Question: Stderr On Samtools Sort
0
gravatar for Masaki MS
5.1 years ago by
Masaki MS30
Masaki MS30 wrote:
Dear all, I'm trying to set up samtools sort command on local Galaxy server. But I can not success to get sorted files from its result. First time, I got error message from Galaxy as.. error at.. [bam_sort_core] merging from 13 files... To resolve this problem, I use discard_stderr_wrapper.sh for modifying my samtools_sort.xml. (http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr) in samtools_sort.xml############################################ discard_stderr_wrapper.sh samtools sort '$input' '$output' ################################################################## Then I can success to finish the samtools sort job. But I can not get sorted file from Galaxy interface. Sorted file exists in the results folder as "dataset_97.dat.bam". But it could not link on Galaxy. Do you have any suggestion for this problem? thanks Masaki MS.
samtools bam • 790 views
ADD COMMENTlink modified 5.1 years ago by Peter Cock1.4k • written 5.1 years ago by Masaki MS30
0
gravatar for Peter Cock
5.1 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
I thought Galaxy tried to keep SAM/BAM files sorted by default... That wiki is out of date now, and should point you to the <stdio>, <regex>, and <exit_code> tag sets documented here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax Using these new features you can avoid a wrapper script just to hide stderr. Peter
ADD COMMENTlink written 5.1 years ago by Peter Cock1.4k
Sorry - the wiki did link to the relevant page in the paragraph at the top. Either I missed it or was seeing an older cache? In anycase, I've reworded this page to try and make it clearer: http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr Peter
ADD REPLYlink written 5.1 years ago by Peter Cock1.4k
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