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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
22 stars 8 forks source link

Error while downloading cgMLST #46

Closed ryobon-dev closed 1 year ago

ryobon-dev commented 1 year ago

Hi,

When I tried to download cgMLST, it requested me "Enter oauth_verifier from browser:" I had registered PubMLST successfully. What is the oauth verifier ?

(confindr) kansensho@DESKTOP-QBEDU0F:/mnt/e/Desktop/genome_analysis/T3OSK/Confindr$ confindr_database_setup -s key.txt 2023-02-09 18:11:32 Removing old databases... 2023-02-09 18:11:32 Downloading cgMLST-derived data for Escherichia, Salmonella, and Listeria... Visit this URL in your browser: http://pubmlst.org/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_rmlst_seqdef&page=authorizeClient&oauth_token=5Aze663Llw77ZY4oZakY6ABj2AGalicg Enter oauth_verifier from browser: 2023-02-09 18:15:13 ERROR: Couldn't get a session token for rMLST database download. Check that your consumer secret and access token files have valid credentials and try again. (confindr) kansensho@DESKTOP-QBEDU0F:/mnt/e/Desktop/genome_analysis/T3OSK/Confindr$ key.txt resistration

pcrxn commented 1 year ago

Hi @ryobon-dev, The confindr_database_setup command is used to download and setup the pubMLST rMLST database, which requires a consumer key and secret (see https://olc-bioinformatics.github.io/ConFindr/install/#downloading-confindr-databases). If you just wish to use the cgMLST databases, you don't have to run the confindr_database_setup step---these databases will be downloaded automatically for you when running confindr.py -i example-data -o output for example.

ryobon-dev commented 1 year ago

Thanks,

Anyway, I could get the oauth_verifier from browser and successfully downloaded DB.