These are chat archives for dereneaton/ipyrad

21st
Oct 2016
Edgardo M. Ortiz
@edgardomortiz
Oct 21 2016 00:31
I have concatenated samples from different runs and lanes and ipyrad didn't complain at any point. The output looks OK too.
vieves
@vieves
Oct 21 2016 00:33
Great news! Thanks @edgardomortiz
Edgardo M. Ortiz
@edgardomortiz
Oct 21 2016 20:07

Hi @dereneaton @isaacovercast, I haven't been able to move beyond step 4 on any paired-end analysis (the single-ends pass just fine), I tried editing the .json files but then it fails again in a different sample, the errors look like this:

   Step 4: Joint estimation of error rate and heterozygosity
  [####################] 100%  inferring [H, E]      | 0:37:20  ERROR:ipyrad.assemble.util:  Sample PIO-Dglut failed with error IndexError(index 13662 is out of bounds for axis 0 with size 13662)

  Step 4: Joint estimation of error rate and heterozygosity
  [####################] 100%  inferring [H, E]      | 0:36:06  ERROR:ipyrad.assemble.util:  Sample DIP-Dmeye-1 failed with error IndexError(index 15927 is out of bounds for axis 0 with size 15927)

  Step 4: Joint estimation of error rate and heterozygosity
  [####################] 100%  inferring [H, E]      | 1:17:51  ERROR:ipyrad.assemble.util:  Sample VAC-Cavbra_EO2401 failed with error IndexError(index 44045 is out of bounds for axis 0 with size 44045)

I was thinking on running step 4 with version 0.4.2 and then running the remaining steps in version 0.4.4 How different are the calculations between versions? What kind of bias could cause on my results? Thanks!