These are chat archives for dereneaton/ipyrad

9th
Feb 2018
Isaac Overcast
@isaacovercast
Feb 09 2018 18:41
@AdRUO So you have paired end RAD data (Baird 2008) with the sonication step? If this is the case check out the FAQ for how to deal with this: http://ipyrad.readthedocs.io/faq.html#why-doesn-t-ipyrad-handle-pe-original-rad
Isaac Overcast
@isaacovercast
Feb 09 2018 20:19
@vsoza Hi Valerie, we'll that sounds like a tricky problem. ipyrad has been tested across a wide array of kernel version (2.6.32.12-0.7 - 4.10.0-42), this is just the range that I know of, so I'm sure the range of kernel versions it's been run on in the wild is actually probably wider. Because ipyrad is python it should be very agnostic about kernel version, but come to think of it we do use several binary distributions internally (vsearch, samtools, bwa, etc). There's a chance one or the other of these internals is having an issue, but i'd be very surprised. You might try updating ipyrad to the newest version, just to see if that helps. What step are you on when it crashes?
It also might help to see the ipyrad_log.txt file after rerunning ipyrad with the -d flag to generate debug output.