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 mfulton@blade12-3-13.gsc.wustl.edu 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)