--refseq flag fails - Githubissues

cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction

Other

145 stars 49 forks source link

--refseq flag fails #128

Closed franciscozorrilla closed 3 years ago

franciscozorrilla commented 3 years ago

Hi Daniel,

Just wanted to report some buggy behavior I ran into when using the --refseq flag (CarveMe version 1.4.1). The flag works as expected in most cases but it fails for some accession numbers, for example GCF_014656585.1:

$ carve -v --refseq GCF_014656585.1 -o GCF_014656585.1.xml

Downloading genome GCF_014656585.1 from NCBI...
Invalid accession code
Failed to download genome from NCBI.

Any idea what could be going wrong?

Best wishes, Francisco

cdanielmachado commented 3 years ago

Hi Francisco,

That's because there is an internal table with accession numbers and the respective ncbi ftp path. I download an updated list from NCBI with every new CarveMe release, so we are always a bit behind.