Hello, I’m having segmentation fault issues with

fasterqdump

on a particular sample from

GSE186322

, I have retried this process several times and still get the same issue. Not sure what’s causing the problems, but it appears to be just this particular sample

SRX12725554_SRR16522901

. I have tried increasing the time and memory allocation to the

fasterqdump

process, but it still results in the same problem.

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX12725554_SRR16522901)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX12725554_SRR16522901)` 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 SRX12725554_SRR16522901 \
       \
      SRR16522901

  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:
  2025-12-22T19:53:42 fasterq-dump.2.11.0 fatal: SIGNAL - Segmentation fault
  fasterq-dump quit with error code 1

Work dir:
  /scratch/incoming/sra/GSE186332_GBM_rnaseq/work/11/ef09c44067394776ec3976158a7965

Container:
  <http://quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0|quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0>

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details