These are chat archives for dereneaton/ipyrad

19th
Jan 2016
Isaac Overcast
@isaacovercast
Jan 19 2016 00:34
I just pushed 0.1.24, a total rewrite of step3 preview mode and refmap unmapped reads handling. Should be much faster, and preview now actually previews all data in step3, rather than just the reference mapping part.
Deren Eaton
@dereneaton
Jan 19 2016 18:07
I tweaking preview mode in step2. Currently when it selects only the first chunk this makes it so that only one processor runs on the data. Instead I'm going to slice a chunk of data out and let zcat_make_tmps still split it into bits to be spread across multiple processors.
Maybe I can generalize preview_truncate_fq to work for both steps 1&2 in this way.
Deren Eaton
@dereneaton
Jan 19 2016 19:58
Nice. step2 preview mode now runs approximately NCPUs X faster.
Isaac Overcast
@isaacovercast
Jan 19 2016 23:26
Very nice.
Did you get a chance to look at the issue with step6? #75 Last time i tried it was crashing on the simulated SE RAD as well.
Isaac Overcast
@isaacovercast
Jan 19 2016 23:33
Also, we should make a plan for thursday. We're trying to leave NYC by 6:30 or 7. Are you gonna to take the train down from New haven thursday morning?