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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 error : databaseeportsmers.kmer_distrib does not exist #273

Open sm-sudo opened 1 month ago

sm-sudo commented 1 month ago

I have a k2report file for which i have run bracken for abundance estimation. when i run the bracken i get the below error

$ bracken -d /mnt/e/krakenindexdb/16S_Silva138_20200326/16S_SILVA138_k2db/ -i reports/10k_16_silva.k2report -r 250 -l G -t 10 -o /mnt/d/metagenomicswork/test/test10k/outputs/10k_16_silva.bracken -reports /mnt/d/metagenomicswork/test/test10k/reports/10k_16_silva.breport

Checking for Valid Options... ERROR: /mnt/e/krakenindexdb/16S_Silva138_20200326/16S_SILVA138_k2db/databaseeportsmers.kmer_distrib does not exist Run bracken-build to generate the kmer distribution file.

database source : pre-available kraken/bracken indexes of 16S_SILVA138_k2db. system info : I am running bracken on wsl2 Ubuntu 22.04.e LTS

I have checked the databasepath and .kerms files exixts. $ ls README.md database100mers.kmer_distrib database200mers.kmer_distrib database50mers.kmer_distrib hash.k2d taxo.k2d bashrc database150mers.kmer_distrib database250mers.kmer_distrib database75mers.kmer_distrib opts.k2d

jenniferlu717 commented 1 month ago

-reports is an incorrect command line option. Please check your command line?

sm-sudo commented 1 month ago

hi,

it worked after correcting the command line option. thank you