Dear all,
I'm not sure but I think I found a bug somewhere. However, I can't tell where the problem is and, so, who to report it to.
This is what I see in paster.log:
----- galaxy.jobs.runners.drmaa DEBUG 2016-08-01 13:02:08,895 (897/193391) state change: job finished normally galaxy.jobs.output_checker INFO 2016-08-01 13:02:09,244 Job 897: Fatal error: Exit code 1 () galaxy.jobs DEBUG 2016-08-01 13:02:09,317 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,354 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,678 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,707 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,738 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,770 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,809 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,846 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,890 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,928 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,964 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:10,001 setting dataset state to ERROR galaxy.jobs INFO 2016-08-01 13:02:11,560 Collecting metrics for Job 897 galaxy.jobs DEBUG 2016-08-01 13:02:11,579 job 897 ended (finish() executed in (2402.377 ms)) -----
As it turns out, there *is* a problem with the run. So, the latter error messages are correct. So, I think the first line is wrong. Or is this expected behaviour?
About what I'm doing. I'm running the IUC Cuffdiff tool and am using it to generate an sqlite database for cummeRbund. It seems that it is running the system-installed version of R and some packages are missing. (I'm having problems installing the R packages, but I'm still investigating this.)
So, there are error messages in the output. Perhaps there is a problem with the error message being returned by the tool to the drmaa (SLURM, in our case)?
Ray