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Run Kraken2 based on BLAST nt databse #26

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LilyAnderssonLee opened this issue Aug 8, 2023 · 3 comments
Closed

Run Kraken2 based on BLAST nt databse #26

LilyAnderssonLee opened this issue Aug 8, 2023 · 3 comments
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@LilyAnderssonLee
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LilyAnderssonLee commented Aug 8, 2023 •
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Since the database plays a very important role in the classification of metagenomics, we would like to test if Kraken2, based on the BLAST NT database, can perform on the server hasta and identify more interesting organisms
@LilyAnderssonLee LilyAnderssonLee self-assigned this Aug 8, 2023
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LilyAnderssonLee commented Aug 8, 2023 •
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Download the blast db and the compressed file is ~480GB
wget https://genome-idx.s3.amazonaws.com/kraken/k2_nt_20230502.tar.gz

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The taxprofiler process was killed due to the memory limit on hasta. Therefore, it's not realistic to run Kraken2 based on the BLAST nt database on hasta due to the extremely large size of the database.

@LilyAnderssonLee LilyAnderssonLee added bug Something isn't working enhancement New feature or request and removed bug Something isn't working labels Aug 8, 2023
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talnor commented Dec 7, 2023

Closing for now until we have at least ~480GB of mem.

@talnor talnor closed this as completed Dec 7, 2023
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