Kraken2-download taxonomy

[PaolaDiGianvito]

Goodmorning, i have installed Kraken version 2.0.7-beta and i'm having difficulties to create a custom database. At the first stem I have to download the taxonomy, but i receive this message. kraken2-build --db fungi --download-taxonomy Downloading nucleotide est accession to taxon map...rsync: link_stat "/taxonomy/accession2taxid/nucl_est.accession2taxid.gz" (in pub) failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1865) [Receiver=3.2.7]

I read that the problem could be the nucl_est.accession2taxid.gz from NCBI site so I have downloaded as suggested the nucl_gb.accession2taxid.gz. I have have saved this file in a directory called taxonomy and a sub directory accession2taxid, but i have this message again kraken2-build --download-taxonomy --db fungi Downloading nucleotide est accession to taxon map...rsync: link_stat "/taxonomy/accession2taxid/nucl_est.accession2taxid.gz" (in pub) failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1865) [Receiver=3.2.7]

Can someone help me?

[SimonHegele]

Seems to be a common issue. Apparently NCBI changed the way the required data can be retrieved and Kraken2 hasn't been adapted to it. Try one of the pre-built databases, some of them include fungi.

https://benlangmead.github.io/aws-indexes/k2

[rawosemo]

@SimonHegele is right. I ran into a similar issue, but it was solved by downloading the pre-built version of the specific database.