Foldseek not liking generate_foldseek_db.py output TSVs about prostt5 HOT 6 CLOSED

Unfortunately, I cannot seem to open your query.fasta.txt file (says 'Not found'). I generated some dummy sequences (all alanin) to run with your 3Di sequences and successfully generated foldseek databases with both our local installation and version 2.8bd520.
Could you double-check that this isn't a file permission error? Is the directory writable for the user you're running the script with?

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Sorry that the fasta file isn't able to be found, I'm unsure why that is. I don't think I have a file permission problem, but I may just not know enough about it. I'm able to make subdirectories, files, etc. in the directory though. Do you have a way to check if this is indeed the problem?

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I came across a similar error a user had with database creation (sokrypton/ColabFold#589). Do you try to run the script on a shell with very strict limits on memory or runtime?

If that's not the issue, you could try commenting out the last three lines of the script (by putting a '#' as the first character) and run again. You should then find the files 'aa.tsv', '3di.tsv' and 'header.tsv' in your directory. If so, please attach them for me to take a look.

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Thank you for troubleshooting this with me! The shell I'm using doesn't have any limits on runtime or memory, and the total amount of RAM is 64 GB. I've attached the 3 .tsv that were generated from the script
test_TSVs.zip

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Actually, I think it has something to do with permissions, since I was just able to successfully generate the DBs on a different computer with just 32GB of RAM

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Good to hear! Thanks for letting us know.

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