These are chat archives for dereneaton/ipyrad

Apr 2018
Anna Page
Apr 26 2018 15:39

Hi all, I've been having some issues calculating D statistics with the ipyrad analysis toolkit using a jupyter notebook. I get an error which I'm not sure how to interpret. I thought it might be due to incorrectly connecting to the cluster I am parallelising the job on but I asked a colleague who had successfully run D stats before and he didn't have any luck either.

Other code works fine, such as generating all valid trees for D stat tests, but when I try to use the parallel client to calculate D stats I get this error

[                    ]   0%  calculating D-stats  | 0:00:07 |  

IPyradErrorTraceback (most recent call last)
<ipython-input-21-0db236d33999> in <module>()
      1 # run all tests linked to bb
----> 2

/scratch/amlp1n13/software/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/baba.pyc in run(self, ipyclient)
    152             An ipyparallel client object to distribute jobs to a cluster.
    153         """
--> 154         self.results_table, self.results_boots = batch(self, ipyclient)
    156         ## skip this for 5-part test results

/scratch/amlp1n13/software/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/baba.pyc in batch(baba, ipyclient)
    324                 if not asyncs[job].successful():
    325                     raise IPyradWarningExit(\
--> 326                         " error: {}: {}".format(job, asyncs[job].exception()))
    327                 ## enter results for successful jobs
    328                 else:

/scratch/amlp1n13/software/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.pyc in __init__(self, *args, **kwargs)
     50     def __init__(self, *args, **kwargs):
     51         if ipyrad.__interactive__:
---> 52             raise IPyradError(*args, **kwargs)
     53         else:
     54             SystemExit.__init__(self, *args, **kwargs)

IPyradError:  error: 0: IndexError(list index out of range)

Has anyone had this error and can shed any light on what's going wrong?