SRATOOLS_FASTERQDUMP failing due to missing fastq file

Description of the bug

I have a list of SRR IDs in a file and am trying to download them using the pipeline. However, I constantly get an error at the SRATOOLS_FASTERQDUMP step.

This is an example of a failing .command.sh

#!/bin/bash -euo pipefail
export NCBI_SETTINGS="$PWD/user-settings.mkfg"

fasterq-dump \
    --split-files --include-technical \
    --threads 6 \
    --outfile SRX12493307_SRR16208975 \
     \
    SRR16208975

pigz \
     \
    --no-name \
    --processes 6 \
    *.fastq

cat <<-END_VERSIONS > versions.yml
"NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
    sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
    pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS

From the log, it seems that no fastq files are found in the folder when attempting to run pigz after faster-dump. Inspecting the working folder, I can see a file named SRX12493307_SRR16208975, which contains reads but has no .fastq extension, and thus, the Pigz command fails.

Command used and terminal output

Command used:


nextflow run nf-core/fetchngs --input SRP340133_accessions.csv --outdir ./SRP340133 -profile conda,ht_cpu -c /ssu/gassu/small_bits/fht_profile.config -c custom.conf

Here, custom.conf is used to set --max-size 50g since some of the datasets are larger than 20Gb.

This is the error message from Nextflow.

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX12493307_SRR162089
75)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX12493307_SRR16208975)` terminated with an
error exit status (1)


Command executed:

  export NCBI_SETTINGS="$PWD/user-settings.mkfg"

  fasterq-dump \
      --split-files --include-technical \
      --threads 6 \
      --outfile SRX12493307_SRR16208975 \
       \
      SRR16208975

  pigz \
       \
      --no-name \
      --processes 6 \
      *.fastq

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
      sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  spots read      : 117,423,804
  reads read      : 117,423,804
  reads written   : 117,423,804
  pigz: skipping: *.fastq does not exist

### Relevant files

_No response_

### System information

Nextflow: 24.04.2
Hardware: HPC
Executor: Slurm
Container engine: Conda
Pipeline version: 1.12

Start by inspecting the SRATOOLS_FASTERQDUMP process that generates the shown .command.sh, focusing on the fasterq-dump --outfile output and the subsequent pigz *.fastq input. Reproduce the command with SRR16208975 and compare the produced filename with pigz's expected files. Done means the process successfully compresses the generated FASTQ output for this case.