#This script was written and run by Dr. Robin Sleith on each cell.

#!/bin/bash
#PBS -k o
#PBS -l nodes=1:ppn=20,vmem=200gb,walltime=59:00
#PBS -M rsleith@smith.edu
#PBS -m abe
#PBS -N Centrifuge
#PBS -j oe
module load centrifuge
database=/N/dc2/scratch/rsleith/nt/nt
cd /N/dc2/scratch/rsleith/katzlab/amoeba/genomes_project/assemblies
for i in *.fasta
do
echo $i
$HOME/bbmap/reformat.sh in="/N/dc2/scratch/rsleith/katzlab/amoeba/genomes_project/assemblies/"$i out="/N/dc2/scratch/rsleith/katzlab/amoeba/genomes_project/assemblies/500_"$i minlength=500 overwrite=T
centrifuge -p 20 -x $database -f "500_"$i \
-S "/N/dc2/scratch/rsleith/centrifuge/amoeba/nt_"$i".tab" --report-file "/N/dc2/scratch/rsleith/centrifuge/amoeba/nt_"$i"_centrifuge_report.tsv"
done