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

[mpozuelo-flomics]

Hey! Hope you are staying safe for those difficult moments.

Do you have any news for this message in a previous issue that was closed??? I'm getting the same error but using the --use-ftp. Although I have cloned the current repository, it tells me that the option --use-wget is not available. Moreover, I have seen, regarding a previous answer for this message that if I print the information in column 20 (ftp_path) of the assembly_summary.txt, it prints for some rows the ftp path but for others shows me words from other columns ("species", "exemplar", "ICTV") or even they are empty.

Do you have any news for this. By the way, I am trying to download the viral database.

####### Previous issue

I am trying to build the standard database using kraken (I can't use kraken2 because of my downstream needs). I used this code: kraken-build --standard --threads 16 --use-wget --db standard.3

and got this error: rsync_from_ncbi.pl: unexpected FTP path (new server?) for na

This code resulted in a directory with this structure:

ls -lhR standard.3
standard.3:
total 0
drwxrwxr-x 3 user user 4.0K Mar  5 07:29 library
drwxrwxr-x 2 user user 4.0K Mar  5 07:29 taxonomy

standard.3/library:
total 0
drwxrwxr-x 2 user user 4.0K Mar  5 07:29 archaea

standard.3/library/archaea:
total 512K
-rw-rw-r-- 1 user user 321K Mar  5 07:29 assembly_summary.txt

standard.3/taxonomy:
total 30G
-rw-rw-r-- 1 user user    0 Mar  5 07:27 accmap.dlflag
-rw-r--r-- 1 user user  18M Mar  5 07:26 citations.dmp
-rw-r--r-- 1 user user 3.9M Mar  5 07:25 delnodes.dmp
-rw-r--r-- 1 user user  452 Mar  5 07:20 division.dmp
-rw-r--r-- 1 user user  16K Mar  5 07:26 gc.prt
-rw-r--r-- 1 user user 4.9K Mar  5 07:20 gencode.dmp
-rw-r--r-- 1 user user 1.1M Mar  5 07:25 merged.dmp
-rw-r--r-- 1 user user 183M Mar  5 07:26 names.dmp
-rw-r--r-- 1 user user 146M Mar  5 07:25 nodes.dmp
-rw-rw-r-- 1 user user 9.1G Mar  5 07:26 nucl_gb.accession2taxid
-rw-rw-r-- 1 user user  20G Mar  5 07:27 nucl_wgs.accession2taxid
-rw-rw---- 1 user user 2.7K Sep 11 15:34 readme.txt
-rw-rw-r-- 1 user user    0 Mar  5 07:27 taxdump.dlflag
-rw-rw-r-- 1 user user  50M Mar  5 07:27 taxdump.tar.gz
-rw-rw-r-- 1 user user    0 Mar  5 07:29 taxdump.untarflag

Am I doing something wrong with the --use-wget switch? Thanks

Originally posted by @jt7670367 in https://github.com/DerrickWood/kraken/issues/114#issuecomment-595254256

[yangm9]

Hi, Man, I also experienced the same issues last night. My solution is to modify the program "rsync_from_ncbi.pl". Insert the following code to the line 32. next unless($ftp_path=~m#^ftp://ftp\.ncbi\.nlm\.nih\.gov#);