Question: Stderr On Samtools Sort
0
Masaki MS • 30 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.
ADD COMMENT
• link
•
modified 6.0 years ago
by
Peter Cock • 1.4k
•
written
6.0 years ago by
Masaki MS • 30
