[mira_talk] Re: empty info files with sssip=1
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 7 Dec 2009 19:03:20 +0100
On Freitag 04 Dezember 2009 David Lambert wrote:
> [...]
> the file test2_info_assembly.txt is empty, and so is the file
> test2_info_debrislist.txt and I can't find the singletons in the
> fasta file or anywhere else. This happens whether I use mira or
> miraSearchESTSNPs, and when I run the same assembly without the sssip
> parameters, the files are there.
> Any suggestions are appreciated, I am stuck.
I'm trying to recall how reads are handled which don't even pass the filter
stage ... I think they don't appear anywhere anymore.
Could you have a look at the clippings file in the log directory and see
whether some reads, which are 'missing', might have suffered the fate of being
killed prematurely? A simple grep for the read name should give you all
relevant information (or post it here if you have questions).
Regards,
Bastien
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