#!/bin/bash
#SBATCH --job-name=snow_fcsgx
#SBATCH --output=/gscratch/scrubbed/lhs3/snow_annotation/fcsgx.out
#SBATCH --account=coenv
#SBATCH --partition=cpu-g2
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --time=2-10:00:00
#SBATCH --mem=175G
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=laura.spencer@noaa.gov
#SBATCH --chdir=/gscratch/scrubbed/lhs3/snow_annotation

# Load python module
module load coenv/python/3.13.11

# Run FCS-GX - clean genome to remove contamination
python3 \
 /gscratch/srlab/containers/fcs.py \
 --image /gscratch/srlab/containers/fcs-gx.sif \
 screen \
 genome --fasta /gscratch/scrubbed/lhs3/snow_annotation/GCA_016584305.1_ASM1658430v1_genomic.fna.gz \
 --out-dir /gscratch/scrubbed/lhs3/snow_annotation/gx/ \
 --gx-db "/gscratch/scrubbed/samwhite/databases/gxdb" \
 --tax-id 41210