Kraken2 error

[jsalas0798]

Hi, i am using kraken from a supercomputer using linux. When i try to download de database i get this error
kraken2-build --standard --db kraken
Downloading nucleotide gb accession to taxon map...rsync: [Receiver] failed to c onnect to ftp.ncbi.nlm.nih.gov (130.14.250.13): Connection timed out (110)
rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (165.112.9.228): Con nection timed out (110)
rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250:: 10): Network is unreachable (101)
rsync: [Receiver] failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250:: 12): Network is unreachable (101)
rsync error: error in socket IO (code 10) at clientserver.c(139) [Receiver=3.2.7 ]

I also tried a variant that i saw that worked for other people:
kraken2-build --download-library bacteria --db bacteria_refseq --use-ftp

But i get this error
rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/128/725/GCF_900128725.1_BCifornacula_v1.0

I dont know hot to solve it. Please help me

[byeollee]

Hey there, I'm stuck at the same spot too.

So, I tried a bunch of different things, and it seems to be working now. Let me tell you what I did.

first, I change the perl script (rsync_from_ncbi.pl) file as below:

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"; }

This from DerrickWood/kraken2#292

And, if you got the error like rsync_from_ncbi.pl: unexpected FTP path (new server?) for na. then you can try second.
second, I change the assembly_summary.txt file using below command
(this file location is in your db/library/bacteria/)

awk -v FS='\t' '$20 != "na" {print $0}' assembly_summary.txt > new_assembly_summary.txt
cp new_assembly_summary.txt assembly_summary.txt

this one also I found github issue. but I cannot found link

and then, you can edit download_genomic_library.sh

rm -f assembly_summary.txt

to

#rm -f assembly_summary.txt

finally, It work! (but when I search, "rsync_from_ncbi.pl: unexpected FTP path (new server?) for na" error was fix in v2.1.3
you can see here : DerrickWood/kraken2@7d9252d

But, in my case not work (maybe my version is older? I don't know I just try git clone...)
anyway, Have good one~