These are chat archives for dereneaton/ipyrad

7th
Dec 2018
Alex Linan
@alx552
Dec 07 2018 16:28

@isaacovercast I am having trouble with ABBA-BABA using a large dataset (~350 taxa). I get the error below:

IPyradError Traceback (most recent call last)

<ipython-input-7-2b4298c2ec4c> in <module>()
8 ]
9 ## run the tests
---> 10 aa.run(ipyclient)
11 aa.results_table

/home/alx552/programs/anaconda2/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)
154
155 ## skip this for 5-part test results

/home/alx552/programs/anaconda2/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:

/home/alx552/programs/anaconda2/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)

at first I thought I had just miscalled a sample name as I wrote out the test by hand (autogenerate would produce a ton of tests) but after checking that doesnt appear to be the case. I was wondering if there is some sort of maximum size dataset allowed? I was able to get the program to work on a small dataset (24 taxa) but I would really like to do it for the full dataset.

Isaac Overcast
@isaacovercast
Dec 07 2018 18:17
@alx552 There's no theoretical reason a large dataset shouldn't work. If you're doing it by hand this increases the probability of it being a typo. You could try running multiple subsets to see if you can isolate whether it's one sample that's causing the problem.
Alex Linan
@alx552
Dec 07 2018 22:34

@isaacovercast I get the same error no matter what sample I put in, but I cant find anything wrong with the input files. print ipa.version

print toyplot.version

print toytree.version

0.7.26
0.16.1
0.1.6

Isaac Overcast
@isaacovercast
Dec 07 2018 23:41
@alx552 "I was able to get the program to work on a small dataset (24 taxa)". So it worked with these taxa? I'm confused, it sounds like it worked before, but now I don't quite understand what you mean by "same error no matter what sample".... Also, it never hurts to be sure you're using the most recent version of ipyrad (0.7.28).