These are chat archives for dereneaton/ipyrad

28th
Feb 2017
letimm
@letimm
Feb 28 2017 16:14
@dereneaton @isaacovercast I am having an issue with step 1 in ipyrad v0.6.4. I have successfully run this step a number of times (usually taking only a few minutes per file), however now it completes the "chunking large files" step, but hangs on "sorting reads". By that, I mean it 100% completes chunking large files, but sticks at 0% sorting reads (for days, if allowed to run that long). It has run successfully on two of my twelve files, the remaining ten exhibit the described issue. There is no error output. I have tried changing relative path to explicit path in the params file, but it did not resolve the issue. Any insight on what might be going on?
Deren Eaton
@dereneaton
Feb 28 2017 16:18
@letimm did you use the -d flag when you ran step 1?
I ask because we accidentally left a debugging statement in the code for step 1 recently that would make it run very slowly if you used -d.
Katherine Silliman
@ksil91
Feb 28 2017 17:11

@dereneaton I just updated to 6.8 using miniconda and am getting an error now with any call to ipyrad:

$ conda update -c ipyrad ipyrad
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /home/ksilliman/miniconda2:
The following packages will be UPDATED:
    ipyrad:   0.6.6-0            ipyrad --> 0.6.8-0            ipyrad
    llvmlite: 0.13.0-py27_0             --> 0.16.0-py27_0            
    numba:    0.28.1-np111py27_0        --> 0.31.0-np111py27_0       

Proceed ([y]/n)? y
llvmlite-0.16. 100% |######################################################| Time: 0:00:00  11.77 MB/s
numba-0.31.0-n 100% |######################################################| Time: 0:00:00  11.90 MB/s
ipyrad-0.6.8-0 100% |######################################################| Time: 0:00:01  11.14 MB/s
$ ipyrad -n c80-66-o5ko6k-CORR
Traceback (most recent call last):
  File "/home/ksilliman/miniconda2/bin/ipyrad", line 6, in <module>
    from pkg_resources import load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2985, in <module>
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2971, in _call_aside
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2998, in _initialize_master_working_set
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 662, in _build_master
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 675, in _build_from_requirements
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 854, in resolve
pkg_resources.DistributionNotFound: The 'notebook>=4.3' distribution was not found and is required by ipyrad

Edit: fixed by updating notebook. Should probably require that version in the conda package, though.

conda update notebook
letimm
@letimm
Feb 28 2017 17:32
@dereneaton I did use the -d. I have amended the run command to exclude this and it seems to have cleared up my issue. Thank you!
Deren Eaton
@dereneaton
Feb 28 2017 17:34
@letimm great, we'll push a fix for that soon.
@ksil91 thanks, I thought we fixed that but I guess it's still missing. Are you on Mac or Linux?