Thank you Peter. I changed the dataset and succeeded this time. Appreciated
for you help.

Cheers,
Tyler

On Thu, Apr 19, 2012 at 12:40 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Thu, Apr 19, 2012 at 7:13 PM, JIE CHEN <jiechenable1...@gmail.com>
> wrote:
> > Hi Peter,
> >
> > Here is the full log:
> >
>
> Excellent :)
>
> The good news is MIRA seems to be installed and running
> fine - it just didn't like your test data, and I understand why:
>
> > ...
> >
> > Sanger will load 1 reads.
> > Longest Sanger: 36
> > Longest 454: 0
> > Longest IonTor: 0
> > Longest PacBio: 0
> > Longest Solexa: 0
> > Longest Solid: 0
> > Longest overall: 36
> > Total reads to load: 1
> > ...
> > Sanger        total bases:36  used bases in used reads: 0
> > 454   total bases:0   used bases in used reads: 0
> > IonTor        total bases:0   used bases in used reads: 0
> > PacBio        total bases:0   used bases in used reads: 0
> > Solexa        total bases:0   used bases in used reads: 0
> > Solid total bases:0   used bases in used reads: 0
> >
> > ..
> >
> > Fatal error (may be due to problems of the input data or parameters):
> >
> > "No read can be used for assembly."
> >
> > ...
>
> Then finally some information my wrapper script adds:
>
> > MIRA took 0.00 minutes
> > Return error code 1 from command:
> > mira --job=denovo,genome,accurate SANGER_SETTINGS
> -LR:lsd=1:mxti=0:ft=fastq
> > -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat
> COMMON_SETTINGS
> > -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1
>
> It appears you are trying to run MIRA with a single 36bp read,
> telling MIRA this is a Sanger read. That is very odd (not least
> because a 36bp read sounds more likely to be an early
> Solexa/Illumina read from the length).
>
> Has something gone wrong with loading the data into Galaxy?
> Or did you just want to try a trivial test case? If so, it was too
> simple and MIRA has stopped because it thinks it is bad input.
>
> The MIRA output log file (which is actually written to the stout
> if you run MIRA yourself at the command line) is quite verbose,
> but it is incredibly useful for diagnosing problems. That is why
> I collect it as one of the output files in Galaxy.
>
> You should be able to try some larger realistic examples, e.g.
> a virus or a bacterial genome depending on your server's
> capabilities. And if they fail, have a look through the log file
> for why MIRA said it failed.
>
> Also keep in mind that the Galaxy wrapper is deliberately a
> simplified front end - MIRA has dozens of command line
> options which are not available via my wrapper for simplicity.
>
> Regards,
>
> Peter
>
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