These are chat archives for dereneaton/ipyrad

9th
Oct 2018
Oliver Stueker
@ostueker
Oct 09 2018 19:26

I'm running the CLI tutorial and on step 2 I'm running into the following error:

  ipyrad [v.0.7.28.1]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  Begin run: 2018-10-09 16:34
  Using args {'preview': False, 'force': False, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': None, 'cores': 1, 'params': 'params-iptest.txt', 'branch': None, 'steps': '2', 'debug': False, 'new': None, 'download': None, 'MPI': False}
  Platform info: ('Linux', 'cedar5.cedar.computecanada.ca', '3.10.0-693.5.2.el7.x86_64', '#1 SMP Fri Oct 20 20:32:50 UTC 2017', 'x86_64')2018-10-09 16:35:05,718        pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,719         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,720         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)
2018-10-09 16:35:05,721         pid=123762      [rawedit.py]    ERROR   error in run_cutadapt(): OSError([Errno 2] No such file or directory)

The version v.0.7.28.1 is v.0.7.28 which includes the patches suggested in #312 and #313.

Any idea where this could come from?
(I'm not going to use ipyrad myself but rather testing for a user for which I'm installing it)
Isaac Overcast
@isaacovercast
Oct 09 2018 20:06
I'm sure this is because the directory with the binaries in it isn't in the $PATH.
Right now it's almost certainly looking for cutadapt and not finding it.
Oliver Stueker
@ostueker
Oct 09 2018 20:50
It's not an explict depenency defined in requirements.txt. I'll try to add it or install manually tomorrow.
Oliver Stueker
@ostueker
Oct 09 2018 21:15
Yes that was the problem. After installing cutadapt I was able to pass steps 2-7.
Thanks!