[mira_talk] Re: miraSearchESTSNPs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 28 May 2009 21:32:20 +0200
On Mittwoch 27 Mai 2009 hegemon78@xxxxxxxxxxxxxx wrote:
> I have some problems with assembling and SNPs (ver:
> mira_2.9.45_dev_linux-gnu_x86_64)
> I use miraSearchESTSNPs pipeline to assemble 454 reads (with 2 strains),
> but the step3_info_snplist.txt file does not contain any SNPs even
> though i can find in log file for example:
> ...
Hmmm ... strange. I'll have to investigate that. Been quite a while since I
looked at that code, I fear that recent changes in the main routines may a
have broken a few things there. But I'm currently busy with some other things,
please remind me beginning of July if you don't hear back from me until then.
> 1. I think in this pipeline, program is parsing parameter file without
> problem only in 1 step (file: me_step1.par), in 2 & 3 step isn't (no
> effect in results, and marks in log files).
> 2. Is there any way to force program to do outputs in GAP4 format for
> step 1 and step 2?
Putting -OUT:org=yes in the me_step*.par file does not work?
Regards,
Bastien
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