NCBI-genome-download not working with no errors

[sepidehalamouti]

I have been using nib-genome-download on anaconda3 environment for awhile. But since yesterday, I noticed that the download package is not working. It gives no error, just going black and nothing happens. Can you please let me know if there is a current issue with the GenBank database? or I have to look into other possibilities causing the issue?

Many thanks,
Sepideh M. Alamouti

[openpaul]

I just installed it with conda:

conda create -n ncbi -c bioconda ncbi-genome-download
conda activate ncbi
ncbi-genome-download -h

And everything works as expected.

I even downloaded a few genomes which worked well as well.
Can you copy paste what you did and the error message?

[sepidehalamouti]

Hello
I was also downloading different genomes before for example using the following command:
~/anaconda3/bin/ncbi-genome-download --section genbank -g mycobacterium bacteria
but now, it doesn't produce anything even no error...

should I try reinstallation, considering nothing has changed in my linux environment....

[openpaul]

Try using the verbose or debug flag to see whats wrong, if you are curious. Else I think reinstalling could solve the issue.

ncbi-genome-download --verbose --debug --section genbank -g mycobacterium bacteria

The debug flag causes a log of information to be printed.

[dturaev]

I had the same problem, the command ncbi-genome-download all --assembly-accessions GCF_004803935.1 -F fasta --verbose --debug 2>log.txt didn't work for me (version 0.2.12). (Program version 0.2.10 worked before.) The logfile was full of messages like

DEBUG: Skipping entry with incompatible assembly accession 'GCF_003672135.1'
DEBUG: Skipping entry with incompatible assembly accession 'GCF_003710045.1'
DEBUG: Skipping entry with incompatible assembly accession 'GCF_011952275.1'

diff showed some differences between ~/.cache/ncbi-genome-download/refseq_bacteria_assembly_summary.txt and the wget-downloaded https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt, so maybe something is off about the formatting (encoding?) of the downloaded file. When I replaced the former by the latter, the download worked.

Btw, there was also a second problem:

DEBUG: Downloading summary for 'refseq'/'metagenomes' uri: 'https://ftp.ncbi.nih.gov/genomes'
DEBUG: Starting new HTTPS connection (1): ftp.ncbi.nih.gov:443
DEBUG: https://ftp.ncbi.nih.gov:443 "GET /genomes/refseq/metagenomes/assembly_summary.txt HTTP/1.1" 404 None

I didn't see a metagenomes folder in https://ftp.ncbi.nih.gov/genomes/refseq/, maybe it doesn't exist anymore?

[peterjc]

Does that mean this is a duplicate of #115?

[matoxxx]

Hello,
I have the same problem but with just refseq section (genbank section downloads without a problem).
ncbi-genome-download --verbose --debug -F features -A Db_hits_GCF.txt -o ./FEATURES_EUTILS/ --flat-output -v -p 4 -r 4 all
results in many messages like this
DEBUG: Skipping entry with incompatible assembly accession 'GCF_011952275.1'