Hi Ann,

A pause function that truly stops an alignment job, permits inspection of intermediate results, then resumes it, is probably not going to be implemented. But we'll send more feedback about that if I have it incorrect.

The best advice I have to consider running a smaller sample of data through as a test set. It can be tricky to make truly "representative" test sets at first pass, but after this run completes, you could probably identify one by coordinates by choosing all of the sequences that fit within a certain "slices" of genomic regions that contain transcript models (or whatever feature you are examining) that are interesting (or difficult!). Then use that with subsequent runs if you want to tune parameters and have it run quicker. This is what I usually do - being sure to include some of the uglier regions. Even if I am never really able to solve them completely, at least I know what they will look like in the end. You don't want to train your parameters on all "ideal" cases. With lower quality data, this might be even more important since you've got a double challenge to manage - query and target. But that's real data!

Good luck with your project,

Galaxy team

On 6/26/13 2:33 PM, Ann Holtz-Morris, M.S. wrote:


I read   https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-new-pause-resume-functionality-in-Dec-2012-Galaxy-td4657331.html&sa=U&ei=KFzLUaHFCaGcjALSq4GQCw&ved=0CAcQFjAA&client=internal-uds-cse&usg=AFQjCNHSziHrbCCmumvDDUtmAeW9RvLRdg  with interest.


I would also like a Pause function as a toggle on/off so I can stop  look at the data being generated. I’m running a BWA alignment that’s been working now for almost 48 hours. It’s a decent sized data set but it had a very low quality second sequencing read. I’ve quality trimmed and length filtered. It ended up being only ~50% of the # of reads in Read1.


I’d love to be able to pause it and see if the data set is  behaving as expected.





Ann Holtz-Morris


de Jong Laboratory

510-428-3885 x 5715



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