I have encountered a problem when I run SVDiscovery pipeline.
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The script of SVDiscovery I had used is:
!/bin/bash
export SV_DIR=/work/SoftW/svtoolkit
runDir=2016006L-3-1
SV_TMPDIR=2016006L-3-1/tmpdir_SVDiscovery
inputFile=2016006L-3-1.dedupped.bam
sites=2016006L-3-1.discovery.vcf
genotypes=2016006L-3-1.genotypes.vcf
These executables must be on your path.
which java > /dev/null || exit 1
which Rscript > /dev/null || exit 1
which samtools > /dev/null || exit 1
For SVAltAlign, you must use the version of bwa compatible with Genome STRiP.
export PATH=${SV_DIR}/bwa:${PATH}
export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
mx="-Xmx4g"
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
mkdir -p ${runDir}/logs || exit 1
mkdir -p ${runDir}/metadata || exit 1
Run discovery.
java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-cp ${classpath} \
-S ${SV_DIR}/qscript/SVDiscovery.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-configFile conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta \
-genomeMaskFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-genderMapFile 2016006L-3-1_gender.map \
-disableGATKTraversal \
-jobLogDir ${runDir}/logs \
-suppressVCFCommandLines \
-startFromScratch \
-minimumSize 100 \
-maximumSize 1000000 \
-I ${inputFile} \
-O ${sites} \
-run
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And the error is:
INFO 20:15:44,178 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 20:15:44,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7.GS-r1748-0-g74bfe0b, Compiled 2017/10/06 08:08:49
INFO 20:15:44,180 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 20:15:44,180 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 20:15:44,180 HelpFormatter - [Fri Jan 26 20:15:44 CST 2018] Executing on Linux 2.6.32-696.6.3.el6.x86_64 amd64
INFO 20:15:44,181 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15
INFO 20:15:44,184 HelpFormatter - Program Args: -T SVDiscoveryWalker -R /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta -O /work1/wsh/4.test/1.perl/1.pipetest/2016006L-1-1/P0001.discovery.vcf.gz -disableGATKTraversal true -md 2016006L-1-1/metadata -configFile conf/genstrip_parameters.txt -runDirectory 2016006L-1-1 -genderMapFile 2016006L-1-1_gender.map -genomeMaskFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta -partitionName P0001 -runFilePrefix P0001 -storeReadPairFile true -L 1:1-249250621 -searchLocus 1:1-249250621 -searchWindow 1:1-249250621 -searchMinimumSize 100 -searchMaximumSize 1000000
INFO 20:15:44,191 HelpFormatter - Executing as wsh@localhost on Linux 2.6.32-696.6.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15.
INFO 20:15:44,191 HelpFormatter - Date/Time: 2018/01/26 20:15:44
INFO 20:15:44,191 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 20:15:44,191 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 20:15:44,197 26-Jan-2018 GenomeAnalysisEngine - Strictness is SILENT
INFO 20:15:44,334 26-Jan-2018 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 20:15:44,354 26-Jan-2018 IntervalUtils - Processing 249250621 bp from intervals
INFO 20:15:44,417 26-Jan-2018 GenomeAnalysisEngine - Preparing for traversal
INFO 20:15:44,424 26-Jan-2018 GenomeAnalysisEngine - Done preparing for traversal
INFO 20:15:44,424 26-Jan-2018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 20:15:44,424 26-Jan-2018 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 20:15:44,424 26-Jan-2018 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 20:15:44,424 26-Jan-2018 SVDiscovery - Initializing SVDiscovery ...
INFO 20:15:44,425 26-Jan-2018 SVDiscovery - Reading configuration file ...
INFO 20:15:44,429 26-Jan-2018 SVDiscovery - Read configuration file.
INFO 20:15:44,429 26-Jan-2018 SVDiscovery - Opening reference sequence ...
INFO 20:15:44,430 26-Jan-2018 SVDiscovery - Opened reference sequence.
INFO 20:15:44,430 26-Jan-2018 SVDiscovery - Opening genome mask ...
INFO 20:15:44,431 26-Jan-2018 SVDiscovery - Opened genome mask.
INFO 20:15:44,431 26-Jan-2018 SVDiscovery - Initializing input data set ...
INFO 20:15:44,452 26-Jan-2018 SVDiscovery - Initialized data set: 1 file, 1 read group, 1 sample.
INFO 20:15:44,453 26-Jan-2018 MetaData - Opening metadata ...
INFO 20:15:44,454 26-Jan-2018 MetaData - Adding metadata location 2016006L-1-1/metadata ...
INFO 20:15:44,455 26-Jan-2018 MetaData - Opened metadata.
INFO 20:15:44,457 26-Jan-2018 SVDiscovery - Opened metadata.
INFO 20:15:44,462 26-Jan-2018 MetaData - Loading insert size histograms ...
INFO 20:15:44,522 26-Jan-2018 SVDiscovery - Processing locus: 1:1-249250621:100-1000000
INFO 20:15:44,522 26-Jan-2018 SVDiscovery - Locus search window: 1:1-249250621
INFO 20:16:14,638 26-Jan-2018 ProgressMeter - Starting 0.0 30.0 s 50.0 w 100.0% 30.0 s 0.0 s
INFO 20:16:44,639 26-Jan-2018 ProgressMeter - Starting 0.0 60.0 s 99.6 w 100.0% 60.0 s 0.0 s
INFO 20:17:14,640 26-Jan-2018 ProgressMeter - Starting 0.0 90.0 s 149.2 w 100.0% 90.0 s 0.0 s
INFO 20:17:40,449 26-Jan-2018 SVDiscovery - Discovery alt home filtering is disabled.
INFO 20:17:40,932 26-Jan-2018 SVDiscovery - Processing clusters ...
ERROR --
ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.sv.metadata.MetaData.computeSampleDoubleMap(MetaData.java:423)
at org.broadinstitute.sv.metadata.MetaData.getSampleFragmentsPerBaseMap(MetaData.java:397)
at org.broadinstitute.sv.discovery.ClusterDepthModule.init(ClusterDepthModule.java:350)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.createDepthModule(DeletionDiscoveryAlgorithm.java:1123)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.initClusterModules(DeletionDiscoveryAlgorithm.java:1056)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:386)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:204)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:107)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:40)
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:115)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:133)
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.sv.main.SVCommandLine.main(SVCommandLine.java:87)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1748-0-g74bfe0b):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
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Can anyone help me? Thank you very much!