#CE8SSJV3N Hi I have 9GB fastq file This is my config file and bash script, is that normal that takes >24 hours to complete rnaseq pipeline on one sample?

#!/usr/bin/env bash

#SBATCH -J rnaseq_S1

#SBATCH -p high_mem

#SBATCH -c 4

#SBATCH --mem=16G

#SBATCH -t 24:00:00

#SBATCH -o slurm-S1-%j.out

#SBATCH -e slurm-S1-%j.err

set -euo pipefail

module purge

module load Java/17.0.6

# If your cluster has apptainer/singularity as a module, uncomment:

# module load apptainer

# Nextflow (self-bootstrap to scratch if missing)

export NXF_HOME=/parallel_scratch/$USER/.nxf

mkdir -p /parallel_scratch/$USER/bin "$NXF_HOME"

if ! command -v nextflow >/dev/null 2>&1; then

cd /parallel_scratch/$USER/bin

curl -fsSL <https://get.nextflow.io> -o nextflow

chmod +x nextflow

export PATH="/parallel_scratch/$USER/bin:$PATH"

fi

nextflow -version

# Fast caches on scratch

export APPTAINER_CACHEDIR=/parallel_scratch/$USER/apti-cache

export NXF_SINGULARITY_CACHEDIR="$APPTAINER_CACHEDIR"

export APPTAINER_TMPDIR=/parallel_scratch/$USER/nfcore/rnaseq_S1/tmp

export NXF_WORK=/parallel_scratch/$USER/nfcore/rnaseq_S1/work

export NXF_TEMP=/parallel_scratch/$USER/nfcore/rnaseq_S1/tmp

export TMPDIR="$NXF_TEMP"

mkdir -p "$APPTAINER_CACHEDIR" "$NXF_WORK" "$NXF_TEMP"

# IMPORTANT: do NOT recreate singlesample.csv here. Use the one in $PWD.

nextflow run nf-core/rnaseq -r 3.21.0 -profile singularity -resume \

--input "$PWD/singlesample.csv" \

--outdir /parallel_scratch/$USER/nfcore/rnaseq_S1/results \

-c "$PWD/nextflow.config"

and my config profiles

{

singularity {

process.executor = 'slurm'

singularity.enabled    = true

singularity.autoMounts = true

// cache location comes from env (set in sbatch)

}

}

process {

// use node-local scratch and keep work dirs on fast storage

scratch = true

// default Slurm partition for most tasks

queue  = 'shared'

errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate' }

maxRetries    = 1

// Give STAR more resources / different partition

withName: 'NFCORE_RNASEQ:ALIGN_STAR:STAR_ALIGN_IGENOMES' {

queue  = 'high_mem'

cpus   = 12

memory = '48 GB'

time   = '24h'

}

}

executor {

// be gentle with the scheduler

submitRateLimit = '8 sec'

}

params {

// ---- I/O ----

input  = "${baseDir}/singlesample.csv"

outdir = "/parallel_scratch/${System.getenv('USER')}/nfcore/rnaseq_S1/results"

// keep useful intermediates

save_trimmed   = true

save_reference = true

// ---- Reference ----

genome        = 'GRCh38'

// If you later rsync iGenomes locally, point here; nf-core will prefer it.

igenomes_base = "/parallel_scratch/${System.getenv('USER')}/ref/igenomes"

// ---- QC / trimming ----

// S007 = paired-name validator (flaky on some flowcells)

extra_fqlint_args     = "--disable-validator S007"

// Your header shows NovaSeq (A00949), so keep NextSeq/NovaSeq trimming

extra_trimgalore_args = "--illumina --stringency 3 --length 30 --trim-n --nextseq 20"

// If you want quantification-only (skip BAM), uncomment:

// aligner = 'salmon'

}

Please could you kindly give me some advice to be more efficient? Thanks a lot in advance

You almost got it right, this question is best asked in #CE8SSJV3N (it is a channel, not a tag)

Thanks a lot, my run finished successfully but I can not see any quantification output, why? I see these stuffs only

$ ls scratch/nfcore/rnaseq_034_5/results/

fastqc  fq_lint  genome  multiqc  pipeline_info  trimgalore

$ ls scratch/nfcore/rnaseq_034_5/results/genome/

genes.filtered.filtered.bed  genes.filtered.filtered.gtf  genome.fa.fai  genome.fa.sizes  genome.transcripts.fa  rsem

$ ls scratch/nfcore/rnaseq_034_5/results/genome/rsem/

genome.chrlist  genome.fa  genome.grp  genome.idx.fa  genome.n2g.idx.fa  genome.seq  genome.ti  genome.transcripts.fa

Thanks for any thought

My wisdom ends here, as I don't regularly use this pipeline. You should rephrase your question to be about the missing outputs and ask it in the #CE8SSJV3N channel, providing the command that you have run and the relevant configuration options