These are chat archives for dereneaton/ipyrad
@dereneaton So I am having significant problems getting ipyrad to work with my dataset - as I mentioned before, I have one lane of PE and 2 lanes of SE data, and after I merged them and tried to run steps 6-7, I got the following error.
[cluster_across.py] INFO maxlen inside build is 419 [cluster_across.py] INFO inarr shape (280, 2605, 419) [assembly.py] ERROR
I thought this might be a problem with the combination of PE and SE, so I tried rerunning the PE lane as SE. Now, it will run steps 6-7, but (even with min individuals for a locus set to 9) all of the samples from the first lane (96) end up with
NaN loci in assembly. I have run that lane by itself in the past and recovered data, so it has to be something to do with merging the files. I have looked through the error file, log file, and json file and can't find anything that sticks out to me in terms of explanations for this problem, but I'm not exactly sure what to look for since there isn't an error.