ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)'

Description of the bug

I am trying to download from SRA some reads for a project for my thesis. When the Fetchngs pipeline arrives at the last steps, it crashes. Download of reads is complete but it doesn't proceed.

I checked, vdb-config is present in my computer; the pipeline should be able to access it.

Command used and terminal output

nextflow run nf-core/fetchngs -resume --input workdir/sample_list.csv -profile conda --outdir workdir/reads/download

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)'                                                                                                                                          
                                                                                                                                                                                                                                                                                          
Caused by:                                                                                                                                                                                                                                                                                
  Process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)` terminated with an error exit status (1)                                                                                                                         
                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                          
Command executed [/home/juri/.nextflow/assets/nf-core/fetchngs/modules/nf-core/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh]:                                                                                                                                            
                                                                                                                                                                                                                                                                                          
  #!/usr/bin/env bash                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                          
  set -u                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                          
  # Get the expected NCBI settings path and define the environment variable                                                                                                                                                                                                               
  # `NCBI_SETTINGS`.                                                                                                                                                                                                                                                                      
  eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                          
  # If the user settings do not exist yet, create a file suitable for `prefetch`                                                                                                                                                                                                          
  # and `fasterq-dump`. If an existing settings file does not contain the required                                                                                                                                                                                                        
  # values, error out with a helpful message.                                                                                                                                                                                                                                             
  if [[ ! -f "${NCBI_SETTINGS}" ]]; then                                                                                                                                                                                                                                                  
      printf '/LIBS/GUID = "9a0fef2a-9c7c-4609-a33c-331cc9e57a16"\n/libs/cloud/report_instance_identity = "true"\n' > 'user-settings.mkfg'                                                                                                                                                
  else                                                                                                                                                                                                                                                                                    
      prefetch --help &> /dev/null                                                                                                                                                                                                                                                        
      if [[ $? = 78 ]]; then                                                                                                                                                                                                                                                              
          echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\                                                                                                                                                                                                         
          "missing the required entries for /LIBS/GUID and"\                                                                                                                                                                                                                              
          "/libs/cloud/report_instance_identity."\                                                                                                                                                                                                                                        
          "Feel free to add the following to your settings file:" >&2                                                                                                                                                                                                                     
          echo "$(printf '/LIBS/GUID = "9a0fef2a-9c7c-4609-a33c-331cc9e57a16"\n/libs/cloud/report_instance_identity = "true"\n')" >&2                                                                                                                                                     
          exit 1                                                                                                                                                                                                                                                                          
      fi                                                                                                                                                                                                                                                                                  
      fasterq-dump --help &> /dev/null                                                                                                                                                                                                                                                    
      if [[ $? = 78 ]]; then                                                                                                                                                                                                                                                              
          echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\                                                                                                                                                                                                         
          "missing the required entries for /LIBS/GUID and"\                                                                                                                                                                                                                              
          "/libs/cloud/report_instance_identity."\                                                                                                                                                                                                                                        
          "Feel free to add the following to your settings file:" >&2                                                                                                                                                                                                                     
          echo "$(printf '/LIBS/GUID = "9a0fef2a-9c7c-4609-a33c-331cc9e57a16"\n/libs/cloud/report_instance_identity = "true"\n')" >&2                                                                                                                                                     
          exit 1                                                                                                                                                                                                                                                                          
      fi                                                                                                                                                                                                                                                                                  
      if [[ "${NCBI_SETTINGS}" != *.mkfg ]]; then                                                                                                                                                                                                                                         
          echo "The detected settings '${NCBI_SETTINGS}' do not have the required"\                                                                                                                                                                                                       
          "file extension '.mkfg'." >&2                                                                                                                                                                                                                                                   
          exit 1                                                                                                                                                                                                                                                                          
      fi                                                                                                                                                                                                                                                                                  
      cp "${NCBI_SETTINGS}" ./
  fi
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS":
      sratools: $(vdb-config --version 2>&1 | grep -Eo '[0-9.]+')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: riga 8: vdb-config: comando non trovato
  .command.sh: riga 13: NCBI_SETTINGS: variabile non assegnata

Work dir:
  workdir/work/94/ec06b566312d77fc613d06fcc048d8 

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

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

Relevant files

No response

System information

No response

Start with modules/nf-core/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh and reproduce the reported command with the conda profile and -resume. Check the vdb-config, prefetch, and fasterq-dump results in the failing ncbi-settings process; done means Fetchngs proceeds past this process and downloads the reads successfully.