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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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wgd dmd error #30

Closed yuzhenpeng closed 4 years ago

yuzhenpeng commented 4 years ago

Dear teams, When I used the wgd dmd, it comes the following error:

Traceback (most recent call last): File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/bin/wgd", line 8, in sys.exit(cli()) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/click/core.py", line 829, in call return self.main(args, kwargs) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/click/core.py", line 610, in invoke return callback(args, *kwargs) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/wgd_cli.py", line 528, in dmd s[0].get_paranome(inflation=inflation, eval=eval) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/wgd/diamond.py", line 94, in get_paranome df = self.run_diamond(self, eval=eval) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/wgd/diamond.py", line 71, in run_diamond self.make_diamond_db() File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/site-pack ages/wgd/diamond.py", line 65, in make_diamond_db out = sp.run(cmd, capture_output=True) File "/Bio/home/Yanglab/Yuzhenpeng/miniconda2/envs/wgd/lib/python3.6/subproces s.py", line 423, in run with Popen(popenargs, **kwargs) as process: TypeError: init() got an unexpected keyword argument 'capture_output'

My computer used the python3 environment. It can run 'wgd mcl' very well. Could you please give me a help. Thank you.

Zhenpeng

arzwa commented 4 years ago

Hi, wgd dmd requires Python3.7 or higher, this error is due to some changes in Python base libraries, so please try again using a newer Python version.