Closed EricSalomaki closed 7 years ago
NCBI is phasing out GI numbers already. Only accession numbers will be supported. Also, only new species will get a taxid - new "strains" will not.
This will require re-engineering of the Kraken code base, or moving to a new software.
The code has been updated to account for the phasing out of GI numbers. If the updated code has any additional issues, please open a new issue.
I recently downloaded all genomes available on ncbi in hopes of making a database that would be as comprehensive as possible for determining taxonomy for a largely unknown eukaryote/prokaryote metagenomic dataset. However, it appears that there are currently no GI number assigned to the files downloaded from ncbi and the headers look like this :
rather than
I noticed for a previous issue that you mentioned that you are working on a better solution that will allow inclusion of sequences that lack GI numbers but have only accession numbers so hopefully that can help fix this issue down the road. However, I was wondering if you had any ideas for a workaround for this issue at this point in time that may make it easier than trying to individually assign taxonomy for the 60,000+ genomes that I am trying to make into a database. Any thoughts are greatly appreciated.
Best, Eric