Issue with --download-library nt

[abdo3a]

Hello, i tried several times to download nt library using:

kraken2-build --threads 16 --download-taxonomy --db kraken_nt kraken2-build --threads 16 --download-library nt --db kraken_nt kraken2-build --build --threads 16 --db kraken_nt

and ends up with all files but non of the .k2d file exist, only taxo.k2d.tmp.

Any suggestions?

[SenyuanGu]

Hi, did you figure out this issue? I camed up with a same problem...

[abdo3a]

@SenyuanGu , i didn't figured out but i download the indexed database from https://benlangmead.github.io/aws-indexes/k2 , and it works

[KeyLllll]

@abdo3a hello, how can I download the taxonomy from https://benlangmead.github.io/aws-indexes/k2?

[abdo3a]

Hi @KeyLllll, in the https://benlangmead.github.io/aws-indexes/k2 page a table for each database and the corresponding URL.

[KeyLllll]

@abdo3a hello, I downloaded the ‘standard’ Kraken 2 / Bracken Refseq indexes, but when I run " kraken2-build --build --threads 16 --db database" , it gives an error, "There is no taxonomy/". Have you encountered this issue? Thanks!

[abdo3a]

You should first download the NCBI taxonomy using:

kraken2-build --download-taxonomy --db $DBNAME

[KeyLllll]

@abdo3a Hello! I ran "kraken2-build --download-taxonomy --db $DBNAME --threads 56 --use-ftp", but encountered an error: Downloading nucleotide gb accession to taxon map... Do you know how to solve it? Thanks!

[abdo3a]

i didn't remember encountering this problem but I had already changed a line in rsync file according to:

https://github.com/DerrickWood/kraken2/issues/508

Cheers

[Ge0rges]

When I use that index to download the DB, I then did kraken2-build --download-taxonomy --db DB and that was successful.