These are chat archives for dereneaton/ipyrad

28th
May 2016
Robin Sleith
@R0cknRobin_twitter
May 28 2016 15:59
Hi folks, I met Isaac last week and he introduced me to ipyrad. I am running gbs on a cluster with sun grid engine to submit jobs. I am having issues with python dependancies and paths. I was able to solve most by adding PATH=/home/rsleith/miniconda2/bin/:$PATH as the first line of my bash script that gets run on compute nodes. I successfully ran steps 1 through 4 but got an error on step 5. ERROR:ipyrad.core.assembly:
Traceback (most recent call last):
File "/home/rsleith/miniconda2/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.2.9', 'console_scripts', 'ipyrad')()
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 364, in main
data.run(steps=steps, force=args.force, preview=args.preview)
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1378, in run
self.step4(force=force)
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1272, in step4
self._clientwrapper(self._step4func, [samples, subsample, force], 45)
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 837, in _clientwrapper
stepfunc(*args)
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1067, in _step4func
assemble.jointestimate.run(self, samples, subsample, force, ipyclient)
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/jointestimate.py", line 316, in run
submit(data, submitted_args, ipyclient)
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/jointestimate.py", line 374, in submit
if jobs[sname].successful():
File "/home/rsleith/miniconda2/lib/python2.7/site-packages/ipyparallel/client/asyncresult.py", line 237, in successful
assert self.ready()
AssertionError The log file gives me 2016-05-27 19:33:22,661 pid=30107 [assembly.py] ERROR Any thoughts on what might be going on here? Thanks!
Isaac Overcast
@isaacovercast
May 28 2016 18:05
Hi robin, thanks for giving ipyrad a try! From the looks of this stack dump this is actually inside step 4 self.step4(force=force), right? I found the problem and fixed it and pushed a new package to conda, 0.2.10. Pull it down and give it a shot and let me know how it goes.