ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)' #346
Description
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 !!
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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
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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