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Arcadia-Science / ProteinCartography

a pipeline to build similarity maps of protein space
MIT License
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BLASTP fails when making too many API calls #4

Closed mezarque closed 1 year ago

mezarque commented 1 year ago

This is probably because of some rate-limiting on NCBI's end. I'm using the BLAST+ command line interface for this query. I could potentially try using the REST API instead.

It would be great to figure out how to limit Snakemake from running the blast query rule repeatedly in quick succession, but I haven't found a straightforward or satisfactory way to do that.

An alternative solution would be to download the nr database locally, but it's pretty large and requires large memory resources to search (afaik). This solution probably wouldn't be ideal for people trying to use the package on their local machines.

mezarque commented 1 year ago

I haven't run into this issue recently; unclear what was causing it, but closing the issue for now.