These are chat archives for dereneaton/ipyrad

7th
Dec 2017
Emily Warschefsky
@ewarschefsky_twitter
Dec 07 2017 02:45

Hey @dereneaton and @isaacovercast : I saw that someone posted this question before, but I don't think it got answered. I am trying to use a pop file on one branch of my dataset (83 individuals) to rerun step 7 and I get the following error:

-------------------------------------------------------------
  ipyrad [v.0.6.11]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  loading Assembly: L123_abbababa1
  from saved path: /scratch/ewars001/ipyrad/Lanes123/L123_abbababa1.json
  host compute node: [8 cores] on n038

  Step 7: Filter and write output files for 83 Samples
  [####################] 100%  filtering loci        | 0:01:57  

  Encountered an error (see details in ./ipyrad_log.txt)
  Error summary is below -------------------------------
error in filter_stacks on chunk 0: IndexError(index 102 is out of bounds for axis 1 with size 83)

I am sure it is the popfile because I went back and deleted it from the params file and deleted the pops info in the .json file and it is running fine now. I updated to v.0.7.19 and it's still giving me the problem.

Isaac Overcast
@isaacovercast
Dec 07 2017 14:23
@ewarschefsky_twitter Can you email me the popsfile?