Hi I am trying to run Humann3 on some metagenomic sequences. I have the software installed and running on a university cluster with the jobs being managed by a SLURM system.
The problem I am having is that the software starts running fine without any errors and is making temp, output and log files but after a day or two the output files just stop being added to. The software has been running for 14 days now with no change but there is no error messages and the software hasn’t obviously crashed or stopped. The script I am running is below:
#SBATCH --ntasks=50 # threads
#SBATCH --nodes=1 # Use x nodes (physical machines)
#SBATCH --job-name=hum2 # sensible name for the job
#SBATCH --mem=120G # Default memory per CPU is 3GB.
#SBATCH --partition=hugemem # Use the verysmallmem-partition for jobs requiring < 10 GB RAM.
#SBATCH --email@example.com # Email me when job is done.
module load Miniconda3
source activate biobakery3
humann --input /net/fs-1/projects01/SoilCyc/SoilCycReads/catfiles/2_combined.fq.gz --threads 50 --output /net/cn-1/mnt/SCRATCH/sivick/humann3_output/
I hope this is informative but let me know if any more details are needed.