ABRicate pre-downloaded databases

[maesaar]

Hi @tseemann,

I have abricate v0.9.9 installed using brew install abricate, but somehow megares is not displayed in the --list. Should the megares database come with installation of abricate?

Thank you!

[dswan]

I have megares downloaded and installed with 0.9.9. I think --list only shows the downloaded databases.

Have you tried:

abricate-get_db --db megares --force

[nbawe]

I had the same issue, but for me it gave an error:

abricate-get_db --db megares --force
Setting up 'megares' in '/usr/local/Cellar/abricate/0.9.9/libexec/db/megares'
Downloading: https://megares.meglab.org/download/megares_v2.00.zip
Result: 501
Destination: megares.zip
Filesize:  bytes
unzip:  cannot find or open megares.zip, megares.zip.zip or megares.zip.ZIP.
load_fasta: 

------------- EXCEPTION -------------
MSG: file argument provided, but with an undefined value
STACK Bio::SeqIO::new /usr/local/opt/bioperl/libexec/lib/perl5/Bio/SeqIO.pm:399
STACK main::load_fasta /usr/local/Cellar/abricate/0.9.9/libexec/bin/abricate-get_db:726
STACK main::get_megares /usr/local/Cellar/abricate/0.9.9/libexec/bin/abricate-get_db:351
STACK toplevel /usr/local/Cellar/abricate/0.9.9/libexec/bin/abricate-get_db:60
---------------

[tseemann]

You are getting a 501 HTTP error. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/501

The HyperText Transfer Protocol (HTTP) 501 Not Implemented server error response code means that the server does not support the functionality required to fulfill the request.

This status can also send a Retry-After header, telling the requester when to check back to see if the functionality is supported by then.

501 is the appropriate response when the server does not recognize the request method and is incapable of supporting it for any resource. The only methods that servers are required to support (and therefore that must not return 501) are GET and HEAD.

[tseemann]

@mmaesaar it seems i forgot to commit the megares database! sorry. @nbawe i have added checks to tell you when download fails (for whatever reason).

[maesaar]

Thank you @tseemann now works perfectly.

[MHassanSaeed]

Hi,

I tried abricate-get_db --db ncbi --force but come up with following error:

Downloading: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMR_CDS HTTP Result: 501 Destination: amr_cds.ffn Filesize: bytes Downloading: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ReferenceGeneCatalog.txt HTTP Result: 501 Destination: amr_cds.tsv Filesize: bytes **ERROR: Can't read TSV file: amr_cds.tsv**