Error executing process > 'DAQ_UMI:FASTP (52944-ND01001_2;L004)'

Caused by:
  Missing output file(s) `52944-ND01001_2/*` expected by process `DAQ_UMI:FASTP (52944-ND01001_2;L004)`


Command executed:

  mkdir -p 52944-ND01001_2
  
  # Determine whether to split based on params.split_fastq and file size
  if [ "true" == "false" ]; then
      split_args=""
  else
      file_size=$(stat -f%z 52944-ND01001_2_S15_R1_001.fastq.gz 2>/dev/null || stat -c%s 52944-ND01001_2_S15_R1_001.fastq.gz)
      if [ 8880000000 -gt 0 ] && [ $file_size -lt 8880000000 ]; then
          split_args=""
      else
          split_args="--split_by_lines 400000000"
      fi
  fi
  
  fastp \
      --in1 52944-ND01001_2_S15_R1_001.fastq.gz \
      --in2 52944-ND01001_2_S15_R2_001.fastq.gz \
      --out1 52944-ND01001_2/52944-ND01001_2_R1.fastq.gz \
      --out2 52944-ND01001_2/52944-ND01001_2_R2.fastq.gz \
      --detect_adapter_for_pe \
      --length_required 15 \
      --umi --umi_loc per_read --umi_len 6 \
      --json 52944-ND01001_2.fastp.json \
      --html 52944-ND01001_2.fastp.html \
      --thread 4 \
      $split_args \
      2> >(tee 52944-ND01001_2.fastp.log >&2)
  
  # Remove empty files created by fastp edge case (when reads/chunk_size == threads)
  find 52944-ND01001_2 -name "*.fastq.gz" -size 0 -delete
  
  fastp_version=$(fastp --version 2>&1 | sed 's/fastp //')
  
  cat <<-END_VERSIONS > versions.yml
  "DAQ_UMI:FASTP":
      fastp: $fastp_version
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
  
  Detecting adapter sequence for read2...
  No adapter detected for read2
  
  Read1 before filtering:
  total reads: 0
  total bases: 0
  Q20 bases: 0(-nan%)
  Q30 bases: 0(-nan%)
  Q40 bases: 0(-nan%)
  
  Read2 before filtering:
  total reads: 0
  total bases: 0
  Q20 bases: 0(-nan%)
  Q30 bases: 0(-nan%)
  Q40 bases: 0(-nan%)
  
  Read1 after filtering:
  total reads: 0
  total bases: 0
  Q20 bases: 0(-nan%)
  Q30 bases: 0(-nan%)
  Q40 bases: 0(-nan%)
  
  Read2 after filtering:
  total reads: 0
  total bases: 0
  Q20 bases: 0(-nan%)
  Q30 bases: 0(-nan%)
  Q40 bases: 0(-nan%)
  
  Filtering result:
  reads passed filter: 0
  reads failed due to low quality: 0
  reads failed due to too many N: 0
  reads failed due to too short: 0
  reads with adapter trimmed: 0
  bases trimmed due to adapters: 0
  
  Duplication rate: 0%
  
  Insert size peak (evaluated by paired-end reads): 0
  
  JSON report: 52944-ND01001_2.fastp.json
  HTML report: 52944-ND01001_2.fastp.html
  
  fastp --in1 52944-ND01001_2_S15_R1_001.fastq.gz --in2 52944-ND01001_2_S15_R2_001.fastq.gz --out1 52944-ND01001_2/52944-ND01001_2_R1.fastq.gz --out2 52944-ND01001_2/52944-ND01001_2_R2.fastq.gz --detect_adapter_for_pe --length_required 15 --umi --umi_loc per_read --umi_len 6 --json 52944-ND01001_2.fastp.json --html 52944-ND01001_2.fastp.html --thread 4 
  fastp v1.0.1, time used: 0 seconds
  ls: cannot access '52944-ND01001_2/*': No such file or directory

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/323a3283d175fdd6cd22e5e159db1c

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/fastp_split:1.0.1

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