Option for metadata file only

[Ahmed-Shibl]

First I want to thank you for this great tool!

I wanted to ask if there was an option to get the metadata file for a list of accessions without downloading the genomes. I would like to refine the number of genomes that I download based on their metadata.

I tried this command in an attempt to generate the ALL_actino_accs_in_tree_metadata.txt file:
ncbi-genome-download --dry-run --section genbank --assembly-level all --assembly-accessions ALL_actino_accs_in_tree.txt --output-folder /Obesity_v2/actinobacteriota/anvio --metadata ALL_actino_accs_in_tree_metadata.txt --progress-bar --verbose bacteria

No file was generated but this was the output:

GCA_007954505.1	Microbacterium sp. CBA3102	       CBA3102
GCA_008122505.1	Agromyces mariniharenae	                NEAU-184
GCA_008123405.1	Nocardioides sp. BGMRC 2183	        BGMRC 2183
GCA_009696325.1	Collinsella sp. WCA1-178-WT-3 (M1)	WCA1-178-WT-3 (M1)
GCA_009696315.1	Cutibacterium porci	                        WCA-380-WT-3A

Please let me know if you would need any other information. Thanks!

[Thomieh73]

Hi, maybe you figured this out. ncbi-genome-download creates a cache file, which contains the metadata you need.
If you run:

ncbi-genome-download -h

it will then produce these lines in the helpfile:

 -N, --no-cache        Don't cache the assembly summary file in
                        /cluster/home/thhaverk/.cache/ncbi-genome-download.   

So if you do a dry run, you will have the metadata file in the cache folder