Hi all,
I am trying to submit my script to run quality control on 5 samples for 16S V4 amplicon sequence data, but my job has been failing due to the time limit. I have increased the time up to 20 hours and I still get the same error. I don't think the issue is actually the time limit, as I ran QC with the same script for 100 samples and it took less than 20 hours. Any idea why this is happening? Please find my script below.
#!/bin/bash --login
########## SBATCH Lines for Resource Request ##########
#SBATCH --time=20:00:00 # limit of wall clock time - how long the job will run (same as -t)
#SBATCH --nodes=1 # number of different nodes - could be an exact number or a range of nodes
#SBATCH --ntasks=1 # number of tasks - how many tasks (nodes) that you require (same as -n)
#SBATCH --cpus-per-task=4 # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem-per-cpu=32G # memory required per allocated CPU (or core)
#SBATCH --mail-user= # type in your email to receive the notification
#SBATCH --mail-type=ALL # the type of emails that you want: for beggiinng and end of the job
#SBATCH --job-name 2ndexperiment-16S-5samples-QC # you can give your job a name for easier identification (same as -J)
########## Command Lines for Job Running ##########
module purge
export CONDA3PATH=~/miniconda3
module load Conda/3
conda activate qiime2 # Activate the QIIME 2 environment
DADA2 denoise-paired command
qiime dada2 denoise-paired
--i-demultiplexed-seqs first5-demux.qza
--p-trim-left-f 7
--p-trim-left-r 7
--p-trunc-len-f 240
--p-trunc-len-r 240
--o-representative-sequences 202516S_5samples-rep-seqs.qza
--o-table 202516S_5samples-table.qza
--o-denoising-stats 202516S_5samples-stats.qza