[mira_talk] Re: Beginner - problem with input file..
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 9 Sep 2009 23:39:51 +0200
On Mittwoch 09 September 2009 Naira Naouar wrote:
> So I have read the requirements for the analysis but is there a way not
> to use the quality and traceinfo files?
There is. But first, please repeat after me three times: "I don't want to
assemble without qualities!"
Done?
Good, please read on.
> I already processed my 454 reads in order to remove tags and low quality
> nucleotides.
> [...]
> I have run the command:
> mira -project=toto -fasta -job=denovo,genome,accurate,454 -notraceinfo
> And the error that I get now is:
> Fatal Error: "No read can be used for assembly."
> ->Thrown: void Assembly::dumpSomeStatistics()
> ->Caught: main
> Program aborted.
> Was the previous version wrong? or is there a way (with the options) to
> do the analysis like the previous version?
The clipping got you. The standard behaviour of MIRA is to *expect* noisy
input (and also decent coverage), therefore it cleans whatever it can. This
fails when
a) no qualities are given
b) low coverage is present
Both cases are present in your example.
What to do? Choose your clipping options carefully (have a look at the log for
which clipping options MIRA uses in your special --job= combination). If
you're really sure on what you are doing, you can also switch off clipping
completely for, e.g., 454 with:
mira ... --job=... --noclipping=454
For low coverage, you might also need to switch of the proposed end clip:
-CL:pec=no
To tell MIRA that no trace info should be loaded, use:
"--notraceinfo"
or, if just for 454 data:
"454_SETTINGS -LR:mxti=no"
Regards,
Bastien
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