These are chat archives for dereneaton/ipyrad

29th
Mar 2017
R2C2.lab
@R2C2_Lab_twitter
Mar 29 2017 15:39
@isaacovercast: I tried two different assembly methods, using the same data set and the version [v.0.6.11] of ipyrad. All parameters were the same in the params file (except the ones referring to the assembly method. The run using denovo-reference is running normally in step 3 but the one using reference gives the following message in ipyrad_log.txt (attached)
Merging reads 100%
Fatal error: More reverse reads than forward reads
Any advise would be much appreciated
Isaac Overcast
@isaacovercast
Mar 29 2017 18:15
@R2C2_Lab_twitter ahhhh, i thought i fixed that! Let me look again.
R2C2.lab
@R2C2_Lab_twitter
Mar 29 2017 18:23
well, the puzzling thing is that the other assembly (denovo-reference) is running ok. Btw, many thanks for all the help you (and other developers) provide
James McDaniel
@jlmcdaniel
Mar 29 2017 22:29
Hi @isaacovercast or @dereneaton, I was wondering if you had a python script available that can parse out phylogenetically informative loci from the .loci file generated by ipyrad? Thanks!
Isaac Overcast
@isaacovercast
Mar 29 2017 22:46
@jlmcdaniel I don't have anything like that, sorry to say. Deren might.
Isaac Overcast
@isaacovercast
Mar 29 2017 22:53
@R2C2_Lab_twitter The denovo-reference assembly is running ok because it's the reference mapping part that's causing problems, so denovo-reference does the mapping, but then throws out the mapped reads, so no problems.