Process `get_software_versions` terminated with an error exit status （1）

#command and err

1. Command line: nextflow run nf-core/clipseq -profile conda
   --input /home/gl/nfclip/bp.txt
   --fasta /mnt/d/f/X101SC21113826-Z01-F001/Genomes/genome.fa.gz
   --genome mm10
   --max_memory '6.GB'

---

2.error:Error executing process > 'get_software_versions'

Caused by:
Process get_software_versions terminated with an error exit status (1)

Command executed:

echo 1.0.0 > v_pipeline.txt
echo 22.10.1 > v_nextflow.txt
fastqc --version > v_fastqc.txt
multiqc --version > v_multiqc.txt
cutadapt --version > v_cutadapt.txt
bowtie2 --version > v_bowtie2.txt
STAR --version > v_star.txt
samtools --version > v_samtools.txt
umi_tools --version > v_umi_tools.txt
bedtools --version > v_bedtools.txt
preseq 2> v_preseq.txt
subread-align -v 2> v_subread.txt
executor > local (2)
[db/361bc7] process > get_software_versions [100%] 1 of 1, failed:1✘
[19/7c4198] process > generate_premap_index (Mus_musculus.smallRNA.fa.gz) [100%] 1 of 1, cached:1✔
[92/12947a] process > decompress_fasta (genome.fa.gz) [100%] 1 of 1, cached:1✔
[- ] process > generate_fai [ 0%] 0 of 1
[81/f04847] process > fastqc (BP_input_1) [100%] 4 of 4, cached: 4 ✔
[8c/e9761e] process > cutadapt (BP_input_2) [100%] 4 of 4, cached: 4 ✔
[- ] process > premap [ 0%] 0 of 4
[- ] process > align -
[- ] process > preseq -
[- ] process > dedup -
[- ] process > rseqc -
[- ] process > get_crosslinks -
[- ] process > clipqc -
[- ] process > multiqc -
[46/85cdc1] process > output_documentation [ 0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'

Caused by:
Process get_software_versions terminated with an error exit status (1)

Command executed:

echo 1.0.0 > v_pipeline.txt
echo 22.10.1 > v_nextflow.txt
fastqc --version > v_fastqc.txt
multiqc --version > v_multiqc.txt
cutadapt --version > v_cutadapt.txt
bowtie2 --version > v_bowtie2.txt
STAR --version > v_star.txt
samtools --version > v_samtools.txt
umi_tools --version > v_umi_tools.txt
bedtools --version > v_bedtools.txt
preseq 2> v_preseq.txt
subread-align -v 2> v_subread.txt
bam2fq.py --version > v_rseqc.txt
iCount --version > v_icount.txt
pureclip --version > v_pureclip.txt
Piranha -about 2> v_piranha.txt
echo "9" > v_paraclu.txt # Paraclu does not output a version
meme -version > v_meme.txt
python --version > v_python.txt
pygmentize -V > v_pygments.txt
pigz --version 2> v_pigz.txt
perl -v > v_perl.txt

scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
1

Command output:
pigz 2.6

Command error:
pigz 2.6

Work dir:
/home/gl/work/db/361bc7d9ad5b1f200ce141bc565c50

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

Genome reference gtf not found: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf

Expected behaviour

work/db/361bc7d9ad5b1f200ce141bc565c50/ v_pigz.txt=null It should be printed pigz 2.6 as Command error mentioned, but it was null. And rest of these version-files are all printed correctly.

Log files

echo 1.0.0 > v_pipeline.txt
echo 22.10.1 > v_nextflow.txt
fastqc --version > v_fastqc.txt
multiqc --version > v_multiqc.txt
cutadapt --version > v_cutadapt.txt
bowtie2 --version > v_bowtie2.txt
STAR --version > v_star.txt
samtools --version > v_samtools.txt
umi_tools --version > v_umi_tools.txt
bedtools --version > v_bedtools.txt
preseq 2> v_preseq.txt
subread-align -v 2> v_subread.txt
bam2fq.py --version > v_rseqc.txt
iCount --version > v_icount.txt
pureclip --version > v_pureclip.txt
Piranha -about 2> v_piranha.txt
echo "9" > v_paraclu.txt # Paraclu does not output a version
meme -version > v_meme.txt
python --version > v_python.txt
pygmentize -V > v_pygments.txt
pigz --version 2> v_pigz.txt
perl -v > v_perl.txt

scrape_software_versions.py &> software_versions_mqc.yaml

System

WSL2
ubuntu 22.04

Nextflow Installation

N E X T F L O W
version 22.10.1 build 5828
created 27-10-2022 16:58 UTC (28-10-2022 00:58 CDT)
cite doi:10.1038/nbt.3820
http://nextflow.io

• Version:

Container engine

• Engine: conda
• version: conda 22.9.0
• Image tag: nf-core/clipseq v1.0.0

Additional context

I've tried many methods about error exit status 1 and that don't work. Is it a written permisson issue? Thx so much~

Start with the get_software_versions process and the mentioned scrape_software_versions.py entry point, then reproduce the supplied Nextflow command in the reported work directory. Check why pigz --version produces v_pigz.txt=null despite the reported output; done means the process exits successfully and records pigz 2.6, while the separate missing GTF message remains accounted for.