These are chat archives for dereneaton/ipyrad

18th
Jan 2017
congliu0514
@congliu0514
Jan 18 2017 00:03
@dereneaton Looking at the _stats.txt is real a good idea ! thanks a lot !
Todd Pierson
@twpierson
Jan 18 2017 15:28
Hi folks. I'm encountering an odd error while trying to run step 2 (v.0.5.10). I have directed ipyrad towards my sorted_fastq_path and left barcodes_path empty, but ipyrad still seems to be looking for a barcodes file. Here's the first error:
2017-01-18 10:14:13,478     pid=22461     [rawedit.py]    WARNING       error adding barcodes info:     Barcodes file not found. You entered:
Any thoughts?
Todd Pierson
@twpierson
Jan 18 2017 17:15
Hmm. I ran steps 1-2 through an interactive node on this cluster, and the problem disappeared. That is, it only existed when submitting through a job file. Now running step 3 through a job file without a problem.
Isaac Overcast
@isaacovercast
Jan 18 2017 20:21
@twpierson That warning message is more or less safe to ignore, depending on how much merging you have in your pairs. If you have lots of small insert sizes with respect to read length then you'll get lots of R2 reading through the 5' end of R1 and including the barcode/cutsite/adapter in the sequence. If you have large inserts with respect to read length then you don't have to worry about this at all.