ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)'

[Luke-ebbis]

Description of the bug

I am trying to download the transcriptomic data for PRJNA121473. From the error message I do not understand what I can change to fix my issue.

Command used and terminal output

Launching `https://github.com/nf-core/fetchngs` [ecstatic_waddington] DSL2 - revision: 8ec2d934f9 [master]

WARN: Invalid config manifest attribute `id`
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/fetchngs v1.12.0-g8ec2d93
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Core Nextflow options
  revision        : master
  runName         : ecstatic_waddington
  containerEngine : singularity
  launchDir       : /home/sibbe/Documents/projects/oomycete-gene-conservation/transcript-presence-absence-conservation
  workDir         : /home/sibbe/Documents/projects/oomycete-gene-conservation/transcript-presence-absence-conservation/work
  projectDir      : /home/sibbe/.nextflow/assets/nf-core/fetchngs
  userName        : sibbe
  profile         : singularity
  configFiles     : 

Input/output options
  input           : /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/ids/plasmopara_viticola_INRA-PV221.identifiers.csv
  nf_core_pipeline: rnaseq
  download_method : sratools
  outdir          : /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/sequences/plasmopara_viticola_INRA-PV221

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.5070524

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (2)
[9e/7719ed] NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (PRJNA121473)                      [100%] 1 of 1 ✔
[a7/1bc8ca] NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)                                [  0%] 0 of 1
executor >  local (2)
[9e/7719ed] NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (PRJNA121473)                      [100%] 1 of 1 ✔
[a7/1bc8ca] NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)                                [  0%] 0 of 1 ✘
executor >  local (2)
[9e/7719ed] NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (PRJNA121473)                      [100%] 1 of 1 ✔
[a7/1bc8ca] NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)                                [  0%] 0 of 1 ✘
[-        ] NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP                                         -
[-        ] NFC…TQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS -
[-        ] NFC…GS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH -
[-        ] NFC…SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP -
[-        ] NFCORE_FETCHNGS:SRA:ASPERA_CLI                                            -
[-        ] NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET                                    -
[-        ] NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                               -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/fetchngs] Pipeline completed with errors-
WARN: =============================================================================
  Please double-check the samplesheet that has been auto-created by the pipeline.

  Public databases don't reliably hold information such as strandedness
  information, controls etc

  All of the sample metadata obtained from the ENA has been appended
  as additional columns to help you manually curate the samplesheet before
  running nf-core/other pipelines.
===================================================================================
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)'

Caused by:
  Missing output file(s) `*.tsv` expected by process `NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)` (note: input files are not included in the default matching set)


Command executed:

  sra_runinfo_to_ftp.py \
      PRJNA121473.runinfo.tsv \
      PRJNA121473.runinfo_ftp.tsv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  INFO:    Cleaning up image...

Work dir:
  /home/sibbe/Documents/projects/oomycete-gene-conservation/transcript-presence-absence-conservation/work/a7/1bc8caf2020933e67ea7937d4d1bdb

Container:
  /home/sibbe/Documents/projects/oomycete-gene-conservation/transcript-presence-absence-conservation/work/singularity/depot.galaxyproject.org-singularity-python-3.9--1.img

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

RuleException:
CalledProcessError in file /home/sibbe/Documents/projects/oomycete-gene-conservation/transcript-presence-absence-conservation/workflow/Snakefile, line 67:
Command 'set -euo pipefail;  
        nextflow run nf-core/fetchngs --input /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/ids/plasmopara_viticola_INRA-PV221.identifiers.csv --outdir /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/sequences/plasmopara_viticola_INRA-PV221 -profile singularity --nf_core_pipeline rnaseq --download_method sratools' returned non-zero exit status 1.
[Mon May 12 14:15:14 2025]
Error in rule download_sra:
    jobid: 3
    input: /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/ids/plasmopara_viticola_INRA-PV221.identifiers.csv
    output: /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/sequences/plasmopara_viticola_INRA-PV221
    shell:
        
        nextflow run nf-core/fetchngs --input /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/ids/plasmopara_viticola_INRA-PV221.identifiers.csv --outdir /net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/sequences/plasmopara_viticola_INRA-PV221 -profile singularity --nf_core_pipeline rnaseq --download_method sratools
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job download_sra since they might be corrupted:
/net/chaperone/linuxhome/michael-group/sibbe/results/rna-presence-absence/sequences/plasmopara_viticola_INRA-PV221
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-05-12T141503.370842.snakemake.log
WorkflowError:
At least one job did not complete successfully.

Relevant files

No response

System information

No response

[Luke-ebbis]

Is there a fix that I can implement on my end until version 1.13.0 is released?