Downloading viral reference genome

Question

[Mesfin]

Hi,

I was trying to download viral reference genome while exercising the 'Advanced FASTQ processing' section of the biostar handbook. Here are the commands I run;

wget -nc http://data.biostarhandbook.com/reads/duplicated-reads.fq.gz
wget -nc ftp://ftp.ncbi.nih.gov/refseq/release/viral/viral.2.1.genomic.fna.gz
wget -nc ftp://ftp.ncbi.nih.gov/refseq/release/viral/viral.2.protein.faa.gz

While I'm successful downloading the first (duplicated-reads), I keep getting error message on the last two, viral genomic and protein seqs. The message looks like this:

$ wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.2.1.genomic.fna.gz
--2024-01-02 16:46:27--  ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.2.1.genomic.fna.gz
           => 'viral.2.1.genomic.fna.gz'
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.13, 130.14.250.12, 2607:f220:41e:250::10, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.13|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /refseq/release/viral ... done.
==> SIZE viral.2.1.genomic.fna.gz ... done.

==> PASV ... done.    ==> RETR viral.2.1.genomic.fna.gz ... 
No such file 'viral.2.1.genomic.fna.gz'.

Thank you,
Mes

[Pierre Lindenbaum]

there is no such viral.2.1.genomic.fna.gz under https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ .

[GenoMax]

You should submit this error to the Biostarshandbook Issues so it can be fixed for everyone: https://github.com/biostars/biostar-handbook/issues

Run these commands instead

wget -nc ftp://ftp.ncbi.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz
wget -nc ftp://ftp.ncbi.nih.gov/refseq/release/viral/viral.1.protein.faa.gz

Answer 1

[Ram]

The files don't exist.

https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/