problems updating the database : HTTP Result: 501

[youngDouble]

Return Code HTTP Result: 501 when abricate-get_db --db ncbi even add --force:
1. abricate-get_db --db ncbi :

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: 500
Destination: amr_cds.tsv
Filesize:  bytes
ERROR: Can't read TSV file: amr_cds.tsv

2. abricate-get_db --db card：

Downloading: https://card.mcmaster.ca/latest/data
HTTP Result: 501
Destination: card.tar.bz2
Filesize:  bytes
tar: card.tar.bz2: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now

I think the bug appears in 89 lines of abricate-get_db ：89 my $ec = mirror($url, $dest);
Perhaps the current website no longer supports LWP::Simple::mirror, but I have no idea how to solve it

[tolot27]

The problem is caused by an older version of the LWP::Simple module. It does not occur if version 6.43 of LWP::Simple is installed.

[theadrija]

Were you able to solve this issue? I'm facing the same problem.

[youngDouble]

If it requires LWP::Simple version 6.43,abricate-get_db may not be able to correctly run (abricate version 1.0.1 installed with conda), because the latest version of the perl-lwp-simple module provided by bioconda is 6.39. Installing an older version of abricate may be helpful, but I have not tested it.

[YiweiZhu]

Hi, I meet the same issue. It can be solved by creating a dedicated conda environment and installing an old version of perl (let's say, v.5.26) at first, and then abricate (v.1.0.1).

[kuheng3]

I used the following code to solve the same issues:
micromamba install -c bioconda abricate
micromamba install -c bioconda perl-lwp-simple
micromamba install perl-LWP-Protocol-https

[erinyoung]

Thank you! I ran into this problem today and it was nice that it was already fixed.

[tseemann]

Yes I had this problem too!

I have replaced LWP::Simple with File::Fetch which can use curl or wget if it can't find the lSWP module sneeded for HTTPS