What's going on with the NCBI ftp?

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5.1 years ago

5heikki 11k

Hi,

If we look e.g. ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/ we see that the file that is supposed to list all the bacterial genome assemblies was last updated 12/03/2019

However, we also see genome assemblies in that dir that were added later than 12/03/2019, just to give a single example, e.g this

So, either something is very broken or then I have missed some announcement..

Edit. This is the only announcement that could have some relevance in the sense that we know they were going to change things. So, I'm leaning towards something breaking..

Edit. I got a response from the NCBI, there was a bug that stopped the assembly summary files from being updated. The bug is now fixed

NCBI • 938 views

ADD COMMENT • link 5.0 years ago by 5heikki 11k

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nice catch, thanks! same is true for one of my favorites, the ASSMEBLY_REPORTS directory

note however, the GENOME_REPORTS was synced end of last week

ADD REPLY • link 5.1 years ago by Carambakaracho ★ 3.2k

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Hah, I only noticed because my db update script failed. This is an edge case I didn't see coming..

ADD REPLY • link 5.1 years ago by 5heikki 11k

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BTW, this correlates with the RefSeq release 93 on March 13th. I don't know for sure, but I strongly believe that the assembly_reports.txt file were updated more frequently than with a full release ...