Process DNAseq:cutadapt (1) terminated with an error exit status (1)

[limin321]

Hi everyone,
I am a brand-newer nextflow user. When I test my scrip, I ran into the following errors:

N E X T F L O W  ~  version 21.10.0
Launching `cutadapt.nf` [determined_saha] - revision: 0c846e6836
executor >  local (1)
[f0/33dad3] process > DNAseq:cutadapt (1) [  0%] 0 of 1
executor >  local (1)
[f0/33dad3] process > DNAseq:cutadapt (1) [100%] 1 of 1, failed: 1 ✘
Error executing process > 'DNAseq:cutadapt (1)'

Caused by:
  Process `DNAseq:cutadapt (1)` terminated with an error exit status (1)
Command executed:
  mkdir -p trimming trimming/logs 
  //cutadapt -j 1 -a GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG -A ACACTCTTTCCCTACACGACGCTCTTCCGATCT -q 20 -m 25 -O 3 -o trimming/SRR359063_1.fastq.gz -p trimming/SRR359063_2.fastq.gz SRR359063_1.fastq.gz SRR359063_2.fastq.gz > trimming/logs/SRR359063.cutadapt.log 2>&1
          cutadapt -j 1 -a GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG -A ACACTCTTTCCCTACACGACGCTCTTCCGATCT -q 20 -m 25 -O 3 -o DNAseq_cutadaptor_1.fastq -p DNAseq_cutadaptor_2.fastq /c4/home/limchen/projects/nextflow/datasets/DNAseq/SRR359063_1.fastq.gz /c4/home/limchen/projects/nextflow/datasets/DNAseq/SRR359063_2.fastq.gz > cutadapt.log 2>&1

Command exit status:
  1
Command output:
  (empty)

Here is my script.

#! /usr/bin/env nextflow

nextflow.enable.dsl=2

// pipeline parameters
params.forward = "GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG"
params.reverse = "ACACTCTTTCCCTACACGACGCTCTTCCGATCT"
params.minQual = 20
params.minLeng = 25
params.minOver = 3
params.input = "/c4/home/limchen/projects/nextflow/datasets/DNAseq"
params.extension = "fastq.gz"
params.output = "/c4/home/limchen/projects/nextflow/TestCodes/DNAseq_nf/"
params.take = "10"


read_path = "${params.input}/*{1,2}.${params.extension}"
READS = Channel.fromFilePairs(read_path)          
process cutadapt {
    publishDir "${params.output}", pattern:"trimming/*.${params.extension}", mode: 'copy', enabled:true
    publishDir "${params.output}", pattern:"trimming/logs/${sample}.cutadapt.log", mode:'move'
    
    
    input:
    tuple val(sample), path(reads)

    output:
    tuple val(sample), path("trimming/*.${params.extension}")
    path "trimming/*.${params.extension}"
    path "trimming/logs/${sample}.cutadapt.log"


    script:
        """
        mkdir -p trimming trimming/logs 
        cutadapt -j 1 -a ${params.forward} -A ${params.reverse} -q ${params.minQual} -m ${params.minLeng} -O ${params.minOver} -o trimming/${reads[0]} -p trimming/${reads[1]} ${reads} > trimming/logs/${sample}.cutadapt.log 2>&1
        """
}

workflow 'DNAseq' {
    take:
    READS

    main:
    cutadapt(READS)
}

workflow {

    main:
        DNAseq(READS)
}

Can anyone help me diagnose what went wrong in my code?
Your help is greatly appreciated.

[bentsherman]

Post is a few months old but since no one answered, I'll answer for posterity. I'm guessing your cutadapt command returned 1 exit code, but you piped stdout and stderr to cutadapt.log. You should check that file to see if it printed an error message.