Error in CUSTOM_DUMPSOFTWAREVERSIONS

[iagooteroc]

Description of the bug

I got an error in the NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS process that has to do with the versions.yml file:

[Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)` terminated with an error exit status (1)
(...)
yaml.scanner.ScannerError: mapping values are not allowed here
in "versions.yml", line 17, column 18

The content of versions.yml clearly shows a problem:

“NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN”:
    bowtie2: perl:
    samtools: samtools: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory
    pigz: pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory

Any idea what could be causing this? I'm using singularity.

Command used and terminal output

$ nextflow run nf-core/cutandrun --input ${INPUT} --fasta ${REF} --bowtie2 ${BOWTIE2} --gtf ${GTF} --normalisation_mode 'CPM' --use_control false --dedup_target_reads --igenomes_ignore --outdir ${OUTDIR} -profile singularity

Relevant files

log_and_yml.zip

System information

• Nextflow 22.10.4
• Hardware: Cluster
• Executor: slurm
• Container engine: Singularity
• OS: Rocky Linux 8.4 (Green Obsidian)
• Version of nf-core/cutandrun 3.1

[iagooteroc]

I have not encountered this problem again, so feel free to close this.

[KunFang93]

Sorry for commenting in this closed thread. I encountered the same problem. I wondered if you could shed some light on how to solve it? Thanks!

Best,
Kun