forest.py produces an empty directory

[miferg]

I installed phylofisher through anaconda in linux and began an analysis on 10 genomes of interest with unknown taxonomic affiliations. I created the input_metadata.tsv file following the Detailed Example Workflow and ran the config.py, fisher.py, informant.py, working_dataset_constructor.py, and sgt_constructor.py without issues.

Now I have to use the forest.py script but the output directory "forest_out_Jul.06.2023" is empty (no SVGs nor TSV files) regardless if the --local_run flag was used.

What could be causing this behavior?

Thanks in advance, Miguel

[atice]

Hi Miguel,

Could you provide me with the exact command you ran. Also are you running this on a headless server or your local machine?

Thanks, Alex

Alexander K. Tice, Ph.D. Department of Biological Sciences Mississippi State University 027 Harned Hall Lab Telephone: 662-325-4008

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From: Miguel F. Romero @.> Sent: Thursday, July 6, 2023 12:26 PM To: TheBrownLab/PhyloFisher @.> Cc: Subscribed @.***> Subject: [TheBrownLab/PhyloFisher] forest.py produces an empty directory (Issue #84)

I installed phylofisher through anaconda in linux and began an analysis on 10 genomes of interest with unknown taxonomic affiliations. I created the input_metadata.tsv file following the Detailed Example Workflow and ran the config.py, fisher.py, informant.py, working_dataset_constructor.py, and sgt_constructor.py without issues.

Now I have to use the forest.py script but the output directory "forest_out_Jul.06.2023" is empty (no SVGs nor TSV files) regardless if the --local_run flag was used.

What could be causing this behavior?

Thanks in advance, Miguel

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[miferg]

Hi Alex,

I ran the previous scripts in a headless server and downloaded the .tar.gz file to my local machine. My local machine runs on linux, so I installed phylofisher using anaconda on it as well. The command that I am using is: forest.py --local_run -i sgt_constructor_out_Jul.04.2023-local.tar.gz

[robert-ervin-jones]

Hi Miguel,

Do you get any errors, or is it just an empty directory with no errors?

Best, Robert

[atice]

Will you try/look into two things for me if you don't mind.

1. Switch the order of the commands first. -i followed by --local_run
2. If that does not work, open the .tar.gz and make sure it has output in it.

Alexander K. Tice, Ph.D. Department of Biological Sciences Mississippi State University 027 Harned Hall Lab Telephone: 662-325-4008

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From: Miguel F. Romero @.> Sent: Thursday, July 6, 2023 12:47 PM To: TheBrownLab/PhyloFisher @.> Cc: Tice, Alex @.>; Comment @.> Subject: Re: [TheBrownLab/PhyloFisher] forest.py produces an empty directory (Issue #84)

Hi Alex,

I ran the previous scripts in a headless server and downloaded the .tar.gz file to my local machine. My local machine runs on linux, so I installed phylofisher using anaconda on it as well. The command that I am using is: forest.py --local_run -i sgt_constructor_out_Jul.04.2023-local.tar.gz

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[miferg]

Hi Robert,

I am not getting any message at all, just the empty output.

Alex:

1. I tried the following command: forest.py -i sgt_constructor_out_Jul.04.2023-local.tar.gz --local_run With the same result.
2. The .tar.gz is not empty. It has the metadata and color files, as well as the trees directory containing the .final, .raxmlbestTree, and .trimmed files for each gene. All of these files look good.

[robert-ervin-jones]

Miguel,

I found a bug in forest.py. It has to do with a recent update to sgt_constructor.py. Your sgt_constructor run should be fine. You will just need to run forest.py again after I can get the bug fixed. I apologize for the headache.

Best, Robert

[miferg]

No problem, it's good to know that the bug has been found. Looking forward to use the updated version of forest.py. Thanks, Miguel

[robert-ervin-jones]

The bug is now fixed. An update should be available from bioconda in the next few days.

Best, Robert