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Always start downloading input-2024-07-18.build7555.tgz when running the program #332

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fugunokaraage opened this issue Jan 27, 2025 · 1 comment

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@fugunokaraage
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Hi,

I already install PGAP at $HOME/.pgap where input-2024-07-18.build7555, test, and test_genomes-2024-07-18.build7555 directories exist.
Whenever I run pgap.py in other directory where input contig files are, downloading input-2024-07-18.build7555.tgz starts, that takes several hours.

When I put
$docker pull ncbi/pgap-utils:2024-07-18.build7555
all images seems to already exist.

How can I run PGAP smoothly without downloading the database?

Fugu

@azat-badretdin
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Thank you for your report, Fugu!

How can I run PGAP smoothly without downloading the database?

You need the database, Fugu, without it PGAP won't work. You already have docker image installed, but that's only the software. You also need the tarballs with reference data.

It's a lot of data, and it looks like you have local system issues that make this process very long. Unfortunately, we can't do anything to help you with this right now.

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