-
Notifications
You must be signed in to change notification settings - Fork 0
/
denoise_dada2.sh
32 lines (27 loc) · 1011 Bytes
/
denoise_dada2.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
#!/bin/bash
#SBATCH --job-name=DADA2_denoise
#SBATCH --ntasks 1
#SBATCH --mem=16G
#SBATCH --output=stdout_denoiseDADA2.Log
#SBATCH --cpus-per-task 8
# Setting the working directory
cd /home/scarpettad
# Setting the path to the singularity container
sing_container=/home/scarpettad/amplicon_2023.9.sif
# Setting the qiime2 artifact to work on
qiime_artifact=/home/scarpettad/second_run/qiime_artifacts/paired_end.qza
# Setting the output directory to store denoised artifacts
output_dir=/home/scarpettad/second_run/denoise_dada2
# Run DADA2 denoising
singularity run ${sing_container} qiime dada2 denoise-paired \
--i-demultiplexed-seqs ${qiime_artifact} \
--p-n-threads 8 \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 0 \
--p-trunc-len-r 0 \
--p-max-ee-f 2.0 \
--p-max-ee-r 2.0 \
--o-representative-sequences ${output_dir}/rep-seqs-dada2.qza \
--o-table ${output_dir}/table-dada2.qza \
--o-denoising-stats ${output_dir}/denoising-stats-dada2.qza