Assembly not in scope for NCBI Datasets

Question

[Valentin]

Hello,

I am trying to download the genome with assembly accession number GCA_015351695.1 using the command line NCBI Datasets. When I run

datasets download genome accession GCA_015351695.1

I get the following error:

Some of the assemblies provided ('GCA_015351695.1') are valid NCBI Assembly Accessions, but are not in scope for NCBI Datasets.

The webpage is here https://www.ncbi.nlm.nih.gov/assembly/GCA_015351695.1/ where I can download it directly. However, I need to download many genomes by their accession numbers, so I can't download each manually. Is there any way I can download this genome from the command line or any program language interface (Python or whatever)? Thank you!

Answer 1

[GenoMax]

You can with use the two other tools mentioned by @shenwei in this answer: How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?

Or

Use EntrezDirect to get the FTP paths for the assemblies and then download them. There are separate paths for GenBank and RefSeq entries. They appear to be the same for these.

$ esearch -db assembly -query "Methanobacterium formicicum" | esummary | xtract -pattern DocumentSummary -element AssemblyAccession,FtpPath_GenBank,FtpPath_RefSeq
GCA_015351695.1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/015/351/695/GCA_015351695.1_ASM1535169v1
GCF_001458655.1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/458/655/GCA_001458655.1_Mb9  ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/458/655/GCF_001458655.1_Mb9
GCF_001316325.1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/316/325/GCA_001316325.1_ASM131632v1  ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/316/325/GCF_001316325.1_ASM131632v1
GCF_000302455.1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/302/455/GCA_000302455.1_ASM30245v1   ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/302/455/GCF_000302455.1_ASM30245v1
GCF_000953115.1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/953/115/GCA_000953115.1_DSM1535  ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/953/115/GCF_000953115.1_DSM1535
GCF_000762265.1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/762/265/GCA_000762265.1_ASM76226v1   ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1

[Valentin]

Thank you it solved it!