These are chat archives for dereneaton/ipyrad

24th
Jan 2016
Deren Eaton
@dereneaton
Jan 24 2016 00:01
did you remember install the update?
deren@oud:~/Documents/ipyrad/tests$ ipyrad -v
ipyrad 0.1.31
deren@oud:~/Documents/ipyrad/tests$ ipyrad -p test_pairgbs-params.txt -s6 -f

 --------------------------------------------------
  ipyrad [v.0.1.31]
  Interactive assembly and analysis of RADseq data
 --------------------------------------------------
  loading Assembly: test_pairgbs [./test_pairgbs.assembly]
  ipyparallel setup: Local connection to 4 Engines

  Step6: Clustering across 12 samples at 0.85 similarity
deren@oud:~/Documents/ipyrad/tests$
Isaac Overcast
@isaacovercast
Jan 24 2016 00:02
Hm. I'll try agian.
Isaac Overcast
@isaacovercast
Jan 24 2016 00:16
false alarm.
works good.
Isaac Overcast
@isaacovercast
Jan 24 2016 01:07
False false alarm. pairgbs works. the plain vanilla sim rad data still doesn't work for me.
in consensus/test.utemp i can see this:
2G_0_984        1B_0_981        +
2G_0_830        1B_0_981        +
two loci from an individual matching against the same seed, this means two sequences from one ind end up in a chunk
Deren Eaton
@dereneaton
Jan 24 2016 01:23
I see. didn't test on that set. working on it.
Deren Eaton
@dereneaton
Jan 24 2016 02:14
I've been running the CLI bit more. It is nice for testing, but it's harding to find bugs when it does crash. As we have it now, you get a fuller traceback in the API. I'll see if I can get the CLI to print out the full traceback instead of hiding it in the compositeError.
Deren Eaton
@dereneaton
Jan 24 2016 03:39
OK -- the following are all good through the CLI .
  • data/simpairgbs_R* :v:
  • data/simrad1_R1 :v:
  • data/simrad2_R1 :v:
  • data/simrad_test_R1 :v:
  • data/testrad_windels_R1 :v:
also, I suppose we should consolidate these sim data sets at some point.
Isaac Overcast
@isaacovercast
Jan 24 2016 18:09
Tight tight tight tight!