These are chat archives for dereneaton/ipyrad

9th
Apr 2016
Isaac Overcast
@isaacovercast
Apr 09 2016 00:13
samtools view always outputs sequence in forward orientation (the actual strand the hit came from is indicated in the results somewhere).
Isaac Overcast
@isaacovercast
Apr 09 2016 01:38
pro tip: it's easier to debug the new step3 massive parallelization if you pass in -c 1 to ipyrad
Deren Eaton
@dereneaton
Apr 09 2016 02:31
ah, good idea. I also left in some [i.get() for i in res_chunk] type statements commented out which otherwise just get the results up to that point in the code, which is helpful for debugging.
Isaac Overcast
@isaacovercast
Apr 09 2016 22:20
Handling exceptions is trickier, since the main proc is spinning in the wait 1 it's harder to figure out where their coming from. More incentive to do better exception handling inside the called functions.
Isaac Overcast
@isaacovercast
Apr 09 2016 23:27
90% done getting denovo+reference working, but i'm seeing an ImpossibleDependency and reconcat is giving up. Seen this before? looks like an ipyparallel thing...
Isaac Overcast
@isaacovercast
Apr 09 2016 23:57
same problem in denovo-reference, but 'denovo' and 'reference' both seem to work good, for SE at least.