GianBen

Awesome, thanks. For now I just did on the plotted tree.

Hello, having the same identical issue. ``` >> Running Bracken >> python src/est_abundance.py -i /mnt/home/benucci/pipe-bac-pb/outputs/taxcalssabund_kraken2-brachen/pbio-2279.20869.bc1020_BAK8B_OA--bc1020_BAK8B_OA.ccs/kraken2_report.txt -o /mnt/home/benucci/pipe-bac-pb/outputs/taxcalssabund_kraken2-brachen/pbio-2279.20869.bc1020_BAK8B_OA--bc1020_BAK8B_OA.ccs/bracken_report.txt -k /mnt/research/bonito_lab/Benucci/databases/kraken2/minikraken2_v1_8GB/database100mers.kmer_distrib -l S -t 10 >> Checking report file: /mnt/home/benucci/pipe-bac-pb/outputs/taxcalssabund_kraken2-brachen/pbio-2279.20869.bc1020_BAK8B_OA--bc1020_BAK8B_OA.ccs/kraken2_report.txt Error: no...

Dear @mziegler12, I just tried and it doesn't work even with `-l D`. Please see the code below. Thanks, G. ``` /mnt/home/benucci/anaconda2/envs/bracken/bin/bracken: illegal option -- - version of Bracken: Usage:...

@tuncK, Thanks, that may makes sense. But if that is the case then a more detailed error message should help users to understand what's happening. Also, I thought Brachen was...

@tunck I run it on a genome with 39 conitgs and worked well at `-l G` or `-l S`. I then run it on a genome with 8 contigs and...

Thank you so much for the answer, I will use `cutadapt`. Gian

Hi @jtackm, thank for your answer and motivations. I understand. I just fell like much more microbial ecologists will have access to it if implemented in a different, more commonly...