bwa: command not found

[xnr13]

Execution cancelled -- Finishing pending tasks before exit Error executing process > 'BWA_INDEX (genome.fasta)'

Caused by: Process BWA_INDEX (genome.fasta) terminated with an error exit status (127)

Command executed:

bwa index -a bwtsw genome.fasta mkdir BWAIndex && mv genome.fasta* BWAIndex

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 2: bwa: command not found

Work dir: /media/ATACseq_nf-core_atacseq/work/61/60251f1c01ef5bdc9f5c81c5cdcc95

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

[xnr13]

nextflow run nf-core/atacseq \
-resume \
--input samplesheet.csv \
--fasta references/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fasta \
--gtf references/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes_custom_annotation.gtf \
--macs_gsize hs \
--outdir resultsDir \
-profile singularity \
--max_cpus 8 \
-r 1.2.2 \

[ewels]

Please post the full Nextflow log, not just the error message. It sounds like something isn't working with the singularity setup for you.

[drpatelh]

Hi @jianxinwang ! Thanks for reporting! We are about to release a much updated version of the pipeline that has been completely refactored to be written in Nextflow DSL2. When this is released, it would be great if you can let us know if the problem still persists and attach the requested files. I will close this issue for now.

This doesn't sound like a pipeline issue so it may be better to get faster, real-time help for these sorts of things in the #atacseq channel on the nf-core Slack workspace. You can join via the link below: https://nf-co.re/join

[xnr13]

I fixed it in the meantime by adding this to nextflow.config:

singularity {
    runOptions = '--env PYTHONPATH="/opt/conda/envs/nf-core-atacseq-1.2.2/lib/python3.7/site-packages/" --env PREPEND_PATH="/opt/conda/envs/nf-core-atacseq-1.2.2/bin/"'
}

Problem does not occur in DSL2 branch it seems, same setup otherwise.