Despite having updated the database*using humann_databases --download chocophlan full ./ --update-config yes I still get the error below. Any ideas how to solve it?
humann3 --threads 20 --nucleotide-database ./chocophlan --bypass-translated-search --input xxx.kneaddata.fastq --output xxxx
CRITICAL ERROR: The directory provided for ChocoPhlAn contains files ( g__Halomonas.s__Halomonas_lutea.centroids.v0.1.1.ffn.gz ) that are not of the expected version. Please install the latest version of the database: 201901
It looks like you’re using HUMAnN 3 but have a HUMAnN 2 database installed. Or potentially a HUMAnN 3 database was downloaded into the same location as an existing HUMAnN 2 database, and HUMAnN 3 is now warning that is sees files that are more consistent with v2.
I installed humann v3.0.0.alpha.4. Then I run
humann_databases --download uniref uniref90_diamond /home/timyerg/Hohenheim/UniRef_db --update-config yes
to download the database.
When I am trying to run humann,
humann --input $inp --protein-database /home/timyerg/Hohenheim/UniRef_db --threads 4 --output $out
I am getting an error:
CRITICAL ERROR: The directory provided for the translated database contains files ( uniref ) that are not of the expected version. Please install the latest version of the database: 201901
I never installed Humann2 before, so it is not likely that I have some files from Humann2 database. How can I download the right database? I thought, that if I am running the command from Humann 3 tutorial and installing it with humann3 version I should get humann3 database. The same error with chocophlan database. Could you please guide me, I am new with shotgun data analysis.
My guess if that there is some other file at that location which HUMAnN is noticing is not something it should be mapping against. Can you show a file tree of the location where you have the database located?
Hi, thank for your reply. I took a look on the structure and realized, that I used path
/home/timyerg/Hohenheim/UniRef_db to install a database, but to use it I should add
/uniref to the path. My mistake .