SPAdes / Trinity running out of space still

Description of the bug

I'm running a bash script (attached below) and SPAdes and Trinity keep running out of space (html of latest run attached below). I changed the configs to what I believe to be enough CPUs and memory for SPAdes (according to SPAdes documentation), but it keeps failing I'm checking the latest run slurm output, and still getting the same error (attached)

slurm_output.zip.

Are there higher versions of than 1.2? (I'm looking at the system information below).

Command used and terminal output

#!/bin/bash
#SBATCH --job-name=spades_denovo
#SBATCH --partition=common       # Use 'scavenger' if needed
#SBATCH --cpus-per-task=16
#SBATCH --mem=250G
#SBATCH --time=7-00:00:00
#SBATCH --output=spades_%j.out
#SBATCH --error=spades_%j.err

conda activate env_nf

nextflow run nf-core/denovotranscript \
    --input Wisse_10855_150PE_samples.csv \
    --outdir nextflow_output \
    --max_memory 250.GB \
    --max_cpus 16 \
    --skip_fastp true \
    --skip_fastq true \
    --remove_ribo_rna true \
    -resume

Relevant files

pipeline_info.zip

nextflow.config.zip

nf_denovo_transcript.sh.zip

System information

Nextflow: version 24.10.5, build 5935 (04-03-2025 17:55 UTC)
Hardware: HPC
Executor: slurm
Container: conda

OS:
NAME="AlmaLinux"
VERSION="9.5 (Teal Serval)"
ID="almalinux"
ID_LIKE="rhel centos fedora"
VERSION_ID="9.5"
PLATFORM_ID="platform:el9"
PRETTY_NAME="AlmaLinux 9.5 (Teal Serval)"
ANSI_COLOR="0;34"
LOGO="fedora-logo-icon"
CPE_NAME="cpe:/o:almalinux:almalinux:9::baseos"
HOME_URL="https://almalinux.org/"
DOCUMENTATION_URL="https://wiki.almalinux.org/"
BUG_REPORT_URL="https://bugs.almalinux.org/"

Version of nf-core/denovotranscript:
ALMALINUX_MANTISBT_PROJECT="AlmaLinux-9"
ALMALINUX_MANTISBT_PROJECT_VERSION="9.5"
REDHAT_SUPPORT_PRODUCT="AlmaLinux"
REDHAT_SUPPORT_PRODUCT_VERSION="9.5"
SUPPORT_END=2032-06-01

project name: nf-core/denovotranscript
repository : https://github.com/nf-core/denovotranscript
local path : /hpc/home/ds394/.nextflow/assets/nf-core/denovotranscript
main script : main.nf
description : A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq
author : Avani Bhojwani and Timothy Little
revisions :

• master (default)
  TEMPLATE
  dev
  nf-core-template-merge-3.0.0
  nf-core-template-merge-3.0.2
  1.0.0 [t]
  1.1.0 [t]
  1.2.0 [t]

Start by reviewing the attached slurm_output.zip and pipeline_info.zip, then inspect nextflow.config.zip and nf_denovo_transcript.sh.zip alongside the reported command. Compare the SPAdes and Trinity failures with the configured --max_memory, --max_cpus, and Slurm resources; done means identifying the cause of the space failures and documenting actionable configuration or system requirements.