download uniref database error

[nain...@gmail.com]

Hi,

I'm trying to download the full uniref50 database (I had the demo one installed originally). I'm typing:
humann2_databases --download uniref uniref50_diamond database

And keep getting this:
ERROR: Please select an available build.

I tried to change to uniref90, uniref100... same error. I just successfully installed the chocophlan database and just cant figure out what I'm supposed to put for the available build here.

Thank you so much!

-Naina

[Eric Franzosa]

Hi Naina,

Based on your follow-up email, I'm wondering if you managed to resolve this error? If not, please let us know. The command you used to get uniref50 looks good to me.

Thanks,

Eric

[Naina Rengarajan(Khandelwal)]

Hi Eric,

I actually wasn't able to resolve the issue. Just found a copy of the database in a different user's folder. I just tried again and same error... any thoughts? 

khandelwals@n097:/scratch/chlab$ humann2_databases --download uniref uniref50_diamond test

ERROR: Please select an available build.

[Eric Franzosa]

Interesting... Can you tell me which version of HUMAnN2 you're using with "./humann2 --version"?

Thanks,

Eric

[Naina Rengarajan(Khandelwal)]

humann2 v0.6.0

[Eric Franzosa]

OK, that's the issue: v0.6.0 only knows to look for one version of the uniref database, which you'd download with:

humann2_databases --download uniref diamond $LOCATION

That said, I'd recommend upgrading to the latest release (0.7.0) because it includes a bunch of extra database options (which is what the current docs reflect). For example, if you're only interested in uniref proteins that map to a known enzymatic reaction, you could download (in 0.7.0):

humann2_databases --download uniref uniref50_ec_filtered_diamond $LOCATION

Which will result in MUCH faster translated search.

Hope this helps!

Thanks,

Eric

[Naina Rengarajan(Khandelwal)]

Ah fantastic. Thank you!