Fetchngs fails with error: terminated with an error exit status (1) -- Execution is retried (1)

[kanekalla]

Description of the bug

I am trying to download metadata associated with a bunch of SRR ids and the fetchngs flow is failing. The code I am using is nextflow run nf-core/fetchngs
-c samples_fetchngs_20250319.config
-profile docker
-r 1.12.0
--skip_fastq_download
--nf_core_pipeline 'rnaseq'
--input gse_accession_20250316_list.csv

My config file is // fetchngs_20250319.config

params { input = 'gse_accession_20250316_list.csv' outdir = '/home/kra/scratch/nf_test/samples_20250316_fetchngs' }

// Docker configuration docker { enabled = true removeContainer = true runOptions = '--network host --dns 8.8.8.8 --dns 8.8.4.4' // Consolidated Docker options }

// Global process config process { cpus = 1 memory = 4.GB time = 4.hour

// Process-specific configurations
withName: 'NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO' {
    maxRetries = 2
    errorStrategy = { task.attempt <= 2 ? 'retry' : 'ignore' }
    memory = { 2.GB * task.attempt }
    time = { 1.hour * task.attempt }
    // Removed containerOptions to avoid duplicate network host
}

withLabel: 'error_retry' {
    errorStrategy = { task.attempt <= 2 ? 'retry' : 'ignore' }
    maxRetries = 2
    memory = { 2.GB * task.attempt }
    time = { 30.min * task.attempt }
}

}

// Trace configuration trace { enabled = true file = "${params.outdir}/pipeline_trace.txt" fields = 'task_i

Command used and terminal output

tput: /scratch/micromamba/envs/geo_access/lib/libtinfo.so.6: version `NCURSES6_TINFO_6.2.current' not found (required by tput)
tput: /scratch/micromamba/envs/geo_access/lib/libtinfo.so.6: version `NCURSES6_TINFO_6.2.current' not found (required by tput)
tput: /scratch/micromamba/envs/geo_access/lib/libtinfo.so.6: version `NCURSES6_TINFO_6.2.current' not found (required by tput)
tput: /scratch/micromamba/envs/geo_access/lib/libtinfo.so.6: version `NCURSES6_TINFO_6.2.current' not found (required by tput)
tput: /scratch/micromamba/envs/geo_access/lib/libtinfo.so.6: version `NCURSES6_TINFO_6.2.current' not found (required by tput)
curl: /scratch/micromamba/envs/geo_access/lib/libcurl.so.4: no version information available (required by curl)

 N E X T F L O W   ~  version 24.10.5

Launching `https://github.com/nf-core/fetchngs` [nasty_kalman] DSL2 - revision: 8ec2d934f9 [1.12.0]

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
------------------------------------------------------
Core Nextflow options
  revision           : 1.12.0
  runName            : nasty_kalman
  containerEngine    : docker
  launchDir          : /home/kra/scratch/nf_test
  workDir            : /home/kra/scratch/nf_test/work
  projectDir         : /home/kra/.nextflow/assets/nf-core/fetchngs
  userName           : kra
  profile            : docker
  configFiles        :

Input/output options
  input              : gse_accession_20250316_list.csv
  nf_core_pipeline   : rnaseq
  skip_fastq_download: true
  outdir             : /home/kishore_anekalla/scratch/nf_test/test_dir

!! 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 (121)
[0e/e30bc8] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR11582363) [  3%] 57 of 1729, failed: 57, retries: 57
executor >  local (122)
[4e/05a8cb] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR11582367) [  3%] 58 of 1730, failed: 58, retries: 58
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP               -
executor >  local (123)
[a4/64a350] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR11582366) [  3%] 59 of 1731, failed: 59, retries: 59
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP               -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET               -
executor >  local (126)
[dc/618409] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR11582370) [  3%] 62 of 1734, failed: 62, retries: 62
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP               -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET               -
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG          -
[fd/382dc5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR10597091)` terminated with an error exit status (1) -- Execution is retried (1)
[0c/9827b7] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR10669477)` terminated with an error exit status (1) -- Execution is retried (1)
executor >  local (127)

Relevant files

No response

System information

No response

[Zhenghongc]

I’ve encountered the same issue, and I think the most likely cause is a network connection problem. You might want to check your connection to the server — sometimes just trying a few more times helps.