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

[apn83]

Hi, I am trying to build the database. But there is this constant issue 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 used both default and --use-ftp option. But still this issue arises. I installed using

conda install -c bioconda kraken2

The folder so far, has only 2 items: taxonomy - 37.1gb library/archea - 449 kb

Kindly help in resolving this. I guess the expected database size is approx. 100 Gb

Thanks.

[mkazanov]

The same is here:

$kraken2-build --download-library bacteria --db /data3/SOFT/kraken2/krakendb 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

How is possible to resolve this problem?

[ffontani]

A solution that worked for me can be found in another issue posted here: https://github.com/DerrickWood/kraken2/issues/292#issuecomment-1206837801

[MaryoHg]

Dear all,

I was having the same issue, however, the answer in #292 didn't help me. You must modify two scripts. I followed the instructions by #525, given by @aeu79 here

Is it solved?

Yes, but there is no new release (I just tested it in a fresh install). After installing with install_kraken2.sh, go to the "KRAKEN2_DIR" and modify these two files:

download_genomic_library.sh (line 17) FTP_SERVER="**ftp**://$NCBI_SERVER" to FTP_SERVER="**https**://$NCBI_SERVER"

rsync_from_ncbi.pl (line 46) if (! ($full_path =~ s#^**ftp**://${qm_server}${qm_server_path}/##)) { to if (! ($full_path =~ s#^**https**://${qm_server}${qm_server_path}/##)) {

Source: Commit 1 Commit 2

Then I ran the two following codes to be able to download both libraries needed: bacteria and archaea, even fungi. $ kraken2-build --download-library bacteria --db dbprok --threads 56 2>&1 | tee log.bact

Note: 2>&1 | tee log.bact send the stderr and stdout to a file called log.bact and at the same time print into the console itself.

Hope it helps.

[tzaquin]

Dear all,

I was having the same issue, however, the answer in #292 didn't help me. You must modify two scripts. I followed the instructions by #525, given by @aeu79 here

Thank you, still running it but it skipped the ftp error