These are chat archives for dereneaton/ipyrad

6th
Nov 2018
arminf
@arminf82
Nov 06 2018 05:43
@dereneaton Thank you. After Structure and PCA/DAPC I checked ABBA-BABA for hybridization in my geographic groups with at least n=6 samples
I think I will just do some tables showing significant test. But thank you anyway, Ipyrad is awesome and has one more citation!!!
Yayan Kusuma
@ywckusuma
Nov 06 2018 06:22
Hello @dereneaton. I have a question about input data types for ipyrad. In case I have demultiplexed data sets SE derived from primer sets (pcr based NGS), so there wont be any restriction overhang. Will it be able to analyze with ipyrad? How about the 'datatype' and 'Restriction overhang' field name in the param file. Will that be okay to leave it blank?
Sarah J Jacobs
@sarahjjacobs
Nov 06 2018 16:42

hello! I'm trying to run tetrad and I'm running into an error that I've seen posted here previously (@tommydevitt Jun 05 12:30). addr181:~ sjjacobs$ python
Python 2.7.15 |Anaconda, Inc.| (default, Oct 23 2018, 13:35:16)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import ipyrad
import toytree
import ipyrad.analysis
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/init.py", line 18, in <module>
from .structure import Structure as structure
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/structure.py", line 12, in <module>
from ipyrad.analysis.tetrad import get_spans
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 63, in <module>
""")
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.py", line 52, in init
raise IPyradError(args, *kwargs)
ipyrad.assemble.util.IPyradError:
Error: tetrad requires the dependency 'toytree', which we haven't yet
included in the ipyrad installation. For now, you can install toytree
using conda with the following command:

conda install toytree -c eaton-lab
ha - sorry about that - hit enter ...
anyway - I installed toy tree and can see it in my directories, but, I guess init.py can't find it for some reason?
heather340
@heather340
Nov 06 2018 18:20
@sarahjjacobs Hi Sarah - I just did this yesterday and also had to install another dependency (matlab I think?). Do you get another error when you try to run Tetrad after installing toytree?
Sarah J Jacobs
@sarahjjacobs
Nov 06 2018 20:32
@heather340 Hi! Yes, different error if I try to run tetrad solo (below). As a side note, toytree looks like it installed Users/sjjacobs/miniconda2/pkgs directory, and not to Users/sjjacobs/miniconda2/bin ... not sure if that matters? Within toytree pkgs/, there's a .egg and a .pth file. addr250:bin sjjacobs$ tetrad
Traceback (most recent call last):
File "/Users/sjjacobs/miniconda2/bin/tetrad", line 11, in <module>
load_entry_point('ipyrad==0.7.28', 'console_scripts', 'tetrad')()
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 484, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 2707, in load_entry_point
return ep.load()
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 2325, in load
return self.resolve()
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 2331, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/init.py", line 18, in <module>
from .structure import Structure as structure
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/structure.py", line 12, in <module>
from ipyrad.analysis.tetrad import get_spans
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 63, in <module>
""")
File "/Users/sjjacobs/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.py", line 52, in init
raise IPyradError(args, *kwargs)
ipyrad.assemble.util.IPyradError:
Error: tetrad requires the dependency 'toytree', which we haven't yet
included in the ipyrad installation. For now, you can install toytree
using conda with the following command:
conda install toytree -c eaton-lab
@heather340 ... also, we have ipyrad and the suite of analysis tools working on a different computer that does not have Matlab. also, the tetrad.assemble set of tools imports just fine.