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bracken error : databaseeportsmers.kmer_distrib does not exist #273

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sm-sudo opened this issue Jul 17, 2024 · 2 comments
Open

bracken error : databaseeportsmers.kmer_distrib does not exist #273

sm-sudo opened this issue Jul 17, 2024 · 2 comments

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@sm-sudo
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sm-sudo commented Jul 17, 2024

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

@sm-sudo sm-sudo changed the title bracken error : bracken error : databaseeportsmers.kmer_distrib does not exist Jul 17, 2024
@jenniferlu717
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-reports is an incorrect command line option. Please check your command line?

@sm-sudo
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sm-sudo commented Aug 9, 2024

hi,

it worked after correcting the command line option. thank you

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