codeml stalling with default tmp folder name

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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codeml stalling with default tmp folder name #1

Closed ricardovialle closed 5 years ago

ricardovialle commented 6 years ago

Hi,

Running the "wgd ks" under default temporary folder name causes codeml to fail to find the .ctrl file. Then it never completes the process. Probably is some character used in the folder name. Specifying a simple name with "-tmp" everything runs smoothly.

Cheers, Ricardo

arzwa commented 5 years ago

Hi Ricardo,

I notice I didn't address this issue. The reason is probably a too long filename, this will be fixed in the next version (which is coming soon). If it is indeed due to a weird character, this is readily fixed by using the -tmp option so I will close this issue.

Best, Arthur