krakenhll-download example doesn't work

[gputzel]

I have tried this example command from the README:

krakenhll-download --db DB --taxa "archaea,bacteria,viral,fungi,protozoa,helminths" --dust --exclude-environmental-taxa

and nothing seems to happen. It just prints the usage information for the program.

This is on Mac OS X 10.13.5.

[fbreitwieser]

Hi @gputzel , you need to specify nt at the end, i.e.

krakenhll-download --db DB --taxa "archaea,bacteria,viral,fungi,protozoa,helminths" --dust --exclude-environmental-taxa nt

[harshameghadri]

Hey florian,

Some error with the download command.

krakenhll-download --db DB --taxa "archaea,bacteria,viral,fungi,protozoa,helminths" --dust --exclude-environmental-taxa nt Unknown database --taxa.

krakenhll-download [] *

[fbreitwieser]

Hi @harshameghadri , which version of KrakenHLL are you using? The nt database was only added to that script in v 0.4.9

[harshameghadri]

@fbreitwieser We have this version on our servers

KrakenHLL/0.4.9

[Krischan]

Hi @harshameghadri, I had the same issue. I believe you need to enter a path for the \<DB> parameter.

[harshameghadri]

This is what i did instead;

krakenhll-download -o centrifugeDB/ 'refseq/archaea' --dust --exclude-environmental-taxa nt

this I will repeat for viruses and bacteria and see how it goes.

maybe @gputzel try this and let me know if it works as well.

[fbreitwieser]

hi @harshameghadri and @Krischan, I think this issue is resolved. If you continue having problems, please feel free to open a new issue.