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jandrewrfarrell / RUFUS

RUFUS k-mer based genomic variant detection
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Broken pipe #23

Closed Dianer92 closed 1 year ago

Dianer92 commented 1 year ago

Hi, I run command "bash mytestrufus.sh" , erorr:

Exclue File Path = ./Intermediates/..generator.V2.ref.RepRefHash
/../../RUFUS/scripts/Overlap.shorter.sh: line 346: 221116 Done                    samtools view ./$NameStub.overlap.hashcount.fastq.bam
     221117                       | perl $AddSA
     221118 Broken pipe             | grep -v chrUn
     221119 Segmentation fault      (core dumped) | $RUFUSinterpret -mob ./Intermediates/$NameStub.overlap.hashcount.fastq.MOB.sam -mod $dumbFix.Jhash.histo.7.7.dist -mQ 10 -r $humanRef -hf $HashList -o ./$NameStub.overlap.hashcount.fastq.bam -m $MaxAlleleSize $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash
cat   mytestrufus.sh
runRufus.sh -s  /CBQSR.bam  -c  /MBQSR.bam -c  /FBQSR.bam  -k 25 -t 40  -r  /Ho_LIST.fasta