Advanced FASTQ processing, Biostar handbook

[Meshesha78]

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'.

Also,I dont see the files at https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

Thanks,

Mes

[ara-rdgz]

Hello!

I was having the same exact problem and, just like you, I checked the NCBI FTP site for said files and could not find them. So, I decided to do the best next thing which was to download the files with similar names to the ones I wanted. If you go to the FTP site you'll see that while the viral.2.1.genomic.fna.gz and viral.2.protein.faa.gz files do not exit, however the files viral.1.1.genomic.fna.gz and viral.1.protein.faa.gz do exist. So, I just downloaded these and used them for the subsequent steps.

[Meshesha78]

Thanks for the tip! I saw that the the viral.2.1.genomic.fna.gz and viral.2.protein.faa.gz files also used by some published work but do not exist at the FTP site anylonger. I did use the availlable 1.1 versions as you suggested and works fine for the purpose.
Thanks again,

Mes