ALIGN:short_read_alignment (10) - ERROR

Hi,

I am currently running

nextflow run matsengrp/phip-flow -r main \
        --sample_table sample_table.csv \
        --peptide_table peptide_table.csv \
        --read_length 189 \
        --oligo_tile_length 189 \
        --output_tall_csv true \
        --output_wide_csv true \
        --results "$(date -I)" \
        -profile docker

and I am getting the following error

executor >  local (29)
[01/9a1585] process > ALIGN:validate_sample_table (1)                        [100%] 1 of 1 ✔
[5d/c9e72c] process > ALIGN:validate_peptide_table (1)                       [100%] 1 of 1 ✔
[c7/a14c72] process > ALIGN:generate_fasta_reference (1)                     [100%] 1 of 1 ✔
[9b/051e5f] process > ALIGN:generate_index (1)                               [100%] 1 of 1 ✔
[df/5f63eb] process > ALIGN:short_read_alignment (12)                        [ 12%] 1 of 8, failed: 1

  set -euo pipefail

  STREAM_FILE_CMD=zcat
  FASTQ=D152-YO-PCD-BREAST_S16_L001_R1_001.fastq
  INDEX=peptide_index/peptide
  ALIGN_OUT_FN=9.sam
  READ_LENGTH=189
  PEPTIDE_LENGTH=117
  CPUS=1
  MM=2
  OP_ARGS="--tryhard --nomaqround --norc --best --sam --quiet"

  if [ ${PEPTIDE_LENGTH} -lt ${READ_LENGTH} ]; then
      let TRIM3=${READ_LENGTH}-${PEPTIDE_LENGTH}
  else
      TRIM3=0
  fi

  echo $OP_ARGS

  $STREAM_FILE_CMD $FASTQ | bowtie \
    --trim3 $TRIM3 \
    --threads $CPUS \
    -n $MM \
    -l $PEPTIDE_LENGTH \
    $OP_ARGS \
    -x $INDEX - > $ALIGN_OUT_FN

Command exit status:
  1

Command error:
  --tryhard --nomaqround --norc --best --sam --quiet
  gzip: D152-YO-PCD-BREAST_S16_L001_R1_001.fastq.gz: No such file or directory
  Error: reads file does not look like a FASTQ file
  Command: /bowtie-1.3.1-linux-x86_64/bowtie-align-s --wrapper basic-0 --trim3 72 --threads 1 -n 2 -l 117 --tryhard --nomaqround --norc --best --sam --quiet -x peptide_index/peptide -

I already verified that the files "missing" are present in the directory

What could I change to make it work? Thanks!

matsengrp / phip-flow

ALIGN:short_read_alignment (10) - ERROR #72