Hello.
I’m having a problem running metaphlan 4 on metagenomic DNA samples extracted from soil microbiota. I’m using the following command:
metaphlan 268577MP_SMG3_1_trimmed_kneaddata_unmatched_1.fastq,268577MP_SMG3_1_trimmed_kneaddata_unmatched_2.fastq --bowtie2out bowtie2.bz --nproc 20 --unclassified_estimation --input_type fastq -o classification.txt
At the default stat_q level, I got no classifications, and at stat_q = 0.10, I got only 1% classifications.
Does anyone know what the problem might be? I think it might have to do with the database?
Any and all help is very much appreciated.