Starting 0.0 114.8 m 11392.6 w 100.0% 114.8 m 0.0 s
    INFO 10:40:10,492 06-Aug-2021 ProgressMeter - Starting 0.0 115.3 m 11442.2 w 100.0% 115.3 m 0.0 s
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    INFO 10:41:10,495 06-Aug-2021 ProgressMeter - Starting 0.0 116.3 m 11541.4 w 100.0% 116.3 m 0.0 s
    INFO 10:41:40,496 06-Aug-2021 ProgressMeter - Starting 0.0 116.8 m 11591.0 w 100.0% 116.8 m 0.0 s
    INFO 10:42:10,497 06-Aug-2021 ProgressMeter - Starting 0.0 117.3 m 11640.6 w 100.0% 117.3 m 0.0 s
    INFO 10:42:40,498 06-Aug-2021 ProgressMeter - Starting 0.0 117.8 m 11690.2 w 100.0% 117.8 m 0.0 s
    INFO 10:43:20,499 06-Aug-2021 ProgressMeter - Starting 0.0 118.5 m 11756.4 w 100.0% 118.5 m 0.0 s
    INFO 10:44:00,499 06-Aug-2021 ProgressMeter - Starting 0.0 119.2 m 11822.5 w 100.0% 119.2 m 0.0 s
    INFO 10:44:30,500 06-Aug-2021 ProgressMeter - Starting 0.0 119.7 m 11872.1 w 100.0% 119.7 m 0.0 s
    INFO 10:45:00,501 06-Aug-2021 ProgressMeter - Starting 0.0 2.0 h 11921.7 w 100.0% 2.0 h 0.0 s
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    INFO 10:48:10,505 06-Aug-2021 ProgressMeter - Starting 0.0 2.1 h 12235.9 w 100.0% 2.1 h 0.0 s
    INFO 10:48:40,507 06-Aug-2021 ProgressMeter - Starting 0.0 2.1 h 12285.5 w 100.0% 2.1 h 0.0 s
    INFO 10:49:10,508 06-Aug-2021 ProgressMeter - Starting 0.0 2.1 h 12335.1 w 100.0% 2.1 h 0.0 s
    INFO 10:49:50,509 06-Aug-2021 ProgressMeter - Starting 0.0 2.1 h 12401.2 w 100.0% 2.1 h 0.0 s
    INFO 10:50:20,509 06-Aug-2021 ProgressMeter - Starting 0.0 2.1 h 12450.8 w 100.0% 2.1 h 0.0 s
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    INFO 10:53:50,516 06-Aug-2021 ProgressMeter - Starting 0.0 2.2 h 12798.1 w 100.0% 2.2 h 0.0 s
    INFO 10:54:30,517 06-Aug-2021 ProgressMeter - Starting 0.0 2.2 h 12864.2 w 100.0% 2.2 h 0.0 s
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    INFO 11:00:00,525 06-Aug-2021 ProgressMeter - Starting 0.0 2.3 h 13409.9 w 100.0% 2.3 h 0.0 s
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    INFO 11:05:40,533 06-Aug-2021 ProgressMeter - Starting 0.0 2.3 h 13972.0 w 100.0% 2.3 h 0.0 s
    INFO 11:06:10,534 06-Aug-2021 ProgressMeter - Starting 0.0 2.4 h 14021.6 w 100.0% 2.4 h 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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    Bob Handsaker

    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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    Jenny Xu

    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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