Question: What is causing this MPileup error in Galaxy?
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bryantl • 90 wrote:
Hello,
I'm new to galaxy and next gen sequencing. I'm trying to generate a VCF file from whole exome sequencing (human). I keep getting an error from MPileup in galaxy. I generate my SAM file using BWA for Illumina and then convert the SAM to BAM using the SAM-to-BAM option under Samtools. I can view my BAM file in UCSC genome browser. When I try to use MPileup on the BAM file, it generates an error.
Fatal error: Exit code 139 (Error) [main] unrecognized command '--version' /galaxy-repl/main/jobdir/010/986/10986949/galaxy_10986949.sh: line 42: 9792 Segmentation fault (core dumped) samtools mpileup -f "/galaxy/data/hg18/sam_index/hg18.fa" "/galaxy-repl/main/files/013/304/dataset_13304420.dat" --VCF --uncompressed -o "40" -e "20" -h "100" -L "250" -m "1" --open-prob "40" -F "0.002" --output "/galaxy-repl/main/files/013/305/dataset_13305726.dat" 2> "/galaxy-repl/main/files/013/305/dataset_13305727.dat"
I am able to use FreeBayes on this BAM file, but I cannot get MPileup to work. Does anyone know what would cause this error?
Thanks!
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modified 3.0 years ago
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Jennifer Hillman Jackson ♦ 25k
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3.0 years ago by
bryantl • 90
