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Colabfold database files missing #137

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Madhumitha0206 opened this issue Mar 21, 2024 · 1 comment
Closed

Colabfold database files missing #137

Madhumitha0206 opened this issue Mar 21, 2024 · 1 comment
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@Madhumitha0206
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Description of the bug

Hi,

I am trying to run proteinfold pipeline with colabfold mode. I am having the supporting db files in s3 and used the colabfold_db param in nextflow.config file to update the s3 URI. I downloaded the db files using the link given in conf/dbs.config which is

colabfold_db_link       = 'http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz'
uniref30_colabfold_link = 'https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2202.tar.gz'

I downloaded the above links and uploaded the untarred files in s3. But, when we run the pipeline, I am getting an error saying
"FileNotFoundError: Database uniref30_2202_db does not exist"

while exploring this, we came across the folders and files structure given by nf-core (https://nf-co.re/proteinfold/dev/docs/usage) which is
image

My question is, where can we download all these files mentioned in the above link? And why does the link mentioned in the dbs.config file not fetching all of these files?

Command used and terminal output

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@Madhumitha0206 Madhumitha0206 added the bug Something isn't working label Mar 21, 2024
@Madhumitha0206
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Closing this issue as we have found the root cause and the fix

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