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

[gl9797]

#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'

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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~