These are chat archives for dereneaton/ipyrad

2nd
Feb 2018
Nitish Narula
@nitishnarula
Feb 02 2018 14:50
Thanks @isaacovercast and @eaton-lab
cwessinger
@cwessinger
Feb 02 2018 17:41
Hi folks. Thanks so much for a fantastic program. Sorry if this question has been asked and answered: is there an easy way to output the number of loci with just a single haplotype? I'm optimizing clustering threshold for my study system. Thanks! @dereneaton @isaacovercast
leclearnm
@leclearnm
Feb 02 2018 20:13
Hi @dereneaton
I am having some issues with the ABBA-BABA test notebook when trying to use my PE reads. More specifically there is an error (see below) with .loci files (ipyrad v.0.7.21) filtered for certain levels of SNPS in step 7.
I tried removing the 'nnnn' separator based on what I saw written about a similar problem earlier in this forum from @ahaponski_twitter, but this threw a different error dealing with array sizes
pe2a60snp = "/home/nathan/Documents/jatropha/analysis/abba_baba/pe-kept-2a_outfiles/pe-kept-2a.loci"

pe85m4 = ipa.baba(data=pe2a60snp, newick=newick85m4)
pe85m4.generate_tests_from_tree(
    constraint_dict={
        "p4": ["gaumeri"],
        #"p2": ["jaimejimenezii"],
        #"p3": ["curcas"],
        "p3": ["elbae"],
        "p1": ["curcas"],
    })
pe85m4.run(ipyclient)

[                    ]   0%  calculating D-stats  | 0:00:00 |  
---------------------------------------------------------------------------
IPyradError                               Traceback (most recent call last)
<ipython-input-27-14e83097c8ff> in <module>()
----> 1 pe85m4.run(ipyclient)
      2 #test1_1.plot(height=500, pct_tree_y=0.2, alpha=4., tree_style='c');
      3 sorted_results_85m4 = fw85m4.results_table.sort_values(by="Z", ascending=False)

/home/nathan/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)
    155 
    156         ## skip this for 5-part test results

/home/nathan/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:

/home/nathan/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: ValueError(cannot assign slice from input of different size)