Problems Task getref xxxxFinder and CARD

[Coldheart79]

We are having problems download the data from CGE (-finder databases)

ariba getref resfinder out.resfinder
Downloading data with:
curl -X POST --data "folder=resfinder&filename=resfinder.zip" -o resfinder.zip https://cge.cbs.dtu.dk/cge/download_data.php
The following command failed with exit code 127
curl -X POST --data "folder=resfinder&filename=resfinder.zip" -o resfinder.zip https://cge.cbs.dtu.dk/cge/download_data.php

The output was:

/bin/sh: 1: curl: not found

[Coldheart79]

I also started experience problems with CARD after their maintenance shut-down last week.

ariba getref card out.card
Getting available CARD versions
Downloading "https://card.mcmaster.ca/download" and saving as "download.html" ... done
Found versions:
1.0.0 https://card.mcmaster.ca/download/0/broadstreet-v1.0.0.tar.bz2
1.0.1 https://card.mcmaster.ca/download/0/broadstreet-v1.0.1.tar.bz2
1.0.2 https://card.mcmaster.ca/download/0/broadstreet-v1.0.2.tar.bz2
1.0.3 https://card.mcmaster.ca/download/0/broadstreet-v1.0.3.tar.bz2
1.0.4 https://card.mcmaster.ca/download/0/broadstreet-v1.0.4.tar.bz2
1.0.5 https://card.mcmaster.ca/download/0/broadstreet-v1.0.5.tar.bz2
1.0.6 https://card.mcmaster.ca/download/0/broadstreet-v1.0.6.tar.bz2
1.0.7 https://card.mcmaster.ca/download/0/broadstreet-v1.0.7.tar.bz2
1.0.8 https://card.mcmaster.ca/download/0/broadstreet-v1.0.8.tar.bz2
1.0.9 https://card.mcmaster.ca/download/0/broadstreet-v1.0.9.tar.bz2
1.1.0 https://card.mcmaster.ca/download/0/broadstreet-v1.1.0.tar.bz2
1.1.1 https://card.mcmaster.ca/download/0/broadstreet-v1.1.1.tar.bz2
1.1.2 https://card.mcmaster.ca/download/0/broadstreet-v1.1.2.tar.bz2
1.1.3 https://card.mcmaster.ca/download/0/broadstreet-v1.1.3.tar.bz2
1.1.4 https://card.mcmaster.ca/download/0/broadstreet-v1.1.4.tar.bz2
1.1.5 https://card.mcmaster.ca/download/0/broadstreet-v1.1.5.tar.bz2
1.1.6 https://card.mcmaster.ca/download/0/broadstreet-v1.1.6.tar.bz2
1.1.7 https://card.mcmaster.ca/download/0/broadstreet-v1.1.7.tar.bz2
1.1.8 https://card.mcmaster.ca/download/0/broadstreet-v1.1.8.tar.bz2
1.1.9 https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.bz2
1.2.0 https://card.mcmaster.ca/download/0/broadstreet-v1.2.0.tar.bz2
1.2.1 https://card.mcmaster.ca/download/0/broadstreet-v2.0.0.tar.gz">DOWNLOAD

DataOctober 2017 release - minor revisions, addition of MCR-1.2, beta-lactamases, APHs1.2.1JSON, TAB ,OBO, FASTA2017-10-10 15:51:53.778226DOWNLOAD

DataOctober 2017 release - minor revisions, addition of MCR-1.2, beta-lactamases, APHs1.2.1JSON, TAB ,OBO, FASTA2017-10-10 15:51:53.778226DOWNLOAD

DataOctober 2017 release - minor revisions, addition of MCR-1.2, beta-lactamases, APHs1.2.1JSON, TAB ,OBO, FASTA2017-10-10 15:51:53.778226DOWNLOAD

DataOctober 2017 release - minor revisions, addition of MCR-1.2, beta-lactamases, APHs1.2.1JSON, TAB ,OBO, FASTA2017-10-10 15:51:53.778226<a href="/download/0/broadstreet-v1.2.1.tar.bz2

The output was:

--2018-02-08 14:35:44-- https://card.mcmaster.ca/download/0/broadstreet-v2.0.0.tar.gz%3EDOWNLOAD%3C/a%3E%3C/td%3E%3C/tr%3E%3Cdiv%20id=other%20class=more
Resolving card.mcmaster.ca (card.mcmaster.ca)... 130.113.77.126
Connecting to card.mcmaster.ca (card.mcmaster.ca)|130.113.77.126|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-02-08 14:35:44 ERROR 404: Not Found.

--2018-02-08 14:35:44-- http://collapse%3E%3Ctr%20class=more/
Resolving collapse><tr class=more (collapse><tr class=more)... failed: Name or service not known.
wget: unable to resolve host address ‘collapse><tr class=more’
--2018-02-08 14:35:46-- http://collapse%3E%3Ctd%3Edata%3C/td%3E%3Ctd%20class=hidden-xs%3EOctober%202017%20release%20-%20minor%20revisions,%20addition%20of%20MCR-1.2,%20beta-lactamases,%20APHs%3C/td%3E%3Ctd%20class=hidden-xs%3E1.2.1%3C/td%3E%3Ctd%20class=hidden-xs%3EJSON,%20TAB%20,OBO,%20FASTA%3C/td%3E%3Ctd%20class=hidden-xs%3E2017-10-10%2015:51:53.778226%3C/td%3E%3Ctd%3E%3Ca%20href=/download/0/broadstreet-v1.2.1.tar.bz2
Resolving collapse>data< (collapse>data<)... failed: Name or service not known.
wget: unable to resolve host address ‘collapse>data<’

[Coldheart79]

Should mention no problems with the other databases, but unable to download any of the ones at CGE or CARD.

[ssjunnebo]

The CARD issue was fixed in the latest version (2.11.1).

For resfinder, you need to install curl.