These are chat archives for dereneaton/ipyrad

May 2017
Edgardo M. Ortiz
May 10 2017 15:46
@toczydlowski that file contains the output from vsearch, if you substract singletons from clusters you get the number of clusters with at least 2 sequences. At this point your clusters have not been filtered by your minsample parameter yet.
May 10 2017 20:37
@isaacovercast I am comparing my results from denovo and reference pipelines. Despite the fact that ~90% of my PE reads overlap, when I look at the clustS, all of the reads look unmerged (R1nnR2). In the reference pipeline are reads being merged before clustering, as is the casefor denovo? Thanks for the clarification.
May 10 2017 21:28
Sorry I meant before mapping.
May 10 2017 22:33

Hi @isaacovercast I ran step 7 but I got the following error. Apparently it is a problem with sample PL105, but I checked the consensus from step 6 an it looks fine.

ipyrad [v.0.6.20]

Interactive assembly and analysis of RAD-seq data

Begin run: 2017-05-10 17:26
Using args {'preview': False, 'force': True, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': False, 'cores': 64, 'params': 'params-PL_95_6b.txt', 'branch': None, 'steps': '7', 'debug': False, 'new': None, 'MPI': True}
Platform info: ('Linux', 'node-19.local', '2.6.32-642.15.1.el6.x86_64', '#1 SMP Fri Feb 24 14:31:22 UTC 2017', 'x86_64')2017-05-10 17:26:59,333 pid=47596 [] ERROR 'PL105'