On Thu, Apr 19, 2012 at 6:35 PM, JIE CHEN <jiechenable1...@gmail.com> wrote:
> Hi Peter,
>
> Thank you for your patience. I checked the error message in the history.
> They all give exactly the same error-- the one i gave in the first thread.

Are you saying this is the entire contents of the MIRA log entry in the history?

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
SOLEXA_SETTINGS -LR:lsd=1: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

I'm pretty sure you are just telling me the error message. I would have expected
more than that, e.g. a line "MIRA took XXX minutes" before that error message.

To try to be even clearer:

1. Start your web browser and goto your Galaxy
2. Upload/import the files
3. Select the MIRA tool from left hand pane
4. Select input files and set parameters
5. Click "Execute"
6. Notice that six new history entries appear: MIRA contigs (FASTA),
MIRA contigs (QUAL)",MIRA contigs (CAF), MIRA contigs (ACE)", MIRA
coverage (Wiggle), MIRA log
7. Wait for MIRA to fail and the six new history entries to go red.
8. Click on the "eye" icon for the red history item "MIRA log"
9. Copy and paste the MIRA log contents to an email.

Also, and perhaps equally useful, can you access this server at the
command line and try the exact same failing command (from a temp
directory - it may create lots of files and folders)?

Peter
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