These are chat archives for dereneaton/ipyrad

8th
Oct 2018
Edgardo M. Ortiz
@edgardomortiz
Oct 08 2018 13:33
Hi again @isaacovercast , this is just a curiosity. Prior to demultiplexing, ipyrad chunks the raw files, but this takes really long compared to the actual sorting. Might this because I am working on a Mac?

 -------------------------------------------------------------
  ipyrad [v.0.7.28]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  New Assembly: deman1
  establishing parallel connection:
  host compute node: [24 cores] on PlantBiodiversitys-Mac-Pro.local

  Step 1: Demultiplexing fastq data to Samples
  [####################] 100%  chunking large files  | 0:41:02
  [####################] 100%  sorting reads         | 0:01:47
  [####################] 100%  writing/compressing   | 0:03:15
Edgardo M. Ortiz
@edgardomortiz
Oct 08 2018 13:56
Update: the split that comes with Mac is ridiculously slow, I am using the homebrew GNU version of split and is super fast (0:01:21)
Isaac Overcast
@isaacovercast
Oct 08 2018 15:54
@edgardomortiz whoa, weird. That's crazy the mac split is so slow.