Question: What is causing this MPileup error in Galaxy?
1
gravatar for bryantl
2.6 years ago by
bryantl90
United States
bryantl90 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!

 

 

galaxy samtools • 1.0k views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by bryantl90
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The Mpileup tool has known issues at this time. Our team is actively working on a correction. Progress can be followed here: https://github.com/galaxyproject/tools-devteam/issues/255

Thank you for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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