Hello, I had a reasonable ''Iterative Alignment Map'' Run which uses Bowtie with a 132MB output that downloads. However I did get the ERROR: ''[bam_sort_core] merging from 3 files...''. Should I repeat with new parameters or maybe fix the 132MB file somehow?
This sounds a lot like recent errors at Galaxy Main (http://usegalaxy.org) a bit over a week ago. There were a few more sporadic errors of this type last week.
In short, this usually means that the alignment failed at some point. The result may only contain the header and/or potential incomplete output. Check the output by converting BAM to SAM if you want (If that tool will even run), or just rerun the job and discard the first.
If this happens again, check your inputs. It is also possible that the job is failing for memory with this type of warning. If the problem is persistent, and you cannot determine the root cause, a bug report or shared history link can be sent in for feedback.
Thanks, Jen, Galaxy team