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SVPreprocess Error: failed to open "md_tempdir/headers.bam" No such file or directory

Dear Genome STRiP users,

I am running SVPreprocess to the range chr16:171000-178000. The SVPreprocess pipeline script is here

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
rundir="/proj/yunligrp/users/minzhi/gs/gs_test_svpreprocess"

java -Xmx4g -cp ${classpath}\
     org.broadinstitute.gatk.queue.QCommandLine\
     -S ${SV_DIR}/qscript/SVPreprocess.q\
     -S ${SV_DIR}/qscript/SVQScript.q\
     -cp ${classpath}\
     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
     -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
     -R /proj/yunligrp/users/minzhi/gs/Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta \
     -L chr16:171000-178000 \
     -I /proj/yunligrp/users/minzhi/gs/gs_script/NWD.recab.list \
     -md md_tempdir \
     -tempDir /proj/yunligrp/users/minzhi/gs/gs_tempdir \
     -runDirectory ${rundir} \
     -ploidyMapFile /proj/yunligrp/users/minzhi/gs/gs_script/standard_ploidy.map \
     -jobLogDir ${rundir}/logs \
     -jobRunner Drmaa \
     -gatkJobRunner Drmaa \
     -jobNative "--mem=5000 --time=5:00:00 --nodes=1 --ntasks-per-node=8" \
     -jobQueue general \
     -run \
     || exit 1

It returned error "samtools index: failed to open "md_tempdir/headers.bam": No such file or directory" during running it (details as below):

ERROR 13:07:15,877 FunctionEdge - Error: samtools index md_tempdir/headers.bam 
ERROR 13:07:15,886 FunctionEdge - Contents of /proj/yunligrp/users/minzhi/gs/gs_test_svpreprocess/logs/SVPreprocess-4.out:
[E::hts_open_format] Failed to open file md_tempdir/headers.bam
samtools index: failed to open "md_tempdir/headers.bam": No such file or directory 

But I successfully completed this pipeline with the same script two months ago. I do not understand when the "headers.bam" will be created, and why it is not in created this time. May I have your suggestions? Thank you very much in advance.

Best regards,
Wusheng

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