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Database extraction error: "ERROR: Could not extract" #358

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Footboard5358 opened this issue Dec 23, 2024 · 2 comments
Open

Database extraction error: "ERROR: Could not extract" #358

Footboard5358 opened this issue Dec 23, 2024 · 2 comments

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@Footboard5358
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Footboard5358 commented Dec 23, 2024

Hi,
I installed Bakta with Conda, downloaded the database, but it doesn't seem to be able to extract files from the database archive.
I didn't try to download it with the --debug option, as this is a very long process to repeat.
Is there anything else I need to do to make it work?

bakta_db download --output ./bakta_database        
                      
fetch DB versions...
	... compatible DB versions: 2
download database: v3.1, 2022-02-03, DOI: 10.5281/zenodo.5961398, URL: https://zenodo.org/record/5961398/files/db.tar.gz...
|████████████████████████████████████████| 28593946/28593946 [100%] in 7:13:33.7 (1099.19/s)
	... done
check MD5 sum...
	...database file OK: 95a140c0c2a40153fdc9794e89860944
extract DB tarball: file=/Users/.../bakta_database/db.tar.gz, output=/Users/.../bakta_database
ERROR: Could not extract /Users/.../bakta_database/db.tar.gz to /Users/.../bakta_database
@Footboard5358
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When I try to unpack the tarball archive manually, the output looks like this:

~/D/A/p/bakta_database ❯❯❯ tar -xvzf db.tar.gz                                                         
x db/
x db/ncRNA-regions.i1p
x db/version.json
x db/rfam-go.tsv
x db/ncRNA-genes.i1i
x db/ncRNA-regions.i1m
x db/pfam.h3i
x db/expert-protein-sequences.dmnd
x db/antifam.h3f
x db/pfam.h3f: truncated gzip input
tar: Error exit delayed from previous errors.

@oschwengers
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Might be trivial (sorry), but are you sure that you have enough free space on your disk?

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