"funannotate remote -m phobius" stops processing my file

[alpargata97]

Hello,

I am using funannotate 1.8.17, the latest version so sar, and I am facing a problem with phobius. When I process my file with funannotate remote -m phobius, the process starts a works perfectly but at one point it just stops processing sequences, it gets stuck in one sequence almost at the end of the process and it won't continue doesn't matter how much time I wait.There are no error logs or warnings, it just stays there for hours. It does not seem to be the queue of the server since if I put another file to process it works until almost the end that stops as well.

Has anyone faced this or know why this happen and how could I fix it?

Thank you very much.

[drdna]

I have the same problem...

[nextgenusfs]

Run phobius locally perhaps. I no longer have university email so I can't download and test.

[drdna]

Thanks for the quick feedback Jon. I have a quick followup question. Antismash also failed but at the retrieving results stage. I have been able to run Phobius locally. Assuming I can get Antismash running locally too, what do I need to do to make sure the results from these external runs will be queried in the Funannotate annotation?

Thanks,

Mark

On Apr 8, 2025, at 11:08 PM, Jon Palmer @.***> wrote:

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Run phobius locally perhaps. I no longer have university email so I can't download and test.

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Run phobius locally perhaps. I no longer have university email so I can't download and test.

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[nextgenusfs]

For antismash it should just be to pass the antismash annotated GBK file from the output folder to the --antismash option in funannotate annotate.