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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