nf-core / nf-core/fetchngs

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

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bug
Dominant language
Nextflow
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202
Forks
93
Avg merge
1d 18m
Merged PRs (30d)
15

Description

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`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  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

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO process and inspect the task logs in work/0e/e30bc8, 4e/05a8cb, a4/64a350, or dc/618409. Compare the failing command output with the Docker and retry configuration shown in the report. Done means the listed SRR metadata tasks complete without exit status 1 and downstream SRA processes begin.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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