start of kraken script for decontamination

kraken.sh

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+#!/bin/bash
+
+#SBATCH --mem 70G
+#SBATCH --job-name kraken
+#SBATCH --mail-user [email protected] ## 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; [email protected]
+
+# ----- 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"