These are chat archives for dereneaton/ipyrad

21st
Nov 2017
joqb
@joqb
Nov 21 2017 14:40
This morning my server was down, probably it was already not functioning properly yesterday. Now it's running fine.
asassone
@asassone
Nov 21 2017 15:44
Hi@dereneaton!! I am trying to run ABBA-BABA, I got this error with my own dataset:
IPyradError: error: 0: IndexError(list index out of range)
I tried to provied netwick, just the tests and also tried with different subsampling, but it is not running. When I tried with a different locifile (my colegue facilitated me his data) it works properly. Do you have any idea which is the problem? Something is wrong with my dataset (I am using the ".loci" as it came out from ipyrad).
Deren Eaton
@dereneaton
Nov 21 2017 16:08
Hi @asassone, the problem is with setting up the tests. You can try creating the tests by hand instead of using the generate function. You can enter tests like this:
## a single test
bb.tests = {
    "p4": ["32082_przewalskii", "33588_przewalskii"],
    "p3": ["29154_superba"], 
    "p2": ["33413_thamno"], 
    "p1": ["40578_rex"],
}

## or, multiple tests
bb.tests = [
    {
     "p4": ["32082_przewalskii", "33588_przewalskii"],
     "p3": ["41954_cyathophylloides"], 
     "p2": ["33413_thamno"], 
     "p1": ["40578_rex"],
    },
    {
     "p4": ["32082_przewalskii", "33588_przewalskii"],
     "p3": ["41478_cyathophylloides"], 
     "p2": ["33413_thamno"], 
     "p1": ["40578_rex"],
    },
]
The generate function should work as well, but it depends on your tree, and how you enter the constraints. It should tell you after you run it how many tests were generated. If you try to use the .run() command when no tests were generated then it will raise an error.
asassone
@asassone
Nov 21 2017 17:03
@dereneaton Thanks for the answer. I don't think that is the problem because I have already used the test incorporated by hand and it is not working. Even more, when using the function generate_tests_from_tree() is telling me the number of test to perform ... but then I got the error when I use run() command.
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