Hi All, 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 Reference: /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index 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 SOAPaligner/soap2 End 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? Cheers -- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm(a)glbrc.wisc.edu