Excessively long running time

[lslochov]

Hi, I'm running the example dataset featured in section 4.1 of the README on an HPC SLURM cluster. I'm seeing MitoHifi's running time exceed 24 hours without finishing, even when I request 16 CPU cores and 32 GB RAM. I doubt that should be happening for a dataset of this size, so I suspect I've misconfigured something, but I'm not sure what. I'd appreciate any help in understanding and resolving this.

[marcelauliano]

can you give all the details of your run please

[lslochov]

I started by downloading reference files for "Deilephila porcellus", per section 4.1 of the README.

python3 findMitoReference.py --species "Deilephila porcellus" --outfolder /home/llochovsky001202/data/deilephila --min_length 14000

Then I ran MitoHifi itself using Deilephila porcellus test data:

python3 mitohifi.py -r ../tests/ilDeiPorc1.reads.100.fa -f /home/llochovsky001202/data/deilephila/NC_079697.1.fasta -g /home/llochovsky001202/data/deilephila/NC_079697.1.gb -t 4 -o 5

I ran this on SLURM with the following config:

#!/bin/bash
#SBATCH --job-name=mitohifi_test
#
#SBATCH --nodes=1
#
#SBATCH --ntasks-per-node=1
#
#SBATCH --cpus-per-task=4
#
#SBATCH --mem=8G
#
#SBATCH --time=24:00:00

The job eventually reaches the 24-hour limit and is killed by SLURM. I tried increasing the CPUs and RAM in the hope that it would speed up the computation, but even with 16 CPU cores and 32 GB RAM, I see the same results.

[marcelauliano]

It should take only a few minutes. It's probably something with your system or installation.