Error while running nf-core/rnaseq pipeline

Question

[eesha28112001]

Hello guys!

I am trying to run the nf-core/rnaseq pipeline with the following parameters:

nextflow run nf-core/rnaseq 
-r 3.10.1 
--input samplesheet.csv 
--outdir output 
--fasta chr22_with_ERCC92.fa 
-profile docker 
--gtf chr22_with_ERCC92.gtf
--max_memory 200GB 

I keep getting a persistent error:

---

WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (chr22_with_ERCC92.fa)'

Caused by:
  Process requirement exceeds available memory -- req: 6 GB; avail: 3.7 GB

Command executed:

  samtools faidx chr22_with_ERCC92.fa
  cut -f 1,2 chr22_with_ERCC92.fa.fai > chr22_with_ERCC92.fa.sizes

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES":
      getchromsizes: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /home/eesha/work/b1/58aad9a09e425462cf3a7c9148c114

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`

 -- Check '.nextflow.log' file for details
ERROR ~ Unexpected error [ClosedByInterruptException]

 -- Check '.nextflow.log' file for details
-[nf-core/rnaseq] Pipeline completed with errors-

---

What could be the workaround for this?

Answer 1

[Maxime Garcia]

Hi, Given the Process requirement exceeds available memory -- req: 6 GB; avail: 3.7 GB error, I would advise using --max_memory 3.7.GB when launching your pipeline. You seem to have asked for more memory than what was available. The --max_* resources params on nf-core are just a limit to ensure that Nextflow is never asking more than what you have available.

[eesha28112001]

Got this after assigning --max_memory 3.7GB and --max_cpus 4:

---

ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (chr22_with_ERCC92.fa)'

Caused by: Process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (chr22_with_ERCC92.fa) terminated with an error exit status (127)

Command executed:

filter_gtf_for_genes_in_genome.py \ --gtf chr22_with_ERCC92.gtf \ --fasta chr22_with_ERCC92.fa \ -o chr22_with_ERCC92_genes.gtf

cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER": python: $(python --version | sed 's/Python //g') END_VERSIONS

Command exit status: 127

Command output: (empty)

Command error: .command.run: line 293: docker: command not found

Work dir: /home/eesha/work/b7/a5ea589e1cc24348816fcff1e9a7bd

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

-- Check '.nextflow.log' file for details

[Maxime Garcia]

Given the docker: command not found I'd say that docker is not installed on your system. I'd check https://nf-co.re/docs/usage/introduction and https://nf-co.re/docs/usage/installation