Error DADA2 in R (return code -9)

Hello everyone, I am new pleasure to meet you!
I ran the following dada2 command on denoising paired-end data.

#SBATCH --job-name=dada

#SBATCH --output=/g100/home/userexternal/MYUSER/miniconda3/envs/script_annamaria/dada_job.out

#SBATCH --error=/g100/home/userexternal/MYUSER/miniconda3/envs/script_annamaria/dada_job.err

#SBATCH --mail-type=ALL

#SBATCH --mail-user=myemail

#SBATCH --time=1:00:00

#SBATCH --nodes=1

#SBATCH --ntasks-per-node=32

#SBATCH --mem=10GB

#SBATCH --partition=g100_usr_prod

#SBATCH --account=myaccount

qiime dada2 denoise-paired --i-demultiplexed-seqs /g100_scratch/userexternal/XXX/esp11r1002l.qza --p-trunc-len-f 299 --p-trunc-len-r 219 --o-table /g100_scratch/userexternal/MYUSER/170124/dada/esp11r1002l_table.qza --o-representative-sequences /g100_scratch/userexternal/MYUSER/170124/dada/esp11r1002l_rep-seqs.qza --o-denoising-stats /g100_scratch/userexternal/MYUSER/170124/dada/esp11r1002l_stats.qza

and I get the following error:
Plugin error from dada2
An error was encountered while running DADA2 in R (return code -9) please inspect stdout and stderr to learn more.

Could someone help me please? :pray:

thank you!!

Hi @Annamaria ,
This message indicates that you are running out of memory. You are already requesting 10GB of RAM, which should be plenty for dada2. You should contact your HPC admin to make sure that the memory request is being set correctly.

If you are indeed exceeding 10 GB of RAM, this is unusual. Either you just have a really large dataset (in which case request more RAM) or you might be using a data type (like shotgun sequence data) that should not be used with dada2.

Beyond this, you can search the forum archive (see the magnifying glass in the corner of the screen) to find troubleshooting advice for reducing memory load with this and other QIIME 2 actions.

Good luck!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.