[Trinity have been running very slow]

[Đức Phúc Trần]

Hello everyone, I was trying to run Trinity v-2.15.2 with about 38 fastq files, setting the parameter: --CPU 64 and --max_memory 256G. The tool runs so slowly, I know it would take a lot of time, but it' been about a week now and only at ~19% completed in phase 2. 

Does anyone have the same issue? Please give me some advice about this situation. Thank you.

This is my code: 

#!/bin/bash
#SBATCH --job-name=trinity_p2
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --mem=256G
#SBATCH --output=inter%j.out
#SBATCH --error=inter%j.err

source /home/phuctran/miniconda3/etc/profile.d/conda.sh

    hdir="/mnt/12T/lobster_project/RNA"
    p_raw="/mnt/12T/lobster_project/RNA/raw"
    p_trim="/mnt/12T/lobster_project/RNA/output/trimmomatic"
    p_out="/mnt/12T/lobster_project/RNA/output"

    files=$(find "$p_trim" -maxdepth 1 -type f -name "*_trimmed_paired.fastq.gz" | grep -v 'trim\.')
    r1=$(echo "$files" | grep '_1' | tr '\n' ',' | sed 's/,$//')
    r2=$(echo "$files" | grep '_2' | tr '\n' ',' | sed 's/,$//')
    echo "Input contains: $r1, $r2"
conda activate trinity
Trinity \
--seqType fq \
--left "$r1" \
--right "$r2" \
--SS_lib_type RF \
--CPU "$SLURM_CPUS_PER_TASK" \
--max_memory 250G \
--output "$p_out/trinity" \

conda deactivate