downloading standard database error

[shashank-KU]

Hi,

I am getting this error while downloading the database through kraken2.
kraken2-build --standard --threads 70 --db kraken2_bacteria_db

Downloading nucleotide gb accession to taxon map...rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (165.112.9.228): Connection timed out (110)
rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (165.112.9.230): Connection timed out (110)
rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250::13): Network is unreachable (101)
rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250::10): Network is unreachable (101)
rsync error: error in socket IO (code 10) at clientserver.c(137) [Receiver=3.2.3]

any suggestions?

[Gogis0]

This issue seems to appear in both conda installation as well as direct installation from this repo.

[shashank-KU]

I have tried other ways for installation, but still getting the error

[jmonroynieto]

This is resolved via the workaround on #508
#508 (comment)

[Gogis0]

@jmonroynieto Is there a way to do in using the conda installation?

[jmonroynieto]

rsync_from_ncbi.pl is a file in your conda environment. To know where that is located you can list your conda env with conda env list or alternatively, activate your kraken environment and use which kraken2.