These are chat archives for dereneaton/ipyrad

Oct 2017
Oct 23 2017 03:29
Hi @dereneaton ,I read the tutorial of ABBA-BABA test,but I don't have that many ideas about what the figure means
could you explain it?(like the different color means)
Oct 23 2017 08:33
Hi @isaacovercast and @dereneaton I am using ipyrad to run a pairddrad dataset for my project, and now for the Step 1,an error occured (argument of type 'numpy.int64' is not iterable),but for other datasets,it ran well.Also,I comfirmed this dataset by md5 value.What's wrong with it?
Ollie White
Oct 23 2017 16:40

Hi @dereneaton @isaacovercast I am trying to run step 7 on a pooled sample list with the aim of running Treemix. But I am getting an error message

  Step 7: Filter and write output files for 68 Samples
  [####################] 100%  filtering loci        | 0:00:47

  Encountered an error (see details in ./ipyrad_log.txt)
  Error summary is below -------------------------------
error in filter_stacks on chunk 0: IndexError(index 71 is out of bounds for axis 1 with size 68)

I can see some others have also had this issue but I wasn't sure the best way forwards? Cheers, Ollie

Isaac Overcast
Oct 23 2017 20:20
@Ollie_W_White_twitter The number of reads_passed_filter is all raw reads, whereas the number of mapped and unmapped reads are totalled up after an initial dereplication step (all identical copies of each read are deduplicated). The number of mapped and unmapped reads will always be much smaller because of this.
@ChaoShenzjs What does the rest of the output look like? Did you try re-running it with -d and looking at the ipyrad_log.txt?