Samtools index error when running Preprocessing on GenomeStrip Release 2.00.1.602.

Hi,

I am running GenomeStrip Release 2.00.1.602.

I did the installtest run and everything works fine.

Currently, I am working on 17 WGS bam files and I am constantly getting the following error.
Error: samtools index /mnt/projects/tanhjj99/drug_response/svtoolkit/installtest/TEST/metadata/headers.bam

I ran this line of command and it works without error.

This is the command which I used to run the preprocessing:

mx="-Xmx4g"
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.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
\ -cp ${classpath}
\ -configFile ${confile}
\ -tempDir ${SV_TMPDIR}
\ -R ${refgenome}
\ -genomeMaskFile ${processingdatapath}/human_g1k_v37.mask.100.fasta
\ -copyNumberMaskFile ${processingdatapath}/cn2_mask_g1k_v37.fasta
\ -genderMapFile ${currentpath}/bamfilegendermap.txt
\ -ploidyMapFile ${processingdatapath}/humgen_g1k_v37_ploidy.map
\ -runDirectory ${runDir}
\ -md ${runDir}/metadata
\ -useMultiStep
\ -reduceInsertSizeDistributions true
\ -computeGCProfiles true
\ -computeReadCounts true
\ -jobLogDir ${runDir}/logs
\ -I SEQUENCINGbamfile.list
\ -run

What should I do to solve this problem?

Thank you very much.

Best regards,
Joanna