Error Running CNVDiscovery Pipeline

mfultonmfulton St. LouisMember

I tried to run the pipeline and it succeeded for the first stage but then failed at the second. It looks like a null pointer exception. What other information would be useful to debug this?

INFO 10:45:23,761 HelpFormatter - ---------------------------------------------------------------------------
INFO 10:45:23,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v, Compiled 2014/11/26 23:42:58
INFO 10:45:23,763 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:45:23,763 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:45:23,768 HelpFormatter - Program Args: -T SVGenotyperWalker -R /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta -O /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19_CNVDiscoveryPipeline__experiment1/cnv_stage2/seq_18/P0133.genotypes.vcf.gz -disableGATKTraversal true -md /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19_SVPreprocess_metadata_experiment1/ -configFile /gscmnt/gc2801/analytics/dlarson/GenomeSTRiP/svtoolkit/conf/genstrip_parameters.txt -P depth.readCountCacheIgnoreGenomeMask:true -P genotyping.modules:depth -runDirectory /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19_CNVDiscoveryPipeline__experiment1/cnv_stage2/seq_18 -ploidyMapFile /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt -genomeMaskFile /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta -genomeMaskFile /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta -vcf /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19_CNVDiscoveryPipeline__experiment1/cnv_stage1/seq_18/seq_18.sites.vcf.gz -partitionName P0133 -partition records:132001-133000 -L 1:1-1
INFO 10:45:23,770 HelpFormatter - Executing as [email protected] on Linux 3.0.0-16-server amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0-b147.
INFO 10:45:23,771 HelpFormatter - Date/Time: 2015/06/09 10:45:23
INFO 10:45:23,771 HelpFormatter - ---------------------------------------------------------------------------
INFO 10:45:23,771 HelpFormatter - ---------------------------------------------------------------------------
INFO 10:45:54,638 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:45:54,769 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 10:45:54,791 IntervalUtils - Processing 1 bp from intervals
INFO 10:45:54,861 GenomeAnalysisEngine - Preparing for traversal
INFO 10:45:54,862 GenomeAnalysisEngine - Done preparing for traversal
INFO 10:45:54,862 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 10:45:54,862 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 10:45:54,863 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 10:45:54,874 SVGenotyper - Opening reference sequence ...
INFO 10:45:54,874 SVGenotyper - Opened reference sequence.
INFO 10:45:54,874 SVGenotyper - Opening genome mask ...
INFO 10:45:54,883 SVGenotyper - Opened genome mask.
INFO 10:45:54,883 SVGenotyper - Initializing input data set ...
INFO 10:45:54,967 SVGenotyper - Initialized data set: 1 file, 159 read groups, 22 samples.
INFO 10:45:54,968 MetaData - Opening metadata ...
INFO 10:45:54,971 MetaData - Adding metadata directory /gscmnt/gc2801/analytics/mfulton/Homo_sapiens_assembly19_SVPreprocess_metadata_experiment1 ...
INFO 10:45:54,986 MetaData - Opened metadata.
INFO 10:45:55,094 SVGenotyper - Using copy number confidence threshold: none
INFO 10:45:55,917 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException
at org.broadinstitute.sv.metadata.MetaData.computeSampleDoubleMap(MetaData.java:447)
at org.broadinstitute.sv.metadata.MetaData.getSampleFragmentsPerBaseMap(MetaData.java:421)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.init(GenotypingDepthModule.java:1799)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initModules(GenotypingAlgorithm.java:522)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initialize(GenotypingAlgorithm.java:87)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR -----------------------

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