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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
87 stars 13 forks source link

conda installed ganon can't use ganon build -g argument? #252

Closed LilyAnderssonLee closed 1 year ago

LilyAnderssonLee commented 1 year ago

Hi, I installed ganon through conda and I am having issues to download the databases through this command line.

ganon build --organism-group archaea bacteria fungi viral protozoa human --threads 12 --complete-genomes --db-prefix abfcph_refseq_cg

error message: ganon: error: unrecognized arguments: --organism-group archaea bacteria fungi viral protozoa human --complete-genomes

I didn't see -g/--organism-group argument in help message of ganon build -h image

pirovc commented 1 year ago

It seems like you are using an outdated ganon version that did not support download of databases directly. Please update it to the latest vesion with conda update ganon to have such functionality.

LilyAnderssonLee commented 1 year ago

Thanks! My ganon version is 0.2.3 and it seems like I'm unable to update to the latest version. This could be due to my outdated version of conda. I will get back to you once I've resolved the version issue.

LilyAnderssonLee commented 1 year ago

Yeah downloading works now after upgrading the ganon version to 1.6.0. Thanks again.