tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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error updating MEGARES #198

Closed stalact closed 1 year ago

stalact commented 1 year ago

I have some issues with updating the MEGARES database:

abricate-get_db --db megares --force Setting up 'megares' in '/abricate-1.0.1/db/megares' Downloading: https://megares.meglab.org/download/megares_v2.00.zip HTTP Result: 200 Destination: megares.zip Filesize: 55162 bytes Archive: megares.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of megares.zip or megares.zip.zip, and cannot find megares.zip.ZIP, period. load_fasta:

------------- EXCEPTION: Bio::Root::Exception ------------- MSG: file argument provided, but with an undefined value STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:394 STACK: main::load_fasta /abricate-1.0.1/bin/abricate-get_db:727 STACK: main::get_megares /abricate-1.0.1/bin/abricate-get_db:352 STACK: /abricate-1.0.1/bin/abricate-get_db:60

is there a proper way for getting the updated database?

pratyaysengupta commented 1 year ago

Also facing the same! With all the databases :(

aastha-batta commented 1 year ago

Hi, The link used to update database is old. Kindly go to line 350 in bin/abricate-get_db and do download('https://www.meglab.org/downloads/megares_v3.00.zip', $zip); This might help.

pratyaysengupta commented 1 year ago

Hi, The link used to update database is old. Kindly go to line 350 in bin/abricate-get_db and do download('https://www.meglab.org/downloads/megares_v3.00.zip', $zip); This might help.

Many Thanks

stalact commented 1 year ago

Thanks for your help! :-)