Has there been any consideration to using fastplong instead of porechop for adapter removal and read QC with Nanopore reads? Running into some challenges. I seem to be getting a terminated for unknown reason error that kills my Nextflow main run but the jobs continue to execute in separate slurm submitted jobs on our HPC cluster. Running 5.4.1 still but didn't see any relevant changes on Github. Caused by: Process

NFCORE_MAG:mag:LONGREAD_PREPROCESSING:PORECHOP_ABI (SH256460017D_27-M-4-G_APW_65C_1min)

terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: porechop_abi \ --input PBK67351_pass_SH256460017D_27-M-4-G_APW_65C_1min_e3fee7f2_00000000_0.fastq.gz \ \ --threads 8 \ \ --output SH256460017D_27-M-4-G_APW_65C_1min_run0_porechop-abi_trimmed.fastq.gz \ | tee SH256460017D_27-M-4-G_APW_65C_1min_run0_porechop-abi_trimmed.log cat <-END_VERSIONS versions.yml "NFCORE_MAG🔍LONGREAD_PREPROCESSING:PORECHOP_ABI": porechop_abi: $( porechop_abi --version ) END_VERSIONS Command exit status: - Command output: (empty)

There is no reason for us to not add more tool alternatives! So you can just make an issue on the repo :). But if you check your

slurm acct

history it should tell you why the job is getting killed. The 'external system' is typically the scheduler. If you are submitting the main run command to the cluster, it could get killed if for whatever reason, but the process jobs will not automatically be killed if they themselves are running happily