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CNVPipeline stage 7 error (unable to read the list of metadata directories)

zihhuafangzihhuafang Switzerland Member
edited December 2019 in GenomeSTRiP
I ran into this issue with reading metadata location when running CNVPipeline.
I have 4 metadata directories, so I put their locations into a list called metadata.list

The error message below can be found from the log file CNVDiscoveryPipeline-10.out and log files from cnv_stage7 where the program org.broadinstitute.sv.genotyping.RefineCNVBoundaries was run.

INFO 14:52:34,256 MetaData - Adding metadata location /cluster/work/pausch/fang/svtoolkit/ucd_sv/ucd_test/metadata.list ...
Exception in thread "main" org.broadinstitute.sv.commandline.ArgumentException: Invalid metadata directory: /cluster/work/pausch/fang/svtoolkit/ucd_sv/ucd_test/metadata.list

I checked log files from stage 1-6. There was no issue reading the list of multiple metadata directories.
Does someone know how to fix this issue?

Below is my script to run CNVPipeline and the log files are attached.

#!/bin/env bash
module load gcc/4.8.5 jdk samtools/1.6 r/3.3.3 htslib/1.6 lsf_drmaa/1.1.1

chrom='1'
SV_TMPDIR=/cluster/work/pausch/temp_scratch/fang/SV_tmp_cnv/chr${chrom}
export SV_DIR='/cluster/work/pausch/fang/svtoolkit'
inputFile='/cluster/work/pausch/fang/svtoolkit/bam.list'
runDir=/cluster/work/pausch/fang/svtoolkit/ucd_sv/ucd_test/cnv_run/chr${chrom}
reference_prefix='/cluster/work/pausch/fang/svtoolkit/reference_meta/ARS-UCD1.2_Btau5.0.1Y'
outdir='/cluster/work/pausch/fang/svtoolkit/ucd_sv/ucd_test/output/cnv'
output_prefix='test'
gendermap='/cluster/work/pausch/fang/svtoolkit/ucd_sv/ucd_test/gendermap.txt'
jobRunner="Drmaa"
jobWrapper="/cluster/work/pausch/fang/test_cnv/queue_lsf_wrapper.sh"

export PATH=${SV_DIR}/bwa:${PATH}
export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}

mkdir -p ${SV_TMPDIR} || exit 1
mkdir -p ${runDir} || exit 1
mkdir -p ${runDir}/logs_cnv || exit 1

mx="-Xmx5g"
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

echo "-- Run CNVPipeline -- "
LC_ALL=C java -cp ${classpath} ${mx} \
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 \
-memLimit 7.0 \
-jobRunner ${jobRunner} \
-gatkJobRunner ${jobRunner} \
-jobWrapperScript ${jobWrapper} \
-jobNative "-W 24:00 -R rusage[mem=8000]" \
--disableJobReport \
-R ${reference_prefix}.fa \
-genomeMaskFile ${reference_prefix}.svmask.fasta \
-genderMapFile ${gendermap} \
-ploidyMapFile ${reference_prefix}.ploidymap.txt \
-md /cluster/work/pausch/fang/svtoolkit/ucd_sv/ucd_test/metadata.list \
-runDirectory ${runDir} \
-jobLogDir ${runDir}/logs_cnv \
-I ${inputFile} \
-intervalList ${chrom} \
-lastStage 7 \
-tilingWindowSize 5000 \
-tilingWindowOverlap 2500 \
-maximumReferenceGapLength 2500 \
-boundaryPrecision 200 \
-minimumRefinedLength 2500 \
-run \
|| exit 1

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