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I'm triying to download some bacteria genomes using the ncbi-genome-download command. But after a while the following error apear:

ERROR: Download from NCBI failed: ConnectionError(ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response')))

I have been looking for a possible solution, but aparently there is nothing I can do, it's NCBI side. I need the genomes to clean some contamination of my reads for an RNA-seq. Any idea how to fix it or any alternative solution?

Apparently NCBI have less trafic on weekends and at night so some people suggest to try it at those times, but didn't work either.

Alonso Cid
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  • For future users this happend when downloading kraken bacterial genome library. For what I know don't have and won't have a solution in the near future. Fortunatly for me I use a server that have kraken2 and it's databases already in. Sorry for those who need it but no solution at the moment :( – Alonso Cid Feb 16 '23 at 12:54

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