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jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
http://ccb.jhu.edu/software/bracken/index.shtml
GNU General Public License v3.0
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bracken-build syntax error #232

Open ythuangmyco opened 1 year ago

ythuangmyco commented 1 year ago

Hi, I am trying to build a bracken database from a kraken database built with this code: kraken2-build --download-taxonomy --db fungi kraken2-build --download-library fungi --db fungi kraken2-build --build -t 8 --db fungi

With this bracken code: bracken-build -d fungi -k 20 -l 3000 -t 8 I got this syntax error message, Screenshot from 2023-09-01 09-24-16 It seems an issue in my downloaded fungi databased from NCBI, though when I deleted the error-making sequence from database.kraken, problem persistent but became another sequence that caused error (in this case, I removed NW_003803360.1, and then NW_003803359.1 became the culprit).

Any idea or does anyone face similar question? Thank you!

ythuangmyco commented 1 year ago

the screen shot is a dirty-and-quick test for getting the error message, so it's just two mers : )

jenniferlu717 commented 11 months ago

Does it say which script is causing the issue? It looks like it might be the generate_kmer_distibution.py script but I cannot be sure