These are chat archives for dereneaton/ipyrad

16th
Apr 2018
Jesse Grismer
@J_Grismer_twitter
Apr 16 2018 14:37

Hey Isaac,

Does ipyrad generate whole phased loci? If so what is the best way to obtain these after Step7 for downstream analyses. Thank you!!

yihanwu
@yihanwu
Apr 16 2018 16:03
Hi @isaacovercast and @dereneaton , I'm running step 3 on a gbs dataset, and will reach the end of my job time limit in a few days. If step 3 is stopped before completed, can I restart where it ended? I'm on the clustering step at the moment which has taken a long time. Thank you!
Isaac Overcast
@isaacovercast
Apr 16 2018 16:11
@J_Grismer_twitter Hi Jesse, yeah ipyrad outputs phased loci to the *.alleles.loci file.
@yihanwu Unfortunately step 3 is not checkpointed. this is something we've been meaning to do, but haven't gotten to it yet. It's possible to subsample your assembly, cluster the subsamples and then merge them after step 3 but that's pretty annoying. Easier if you can allocate more RAM and more cores to the job and see if you can get it to finish under the wall time limit.
yihanwu
@yihanwu
Apr 16 2018 16:22
@isaacovercast thank you.
Isaac Overcast
@isaacovercast
Apr 16 2018 16:23
@pbpearman Did you resolve your issue with demultiplexing samples? I thought I saw a question here from you about empty samples, but i don't see it here now.