Fetchngs fails with error: terminated with an error exit status (1) -- Execution is retried (1)
bug
### 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
```console
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_
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