Hi,

I find this tool [https://github.com/kblin/ncbi-genome-download][1] in github for downloading the bacteria genomes.

    ncbi-genome-download bacteria

it downloades  ---> refseq/bacteria/GCF_940077525.1

from GCF_ * how do I get fasta files ?

Then I tried this, cmd, it unables to download the fasta files.

    ncbi-genome-download --formats fasta bacteria --parallel 16
    
    WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_023646435.1'

Inaddition, I tried to download sequences directly from ncbi ftp site.

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

    wget ftp://ftp.ncbi.nih.gov/refseq/release/bacteria/ 
    generates ----> index.html file

The html file contains all the ftp links related to the bacterial genomes.

How do I download the sequences using the index.html file ? 
Is their any easy way to download the bacterial, viral genomes ?

    <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
    <html>
    <head>
    <title>Index of /refseq/release/bacteria on ftp.ncbi.nih.gov:21</title>
    </head>
    <body>
    <h1>Index of /refseq/release/bacteria on ftp.ncbi.nih.gov:21</h1>
    <hr>
    <pre>
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1.1.genomic.fna.gz">bacteria.1.1.genomic.fna.gz</a>  (112297068 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1.genomic.gbff.gz">bacteria.1.genomic.gbff.gz</a>  (90133141 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.10.1.genomic.fna.gz">bacteria.10.1.genomic.fna.gz</a>  (2647137 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.10.genomic.gbff.gz">bacteria.10.genomic.gbff.gz</a>  (2242108 bytes)
      2022 May 05 22:45  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.100.1.genomic.fna.gz">bacteria.100.1.genomic.fna.gz</a>  (94215320 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.100.genomic.gbff.gz">bacteria.100.genomic.gbff.gz</a>  (82718913 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1000.1.genomic.fna.gz">bacteria.1000.1.genomic.fna.gz</a>  (120745492 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1000.genomic.gbff.gz">bacteria.1000.genomic.gbff.gz</a>  (104026228 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1001.1.genomic.fna.gz">bacteria.1001.1.genomic.fna.gz</a>  (120374412 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1001.genomic.gbff.gz">bacteria.1001.genomic.gbff.gz</a>  (102935563 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1002.1.genomic.fna.gz">bacteria.1002.1.genomic.fna.gz</a>  (116037436 bytes)
      2022 May 05 22:46  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1002.genomic.gbff.gz">bacteria.1002.genomic.gbff.gz</a>  (100084701 bytes)
      2022 May 05 22:45  File        <a href="ftp://ftp.ncbi.nih.gov:21/refseq/release/bacteria/bacteria.1003.1.genomic.fna.gz">bacteria.1003.

  [1]: https://github.com/kblin/ncbi-genome-download


There is always a way directly from the FTP site:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/940/077/525/GCF_940077525.1_ASM94007752v1/

You likely need the file that ends in `genomic.fna.gz`.

You may want to try this program:

https://github.com/pirovc/genome_updater

Beware that going with 16 parallel downloads will likely cause NCBI to throttle down your IP number as you may be considered to abuse their resources. Sometimes going with 4-8 parallel downloads will get the job done faster than with 16.