[mira_talk] Re: empty info files with sssip=1
- From: David Lambert <dlamber2@xxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 09 Dec 2009 17:38:39 -0500
Hi,
I looked at the clippings file and a few are being filtered out at
this stage. There are a few singletons in the output, but it seems
like there are not enough-- like 93 in a test assembly of 105,000
titanium reads that assembled 65,000 reads. I don't think that the
sssip function is working for me. Especially since I am getting this
strange result where the info and debris list files are empty.
Does the following seem like a functional command line:
miraSearchESTSNPs -project=test2 -fasta
-job=denovo,est,normal,sanger,454 SANGER_SETTINGS -OUT:sssip=1
454_SETTINGS -OUT:sssip=1
If so, then maybe I should remake my installation of mira?
Thanks!
Dave
At 01:03 PM 12/7/2009, you wrote:
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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