These are chat archives for dereneaton/ipyrad

Feb 2018
Valerie Soza
Feb 13 2018 01:13 UTC
@isaacovercast, thanks for that info. I was running step 6 on a denovo assembled dataset and did have the -d flag on. I could send you the ipyrad_log.txt that I got from version 0.7.17, or should I upgrade first and try rerunning? FYI, the last two lines from the job that exited due to signal 7 bus errors in the ipyrad_log.txt were "2018-02-02 22:05:11,504 pid=11271 [] ERROR [Errno 116] Stale file handle
2018-02-05 09:29:38,924 pid=29329 [] INFO debugging turned on and registered to be turned off at exit"
Deren Eaton
Feb 13 2018 15:21 UTC
Hi @DylanHCohen_twitter , that looks like a bug on the git master branch. I just pushed a fix that you can get with git pull.
Deren Eaton
Feb 13 2018 15:29 UTC
@vsoza This Stale file handle error seems to be caused by a directory being moved or removed and then trying to query a file in it. I'm not sure that it is related to any kernel issues, but more likely to some change in the filesystem mounting perhaps. If step 6 was being restarted from having stopped without finishing it tries to restart from the 'substep' part of step 6 that it was on, and so perhaps this is creating some error when looking for a temporary file... just dropping ideas here. If that was the problem you could try forcing a hard restart of step 6 by using the -f flag. Upgrading is advised as well.
Isaac Overcast
Feb 13 2018 16:25 UTC
@vsoza Yeah, the stale file handle error could very well be downstream from the real problem, it's hard to say. If you send me the ipyrad_log.txt file I'll take a look at it, but certainly updating and rerunning with -f to try a clean run from the start would be something to try.
@LilyRobertLewis_twitter I agree that the "skip step one, but you still have to run step 1" thing is a little confusing, but glad you got it sorted out.
Valerie Soza
Feb 13 2018 18:17 UTC
@isaacovercast, thanks. Step 6 was in the clustering across step and had not finished so when I have tried restarting step 6 it starts from scratch. I will send you the ipyrad_log.txt files because I had another run killed that did not say "stale file handle" at the end. I'm trying to use the same version of ipyrad for comparison purposes with a previous analysis. ll give you more details in the email.
Gissella Pineda
Feb 13 2018 21:34 UTC
Hi, I'm trying to run the step 1 of ipyrad, but i have this error: (' error in %s: %s', ['split', '-a', '4', '-l', '8000000', '-', '/home/ellavazquez/Giss/tmp-chunks-Chaeto_1/chunk1_0_'], 'split: /home/ellavazquez/Giss/tmp-chunks-Chaeto_1/chunk1_0_aacd: No space left on device\n'). I used some commands like killall or lsof | grep deleted to fix it but doesn't work. I am a new user, someone could help me? any idea? Thanks