I have been working to integrate SOAPaligner/soap2 into my Galaxy
instance, and now have it mostly working thanks to some good advice from
this list. However when I execute my tool, the history item for the
resulting dataset turns red and says an error occured while running the
job. When I look at the error message, it is simply the output of the
soap2 tool, as follows:
Begin Program SOAPaligner/soap2
Thu Aug 19 09:27:43 2010
Query File a: /home/galaxy/galaxy_dist/database/files/000/dataset_150.dat
Output File: /home/galaxy/galaxy_dist/database/files/000/dataset_151.dat
Load Index Table ...
Load Index Table OK
Begin Alignment ...
131072 ok 0.46 sec
262144 ok 0.43 sec
393216 ok 0.44 sec
524288 ok 0.45 sec
655360 ok 0.44 sec
702613 ok 0.19 sec
Total Reads: 702613
Alignment: 672995 (95.78%)
Total Elapsed Time: 5.03
- Load Index Table: 0.48
- Alignment: 4.55
Thu Aug 19 09:27:48 2010
Additionally, the resulting dataset is a correct, and I can view it by
clicking on the eye icon for that history item. I've also taken the
exact command from paster.log and run it as the galaxy user, and the
script does have a 0 return code.
So why is Galaxy thinking there was an error generating the dataset? Do
I have to suppress output from soap2 using a wrapper?
Great Lakes Bioenergy Research Center
University of Wisconsin