These are chat archives for dereneaton/ipyrad

Mar 2017
Emily Warschefsky
Mar 04 2017 17:08

@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.

[]    INFO     maxlen inside build is 419
[]    INFO     inarr shape (280, 2605, 419)
[]    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.

Isaac Overcast
Mar 04 2017 22:23
Merging PE and SE probably will do weird things, it's not a use case we ever designed for. In terms of rerunning PE as SE, that should work, i've tried it before and it worked for me, all you're really doing at that point is ignoring R2. Did you rerun the PE as SE from step 1? When you say: "all of the samples from the first lane (96) end up with NaN loci", are you referring to the PE-as-SE or the SE assembly here?
What's the datatype? Did you use the same restriction enzymes for all three lanes?