These are chat archives for dereneaton/ipyrad

23rd
Nov 2016
R2C2.lab
@R2C2_Lab_twitter
Nov 23 2016 12:37
Hi @edgardomortiz I tried your suggestion of running step 6 with the -c 10 flag because of a memory issue but after 10 hours seems to be still running

ipyrad [v.0.4.1]

Interactive assembly and analysis of RAD-seq data

loading Assembly: individual
from saved path: ~/ipyrad_individual/individual.json
local compute node: [10 cores] on ccmar-r2c2-01

Step 6: Clustering across 5 samples at 0.85 similarity
[####################] 100% concat/shuffle input | 0:00:39
[####################] 100% clustering across | 10:18:26
[####################] 100% building clusters | 0:00:27
[####################] 100% aligning clusters | 0:25:37
[####################] 100% database indels | 0:03:16
[####################] 100% indexing clusters | 0:26:50
[####################] 100% building database | 0:01:34

Any suggestion?
Deren Eaton
@dereneaton
Nov 23 2016 16:04
Hey @R2C2_Lab_twitter, It looks like step 6 finished successfully. Have you tried running step 7? Also, for now, you should check for updates fairly frequently, since ipyrad is under pretty active development. You can upgrade by entering conda update -c ipyrad ipyrad. It looks like you are on v.0.4.1, the current release is v.0.5.5.
R2C2.lab
@R2C2_Lab_twitter
Nov 23 2016 16:32
Hi @dereneaton it looks like it has finished but the prompt (regina@ccmar-r2c2-01:~/ipyrad_individual>) is not appearing after [####################] 100% building database | 0:01:34 ; I will upgrade ipyrad to the current version today
and when check if it’s running (htop) it’s still running
James Clugston
@Cycadales_twitter
Nov 23 2016 20:29
@dereneaton @isaacovercast Quick question I have been having a lot of trouble during step 6 where it keeps crashing or giving an error when indexing reads. I did think it was down to RAM usage during step 6 . So I am running a large run on a cluster the specs of the cluster are as follows 7 x 12 core nodes each with 64gb of RAM. Do you guys think this should be enough during step 6? the data set is 86 samples 150 PE read.