kraken2: rsync_from_ncbi.pl: unexpected FTP path (new server?) for na

The strangest thing is that this worked just yesterday. I then deleted the database because something wasn’t working in one of the downstream steps, tried to re-download it

kraken2-build --download-library bacteria --db data-base --threads 32

and the title error message is what I get. I’ve also tried using --use-ftp, but I still get an identical error message. Help would be appreciated!

EDIT: Problem solved! I didn’t change anything about my code and it worked. I guess there might’ve been issues on the NCBI side. EDIT2: It stopped working again.

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 19

Commits related to this issue

Fix rsync bug. cf https://github.com/DerrickWood/kraken2/issues/292 — committed to olsonanl/kraken2 by olsonanl 2 years ago

Most upvoted comments

This worked for me. Within the 'rsync_from_ncbi.pl’ script, there is a pattern matching operation for the ftp site. However, the returned addresses (stored in $full_path within the script) actually start with an ‘https://’ instead of ‘ftp://’ . Thus, I changed the following if statement regexp match line:

if (! ($full_path =~ s#^ftp://${qm_server}${qm_server_path}/##)) { die "$PROG: unexpected FTP path (new server?) for $ftp_path\n"; }

to:

if (! ($full_path =~ s#^https://${qm_server}${qm_server_path}/##)) { die "$PROG: unexpected FTP path (new server?) for $ftp_path\n"; }

+20

sbs87 on Aug 5, 2022

Same problem here. When running: kraken2-build --download-library bacteria --db $DBNAME I obtain: rsync_from_ncbi.pl: unexpected FTP path (new server?) for na

Any solutions?

Gandasegui on Aug 2, 2021

I’m running into the exact same problem as harshitakarri kraken2-build --standard --threads 24 --db $DB --use-ftp

Downloading nucleotide wgs accession to taxon map... done.
Downloaded accession to taxon map(s)
Downloading taxonomy tree data... done.
Uncompressing taxonomy data... done.
Untarring taxonomy tree data... done.
rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1

I installed kraken2 via conda. I saw on github that the scripts rsync_from_ncbi.pl and download_genomic_library.sh were last edited 2 months ago, so I also tried to replace these scripts in my conda installation. However, no luck.

Any solutions for this? Many thanks!

Cryphonectria on Jul 18, 2022

I am using the latest version of Kraken2, and am still having this issue. Can you help?

sneha-nishtala on Nov 5, 2020

I am trying to create standard database in kraken2 for bacteria. Databases have been downloaded but i am encountering the obstacle when i am trying to build the database. rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1 This is the error I have encountered.Kindly guide how to resolve the issue

harshitakarri on Jun 29, 2022

We have just updated the code to include a fix for this issue. If you continue to have problems with the newest code update, please open a new issue.

jenniferlu717 on Sep 10, 2020