These are chat archives for dereneaton/ipyrad

6th
Nov 2016
Edgardo M. Ortiz
@edgardomortiz
Nov 06 2016 00:17
Really puzzled now:

 -------------------------------------------------------------
  ipyrad [v.0.4.9]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  loading Assembly: ast-PE100-85-test
  from saved path: /scratch/02728/emo347/ddRAD/astereae/e_read-lengths_ipyrad/ast-PE100-85-test.json
  host compute node: [24 cores] on nid00622

  Step 3: Clustering/Mapping reads
  [####################] 100%  dereplicating         | 0:09:48
  [####################] 100%  clustering            | 0:18:00
  [####################] 100%  building clusters     | 0:02:46
  [####################] 100%  chunking              | 0:00:09
  [####################] 100%  aligning              | 1:37:45
  [####################] 100%  concatenating         | 0:00:41

  Step 4: Joint estimation of error rate and heterozygosity
  [####################] 100%  inferring [H, E]      | 0:03:34  ERROR:ipyrad.assemble.util:  Sample PIO-Dcine failed with error IndexError(index 123 is out of bounds for axis 0 with size 123)


  Encountered an error, see ./ipyrad_log.txt.
    Sample PIO-Dcine failed step 4
Edgardo M. Ortiz
@edgardomortiz
Nov 06 2016 01:52
Maybe enforce the recalculation even when parameters don't change?
Deren Eaton
@dereneaton
Nov 06 2016 17:24
@edgardomortiz I'll give it another try today
James Clugston
@Cycadales_twitter
Nov 06 2016 20:35
@dereneaton Hi Deren, just question with regards to the recent update (0.4.7). I followed your raecomentdions and changed the max_fragment_length in the .json file for the length of my input data. 150 PE which was 120bp PE after trimming so I changed this value to 120. However step 6 seems to be taking a long time...usually takes around 2 days but just the clustering step has been going over three days now. This might be that this time I am going to get luck and not encounter an error (as every run so far I have not been able to complete and has had to be restarted).
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