These are chat archives for dereneaton/ipyrad

Jun 2018
Anna Page
Jun 28 2018 11:58

Hi all, I've posted before about trying to calculate 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 my installation or that I was incorrectly connecting to the cluster I am parallelising the job on. But I asked a colleague who had successfully run D stats before to try and run my data on his machine and he didn't have any luck either. It was suggested this was an error from a previous version of ipyrad, but I am using the most recent version (0.7.28) and still getting it.

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  | 0:00:09 |  

IPyradErrorTraceback (most recent call last)
<ipython-input-18-0db236d33999> 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)
    151             An ipyparallel client object to distribute jobs to a cluster.
    152         """
--> 153         self.results_table, self.results_boots = batch(self, ipyclient)
    155         ## skip this for 5-part test results

/scratch/amlp1n13/software/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/baba.pyc in batch(baba, ipyclient)
    383                 if not asyncs[job].successful():
    384                     raise IPyradWarningExit(\
--> 385                         " error: {}: {}".format(job, asyncs[job].exception()))
    386                 ## enter results for successful jobs
    387                 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: 14: IndexError(list index out of range)

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