[mira_talk] No output files in mapping mode when nothing maps?
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 6 Apr 2011 15:18:53 +0100
Hi Bastien,
I just had a pipeline fall over when a MIRA mapping ran, finished
cleanly (zero return code, no error messages), but did not write
any files to the project's results folder.
Based on the stdout log, I think what happened was that none
of the reads mapped to my reference (curses - this is already
the second attempt at sequencing this biological sample):
...
Skim summary:
accepted: 0
possible: 19
permbans: 0
Hits chosen: 0
...
Does this sound reasonable (no hits mapped-> no output)?
If so, could you write some "empty" output files anyway please?
In the case of the contigs summary for example, I would expect
a boring table with everything tagged MCVc (Missing CoVerage
in Consenus). Similarly the coverage wiggle file would all be
zeroes, while the contigs would be just the reference sequences.
Alternatively, how about printing a warning/error message and
giving a non-zero return code?
Regards,
Peter
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