I have installed wgd on python 3.6.4, with all the prerequisites. OS linux, centos 6.6. The error I had is below. Your help is appreciated
[ashermoshe@lecs2 ~/dorothee]$ wgd --verbosity debug ksd schlosseri.mcl Botryllus_schlosseri.fas
2019-02-26 11:14:26: DEBUG CACHEDIR=/groups/pupko/ashermoshe/.cache/matplotlib
2019-02-26 11:14:26: DEBUG Using fontManager instance from /groups/pupko/ashermoshe/.cache/matplotlib/fontList.json
2019-02-26 11:14:26: DEBUG backend agg version v2.2
2019-02-26 11:14:27: INFO
2019-02-26 11:14:27: INFO codeml found
2019-02-26 11:14:27: INFO MUSCLE v3.7 by Robert C. Edgar
2019-02-26 11:14:27: INFO
2019-02-26 11:14:27: WARNING Output directory exists, will possibly overwrite
2019-02-26 11:14:27: DEBUG Reading CDS sequences
2019-02-26 11:14:28: INFO Translating CDS file
2019-02-26 11:14:28: DEBUG wrapping excepthook
100% (65587 of 65587) |#################################################| Elapsed Time: 0:00:21 Time: 0:00:21
2019-02-26 11:14:49: WARNING There were 0 warnings during translation
2019-02-26 11:14:49: INFO Started whole paranome Ks analysis
2019-02-26 11:14:49: WARNING Filtered out the 0 largest gene families because n*(n-1)/2 > `max_pairwise`
2019-02-26 11:14:49: WARNING If you want to analyse these large families anyhow, please raise the `max_pairwise` parameter.
2019-02-26 11:14:49: INFO Started analysis in parallel (n_threads = 4)
2019-02-26 11:14:50: INFO Analysis done
2019-02-26 11:14:50: INFO Making results data frame
2019-02-26 11:14:50: INFO Removing tmp directory
2019-02-26 11:14:50: INFO Computing weights, outlier cut-off at Ks > 5
Traceback (most recent call last):
File "/share/apps/anaconda3-5.1.0/bin/wgd", line 11, in <module>
sys.exit(cli())
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/wgd_cli.py", line 545, in ksd
max_pairwise=max_pairwise
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/wgd_cli.py", line 686, in ksd_
max_pairwise=max_pairwise,
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/wgd/ks_distribution.py", line 665, in ks_analysis_paranome
results_frame = compute_weights(results_frame)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/wgd/ks_distribution.py", line 709, in compute_weights
df["WeightOutliersIncluded"] = 1 / df.groupby(['Family', 'Node'])[
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/pandas/core/generic.py", line 5162, in groupby
**kwargs)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/pandas/core/groupby.py", line 1848, in groupby
return klass(obj, by, **kwds)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/pandas/core/groupby.py", line 516, in __init__
mutated=self.mutated)
File "/share/apps/anaconda3-5.1.0/lib/python3.6/site-packages/pandas/core/groupby.py", line 2934, in _get_grouper
raise KeyError(gpr)
KeyError: 'Node'
This seems like the analysis didn't start for some reason, I would suspect it has something to do with the files. Could you show a head output for schlosseri.mcl and Botryllus_schlosseri.fas?
I have installed wgd on python 3.6.4, with all the prerequisites. OS linux, centos 6.6. The error I had is below. Your help is appreciated