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Kraken Database Size #40
Description
Hello,
I was able to run the MEDI build pipeline without getting an error message (although I had to use the K2 functions instead of kraken2-build as I otherwise had rsync problems).
While I am able to run the quant script now and MEDI will produce an output, I believe that there could be an issue with my database size. I specified a max size of 500GB in my script; however, my final hash.k2d file was roughly 354GB and the database.kraken is 155GB.
I would imagine that this could impact the sensitivity of the results as I ran a few test samples an the only food matches in the output were Teas.
Is this an issue you have experienced or do you have any thoughts on why there is a large database size mismatch?
Thank you in advance,
Activity
cdiener commentedon Aug 4, 2026
Sorry for not seeing this earlier. That depends a lot on when you downloaded the data and how much could be downloaded successfully. The updates from today make this much more apparent now. As a reference here are my file sizes for a recent build:
total 566G drwxrws--- 3 o_diener dienerlab 377 Nov 17 2025 . drwxrws--- 12 o_diener dienerlab 1,4K Aug 3 13:02 .. -rwxrwx--- 1 o_diener dienerlab 5,2M Nov 17 2025 database100mers.kmer_distrib -rwxrwx--- 1 o_diener dienerlab 4,8M Nov 17 2025 database150mers.kmer_distrib -rwxrwx--- 1 o_diener dienerlab 4,1M Nov 17 2025 database250mers.kmer_distrib -rwxrwx--- 1 o_diener dienerlab 149M Nov 17 2025 food_contents.csv.gz -rwxrwx--- 1 o_diener dienerlab 90K Nov 17 2025 food_matches.csv -rwxrwx--- 1 o_diener dienerlab 496G Nov 17 2025 hash.k2d -rwxrwx--- 1 o_diener dienerlab 169K Nov 17 2025 manifest.csv -rwxrwx--- 1 o_diener dienerlab 64 Nov 17 2025 opts.k2d -rwxrwx--- 1 o_diener dienerlab 1,2G Nov 17 2025 seqid2taxid.map -rwxrwx--- 1 o_diener dienerlab 4,5M Nov 17 2025 taxo.k2d drwxrws--- 2 o_diener dienerlab 527 Nov 17 2025 taxonomy