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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 giving no reads as an error constantly #215

Open suvekshya21 opened 1 year ago

suvekshya21 commented 1 year ago

Hi,

I am new to bioinformatics and very new to kraken and bracken. I am working on it for one of my project and was able to get kraken report as an output so it seems as tho kraken2 is working on the samples I have but bracken is not working. It just gives ' no reads ' as an error. Please help me with this.

For bracken database building, I used :

bracken-build -d ${KRAKEN_DB} -t ${THREADS} -k ${KMER_LEN} -l ${READ_LEN}

For running bracken I used:

bracken -d ${KRAKEN_DB} -i ${SAMPLE}.kreport -o ${SAMPLE}.bracken -r ${READ_LEN} -l ${LEVEL} -t ${THRESHOLD}

I just got no reads . Please help

m-crown commented 1 year ago

There needs to be at least one taxa at LEVEL which has at least THRESHOLD reads. Suggest checking that you have this first. @jenniferlu717 there are lots of issues related to a misunderstanding of this part of Bracken - could you provide a clarification or if I make a pull request to the readme could this be integrated? See also #117