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TheBrownLab / PhyloFisher

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.
MIT License
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forest_local.py creates empty output folder #91

Closed anoukwillemsen closed 1 year ago

anoukwillemsen commented 1 year ago

Hello,

After downloading sgt_constructorout<M.D.Y>-local.tar.gz to my local machine I am running the forest.py script on Ubuntu 22.04.3 with the command: python3 forest_local.py -t 3 -i sgt_constructor_out_Aug.16.2023-local.tar.gz

This creates the forestout<M.D.Y> folder, however this folder is empty. I do not receive any error or warning messages, and I have not been able to identify the problem yet.

All the best,

Anouk

robert-ervin-jones commented 1 year ago

Hi Anouk,

What version of PhyloFisher are you using? You can find this by running conda list phylofisher with the cona environment activte where PhyloFisher is installed.

Best, Robert

anoukwillemsen commented 1 year ago

Hi Robert,

Thanks for your quick reply. The trees were created with the newest version of PhyloFisher (v.1.2.11). However, I am using the standalone version of forest.py on my own machine.

I just tried to run the forest.py script on the server the trees were generated with PhyloFisher v.1.2.11, but it also gives an empty output folder.

Best, Anouk

robert-ervin-jones commented 1 year ago

Hi Anouk,

We just updated the local version of forest.py. If you could re-download it and try again that would be great. I'm not surprised that it didn't work on your server. Funny things start happening when trying to render graphics on headless servers.

Let me know if you have any more issues.

Best, Robert

anoukwillemsen commented 1 year ago

Hi Robert, The updated local version of forest.py worked for me. Thanks! Best, Anouk