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CNVDiscovery Troubleshooting

Hello,

We are trying to use Genome Strip to process our data and seem to be encountering some errors when running CNVDiscovery. To assist with troubleshooting, a log file has been attached below.

Computing Environment

-- HPCC running Red Hat Enterprise Linux Server 6.9
-- Workflow manager: SLURM
-- Java:
openjdk version "1.8.0_144"
OpenJDK Runtime Environment (build 1.8.0_144-b01)
OpenJDK 64-Bit Server VM (build 25.144-b01, mixed mode)
-- Input: 41 BAM files, ~120GB each

SLURM script

SBATCH -J cnvd
SBATCH --time=320:00:00
SBATCH --nodes=1
SBATCH --cpus-per-task=12
SBATCH --mem=23gb # Memory per node.
SBATCH --array=1-1%1
SBATCH -o cnvd_%A_%a.out

genome='/bin/genome_strip/svtoolkit/metadata/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta'

input_bam_list='input_bams_2.list'

interval_list='ref_chr_7.list'

gender_map_file='gender_map_file_2.tsv'

metadata_dir='genome_strip_sv_preprocess'

output_dir='genome_strip_cnv_discovery_chr7'

module load slurm-drmaa/1.0.7
module load R/3.3.2

export SV_DIR=/bin/genome_strip/svtoolkit
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

time java -Xmx23g -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 ${SV_DIR}/conf/genstrip_parameters.txt \
-R "${genome}" \
-I "${input_bam_list}" \
-md "${metadata_dir}" \
-runDirectory "${output_dir}" \
-jobLogDir "${output_dir}"/logs \
-intervalList "${interval_list}" \
-genderMapFile "${gender_map_file}" \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-jobRunner Drmaa \
-gatkJobRunner Drmaa \
-jobNative '--mem=23000' \
-run

Result

The job finishes after ~10 hours. The SLURM log file is attached as log.txt.
Within log.txt, the following error occurs:

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.genotyping.GenotypingDepthModule.init(GenotypingDepthModule.java:1810)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initModules(GenotypingAlgorithm.java:534)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.initialize(GenotypingAlgorithm.java:95)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:211)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
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.SVGenotyper.main(SVGenotyper.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 ------------------------------------------------------------------------------------------

Answers

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