#!/bin/env bash

for confidence in 10 20 30; do 
	for fastq in *.fastq; do
		kraken2 --db /mounts/tmpfs/kraken2-core_nt --output - --threads 16 --classified-out ${fastq%.*}-classified-$confidence.out \
		--unclassified-out ${fastq%.*}-unclassified-$confidence.out --memory-mapping --confidence 0.$confidence --report-zero-counts \
		--report S1-report-$confidence.out --use-names $fastq;
	done
done