From 321f764cb3eafcbdca4a204c5fb15ded692f5063 Mon Sep 17 00:00:00 2001 From: Negin Valizadegan Date: Thu, 14 Oct 2021 15:31:54 -0500 Subject: [PATCH] start of kraken script for decontamination --- kraken.sh | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 kraken.sh diff --git a/kraken.sh b/kraken.sh new file mode 100644 index 0000000..87e69ea --- /dev/null +++ b/kraken.sh @@ -0,0 +1,48 @@ +#!/bin/bash + +#SBATCH --mem 70G +#SBATCH --job-name kraken +#SBATCH --mail-user valizad2@illinois.edu ## CHANGE THIS TO YOUR EMAIL +#SBATCH --mail-type ALL +#SBATCH --output slurm-%j.out +#SBATCH -n 6 +#SBATCH -N 1 +#SBATCH -A h3abionet +#SBATCH -o /home/groups/h3abionet/RefGraph/results/NeginV_Test_Summer2021/slurm_output/slurm-%j.out + + + +# HPCBio UIUC Kraken; Created by Negin Valizadegan Oct 6, 2021; valizad2@illinois.edu + +# ----- Load necessary modules ------ +module load Kraken2/2.0.8-beta-IGB-gcc-4.9.4 + +echo "Input directory is set to" | tr '\n' ' ' && pwd + + +# Set working directory ------ +cd /home/groups/h3abionet/RefGraph/results/NeginV_Test_Summer2021/results/ + + +# Create a directory for outputs ---- +mkdir -p annotation/kraken/masurca +mkdir -p annotation/kraken/megahit + +echo "Start of kraken process masurca" + +# Masurca ----- + +# Run Kraken ------ + +# kraken2 --use-names --threads 6 --quick \ +# --db /home/groups/h3abionet/RefGraph/data/kraken2/human \ +# annotation/seqkit/masurca/HG03563.masurca.filtered.fasta + +kraken2 --use-names --threads 6 --quick \ +--report annotation/kraken/masurca/HG03563_kraken2_report.txt \ +--classified-out annotation/kraken/masurca/HG03563_masurca_kraken2_classified.fasta \ +--unclassified-out annotation/kraken/masurca/HG03563_masurca_kraken2_unclassified.fasta \ +--db /home/groups/h3abionet/RefGraph/data/kraken2/pluspf_20200919 \ +annotation/seqkit/masurca/HG03563.masurca.filtered.fasta > annotation/kraken/masurca/HG03563_masurca_kraken2_output.txt + +echo "End of kraken process masurca" \ No newline at end of file