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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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Error running dmd #89

Open hyyuu opened 5 months ago

hyyuu commented 5 months ago

Hello , thank you very much for the program ! However , I faced an error at the first step running wgd dmd. 

Traceback (most recent call last):
  File "/home/hiuyan/.pyenv/versions/3.6.12/bin/wgd", line 11, in <module>
    load_entry_point('wgd==2.0.24', 'console_scripts', 'wgd')()
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/cli.py", line 113, in dmd
    _dmd(**kwargs)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/cli.py", line 140, in _dmd
    s[0].get_paranome(inflation=inflation, eval=eval)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/wgd/core.py", line 410, in get_paranome
    mcl_out = gf.run_mcl(inflation=inflation)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/site-packages/wgd/core.py", line 495, in run_mcl
    out = sp.run(command, stdout=sp.PIPE, stderr=sp.PIPE)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/subprocess.py", line 423, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/home/hiuyan/.pyenv/versions/3.6.12/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mcxload': 'mcxload'

I tried with two different cds files, they all returned the same error messages. Could you please help me to fix this error? I installed wgd v2 via pip.

Thank you very much for your help!

Regards, Alex

arzwa commented 5 months ago

Please raise issues with wgd v2 here