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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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guidance replacing Standard kraken2 database with PlusPF #634

Open sheila-adams-sapper opened 1 year ago

sheila-adams-sapper commented 1 year ago

I have had kraken2 standard installed for a couple of years and have used it with no issues. I would like to add fungal identification to my analysis, so I would like to replace the standard kraken2 database with the PlusPF. I downloaded the tar ball from the Index Zone page. The file itself is dated 20220607 even though the index zone date is 9/8/2022.

The files listed in the manual as essential to a kraken database are there: hash.k2d, opts.k2d, taxo.k2d, as well as the kmer_distrib files and a seqid2taxid.map file. I'm unsure of the next step and it is not clear in the manual how to proceed. I can't used kraken2-build with the contents of this directory, I can't directly classify with the contents of this directory (error, database.kdb is missing). I can't work out the combination of commands to build the proper database. I don't want to overwrite the directory where the standard kraken2 database is with these files in case this causes an error, in which case I won't be able to use kraken at all.

Can you untangle this for me?

kmmehjabin commented 5 months ago

hi, were you able to get the .kdb file later? If yes, can you please say how?