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Skill 02 · Nextflow Development
Subchapter 2.6
references/troubleshooting.mdMarkdown3 KBView on GitHub
Quick fixes for common nf-core pipeline issues.
Common exit codes indicating resource issues (per nf-core docs (opens in a new tab)):
| Code | Cause | Fix |
|---|---|---|
| 137 | Out of memory | --max_memory '32.GB' or '64.GB' for WGS |
| 143 | Out of memory | --max_memory '32.GB' or '64.GB' for WGS |
| 104, 134, 139, 247 | Out of memory | Increase --max_memory |
| 1 | General error | Check .nextflow.log for details |
Most pipelines auto-retry with 2x then 3x resources before failing.
export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"
mkdir -p $NXF_SINGULARITY_CACHEDIROn HPC systems without Docker, use Singularity:
nextflow run nf-core/<pipeline> -profile singularity ...Note: For basic environment setup (Docker, Nextflow, Java installation), see the inline instructions in Step 1 of SKILL.md.
-profile singularity instead of dockernf-core download <pipeline> -r <version>ls /path/to/file# Check work directory exists
ls -la work/
# Force clean restart (loses cache)
rm -rf work/ .nextflow*
nextflow run nf-core/<pipeline> ...--max_memory '64.GB'--star_index /path/to/star/--aligner hisat2--strandedness reverseforward, reverse, unstranded--skip_bqsrstatus column: 0=normal, 1=tumor--max_memory '128.GB' --max_cpus 16plotFingerprint/--macs_qvalue 0.1--narrow_peak false--max_cpus 8 --max_memory '32.GB' --max_time '24.h'# CPUs
nproc
# Memory
free -h
# Disk
df -h ..nextflow.log for error details