[mira_talk] Re: Run MIRA in Galaxy....
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "J. Cristobal Vera" <jcv128@xxxxxxx>
- Date: Tue, 20 Dec 2011 10:51:07 +0000
On Tue, Dec 20, 2011 at 7:30 AM, J. Cristobal Vera <jcv128@xxxxxxx> wrote:
> Hi,
> I ran the assembly again and it looks like only the wig file is missing.
> The ace and caf files are there, which are pretty vital. Guess if you can
> fix the wig file issue everything else is working. Galaxy still outlines
> all the results in history as all errors, which could be confusing to
> people.
Galaxy currently assigned success/failure at the job level, not
the output file level. In this case, I was treating a missing wig
file as an error. In an update yesterday I realised a missing wig
file would mean I didn't collect the ACE or CAF output either,
which is now fixed:
https://bitbucket.org/peterjc/galaxy-central/changeset/1c5c6d4ab3c8
Now the question is why isn't there a wiggle file? Since you
sent me the stdout log, I can see that MIRA deliberately
didn't write it:
Parsing parameters: --job=denovo,est,accurate 454_SETTINGS -LR:lsd=yes
-LR:mxti=no -LR:ft=fastq
-FN:fqi=/home/cris/Desktop/Galaxy/galaxy-dist/database/files/000/dataset_29.dat
COMMON_SETTINGS -OUT:rrot=yes -OUT:rtd=yes
...
Result files:
Saved as CAF (orc) : yes
Saved as MAF (orm) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : yes
Saved as GFF3 (org3) : no
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : no
Saved as wiggle (orw) : no
Perhaps I didn't notice this before, but it appears MIRA doesn't
write out a wiggle file by default in EST mode. Would it be
useful to you? I can change the command line to explicitly
request this (and the other files I try to collect).
> I don't have a strong preference either way for fastq or qual, but fastq has
> three different formats for q scores, so that would need to be made clear i
> guess.
Easily done - Galaxy has separate datatypes for the main FASTQ
variants, so we can make it explicit that Sanger FASTQ encoding
was being used.
> Also, how difficult would it be to adapt the py and xml code for the
> mirasearchestsSNPs script? I read it run very similar to mira, although I
> haven't run it yet (I plan on using it soon).
> Cheers,
> Cris
I've never used mirasearchestsSNPs so can't immediately
comment.
Peter
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