SVPreprocess error

hykuohykuo TaiwanMember

Hi Bob and all,

I try to use the GenomeSTRiP recently.
I got some error while I am running SVPreprocess.
I modify the installtest/discovery.sh as my svpreprocess script.

Here are the script content :

export SV_DIR=/home/hykuo/Desktop/svtoolkit
SV_TMPDIR=./tempdir
inputType=bam

GenomeSTRiP=/home/hykuo/Desktop/GenomeSTRiP
runDir=${GenomeSTRiP}/SVPreprocess
inputFile=${GenomeSTRiP}/raw_data/P-C-Wu.${inputType}
sites=test1.discovery.vcf
genotypes=test1.genotypes.vcf

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

mx="-Xmx32g"
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

java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar

java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
--disableJobReport \
-cp ${classpath} \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R ${SV_METADATA_DIR}/Homo_sapiens_assembly19.fasta \
-genomeMaskFile ${SV_METADATA_DIR}/Homo_sapiens_assembly19.svmask.fasta \
-copyNumberMaskFile ${SV_METADATA_DIR}/Homo_sapiens_assembly19.gcmask.fasta \
-runDirectory ${runDir} \
-md ${runDir}/metadata \
-disableGATKTraversal \
-useMultiStep \
-reduceInsertSizeDistributions false \
-computeGCProfiles true \
-computeReadCounts true \
-jobLogDir ${runDir}/logs \
-I ${inputFile} \
-run \
|| exit 1


The first error is about header.bam file

Here are the content in the SVPreprocess-3.out

[E::hts_open_format] fail to open file '/home/hykuo/Desktop/GenomeSTRiP/SVPreprocess/metadata/headers.bam'
samtools index: failed to open '/home/hykuo/Desktop/GenomeSTRiP/SVPreprocess/metadata/headers.bam": No such file or directory


Should I generate the header.bam file by myself or I get something wrong?

The other error I don't know how it generate

ERROR 23:27:36,172 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-X:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/hykuo/Desktop/GenomeSTRiP/SVPreprocess/tempdir' '-cp' /home/hykuo/Desktop/svtoolkit/lib/SVToolkit.jar:/home/hykuo/Desktop/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/hykuo/Desktop/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' /home/hykuo/Desktop/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta' '-I' '/home/hykuo/Desktop/GenomeSTRiP/raw_data/P-C-Wu.bam' '-O' '/home/hykuo/Desktop/GenomeSTRiP/SVPreprocess/metadata/depth/P-C-Wu.depth.txt' '-disableGATKTraversal' 'true' '-md' '/home/hykuo/Desktop/GenomeSTRiP/SVPreprocess/metadata' '-ploidyMapFile' '/home/hykuo/Desktop/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' /home/hykuo/Desktop/svtoolkit/conf/genstrip_parameters.txt' '-genomeMaskFile' '/home/hykuo/Desktop/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' /home/hykuo/Desktop/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0'
ERROR 23:27:36,174 FunctionEdge - Contents of /home/hykuo/Desktop/GenomeSTRiP/SVPreprocess/logs/SVPreprocess-9.out:


attach file is my full log.
I am not sure why I can't use "sh script.sh | tee result" to write the stdout to the file.
Hence I copy the logs to the file, the format is ugly somewhere.
I am not friendly with Post in the forum,too
Sorry for the unfriendly post format

Look forward for your help
Thanks a lot

log.txt 42.5K
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