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rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Change GTDB URL to use mirror site for much faster database downloads. #174

Closed LeeBergstrand closed 1 month ago

LeeBergstrand commented 1 month ago

Could you change the GTDB URL to the mirror site instead of the primary download site?

@jmtsuji I found that downloading GTDB from the primary site (https://data.gtdb.ecogenomic.org/) is slow because the server is overloaded. Its download rate is currently kilobytes per second (May 2024). It would take multiple days to download this data at that speed. I changed the GTDB URL to use their mirror site (https://data.ace.uq.edu.au/public/gtdb/data/releases/) for order of magnitude faster GTDB database download speeds.

LeeBergstrand commented 1 month ago

@jmtsuji If this becomes a persistent issue, then we can perhaps add the GTDB data to Zenodo