Kraken2 standard database can not connect to NCBI ftp

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3.0 years ago

nonaddldy ▴ 10

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I can open https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1 successfully in Google Chrome, but it doesn't work in Kraken2 enter image description here

Kraken2 • 2.2k views

ADD COMMENT • link 3.0 years ago by nonaddldy ▴ 10

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There seem to be multiple issues reported on kraken2 GitHub issues section regarding db download problems. You can either add your vote there or keep an eye on the issues to see when they may be fixed. Considering it is the end of the year and people are on their winter break in the US this may not get fixed until early January,

ADD REPLY • link 3.0 years ago by GenoMax 148k

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Thanks, I read about the kraken2 issue 1 day ago, and solved this problem with modifying the corresponding perl file.

ADD REPLY • link 3.0 years ago by nonaddldy ▴ 10

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Can you post the fix either here or in github section of the tool? It might be useful to other users.

ADD REPLY • link 3.0 years ago by cpad0112 21k

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In this github issue, https://github.com/DerrickWood/kraken2/issues/518, there is a method to solve the problem

ADD REPLY • link 3.0 years ago by nonaddldy ▴ 10

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