Question: galaxy biomina RSeQC bam/sam mapping stats error
0
gravatar for doiremac
4.3 years ago by
doiremac0
uk
doiremac0 wrote:

I am trying to run the Galaxy Biomina RseQC BAM/SAM mapping quality stats

I have selected my uploaded bam file (generated using Tophat on the main Galaxy instance to map the BodyMap brain tissue paired end fastq files, provided in the shared data).

To make a smaller file for trial analysis, I am using only the reads that map to chr22

(ie. bam>sam> filter for c3=='chr22' and sam>bam)

I have selected 50 for the mapping quality minimum for unique reads (which I believe is the case for Tophat)

BUT

I get the following stderror

Fatal error: Exit code 127 (An error occured during execution, see stderr and stdout for more information)

Can anyone suggest what the problem might be?

Doiremac

rseqc biomina galaxy • 1.3k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by doiremac0

Try clicking on stderr and/or stdout in Galaxy, since that'll give more useful information. You may want to post questions like this on the Galaxy forum.

ADD REPLYlink written 4.3 years ago by Devon Ryan92k
0
gravatar for doiremac
4.3 years ago by
doiremac0
uk
doiremac0 wrote:

That's what I get with the stderr. I get blank with stdout.

I'll repost this on the Galaxy forum

Thanks

Doiremac

ADD COMMENTlink written 4.3 years ago by doiremac0
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