good news

All good on my side, reads downloaded, ready to fire up the rnaseq pipeline

Hello! I've been having trouble getting fetchngs to complete today. When using the

apptainer

profile the full error message reads:

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

Caused by:
  Cannot invoke "nextflow.util.Duration.toMillis()" because "this.pullTimeout" is null

The pipeline doesn't appear to get far enough to generate any files in a work directory but I found the following line in the

.nextflow.log

file:

Caused by: java.lang.NullPointerException: Cannot invoke "nextflow.util.Duration.toMillis()" because "this.pullTimeout" is null

I'm not sure if this issue is related to apptainer or fetchngs, but any guidance would be appreciated!

Hi all, Even if I do not have a lot of experience in the nf-core community I will be joining the hackathon at the end of October. I submitted a proposal to work on improving scrnaseq support in fetchngs. If anyone else is interested I believe that by the end of the hackathon we could have a decent pull request, or at least a good draft. Additionally, if anyone with more experience in this pipeline was willing to lead this proposal I’d happy to take a supporting role, no egos on my end :-) https://nfcore.slack.com/archives/C09ADKQ2CHZ/p1760465890442459 Thanks for your attention and looking forward to meeting you!

Hej everyone, I am a newbie in the nextflow space currently attending the virtual summit. I hope many of you are in 🙂. I just had an idea, that it would be a lot of fun to integrate the European Genome-Phenome Archive to fetchngs.

You have to request access for ethical reasons and then you go through the steps listed in "download data" on https://ega-archive.org/

Is it possible to fetch data from GEO that is still private? If you have access to the data via your account or a reviewer access token.

Hi, does fetchngs always check ENA rather than NCBI SRA? is there a way to redirect it? i have an SRR id (SRR32812291) that is available on ncbi but not ena (i know it can take a few days to synchronise, but the dataset was released on 24-10-2025, and some SRRs are available, others are not). Currently using nextflow v25.04.8 and fetchngs v1.12.0 as i have been having problems with singularity/apptainer pulls with the more recent versions (nextflow 25.10.0 and fetchngs dev version), even with the test data.

Hello, I’m having segmentation fault issues with

fasterqdump

on a particular sample from

GSE186322

, I have retried this process several times and still get the same issue. Not sure what’s causing the problems, but it appears to be just this particular sample

SRX12725554_SRR16522901

. I have tried increasing the time and memory allocation to the

fasterqdump

process, but it still results in the same problem.

ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX12725554_SRR16522901)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX12725554_SRR16522901)` terminated with an error exit status (1)


Command executed:

  export NCBI_SETTINGS="$PWD/user-settings.mkfg"

  fasterq-dump \
      --split-files --include-technical \
      --threads 6 \
      --outfile SRX12725554_SRR16522901 \
       \
      SRR16522901

  pigz \
       \
      --no-name \
      --processes 6 \
      *.fastq

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
      sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  2025-12-22T19:53:42 fasterq-dump.2.11.0 fatal: SIGNAL - Segmentation fault
  fasterq-dump quit with error code 1

Work dir:
  /scratch/incoming/sra/GSE186332_GBM_rnaseq/work/11/ef09c44067394776ec3976158a7965

Container:
  <http://quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0|quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0>

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

how can I fix the below error?

export NCBI_SETTINGS="$PWD/user-settings.mkfg"
  
  retry_with_backoff 5 1 100 \
      prefetch \
       \
      SRR35463766
  
  [ -f SRR35463766.sralite ] && vdb-validate SRR35463766.sralite || vdb-validate SRR35463766
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH":
      sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
  END_VERSIONS

Command exit status:
  0

Command output:
  
  
  Download of some files was skipped because they are too large
  You can change size download limit by setting
  --min-size and --max-size command line arguments


Command error:
  WARNING: Not virtualizing pid namespace by configuration
  2026-01-15T20:17:43 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
  2026-01-15T20:17:43 prefetch.3.0.8 warn: Maximum file size download limit is 20GB 
  2026-01-15T20:17:43 prefetch.3.0.8: 1) 'SRR35463766' (26GB) is larger than maximum allowed: skipped 
  2026-01-15T20:17:43 vdb-validate.3.0.8 info: 'SRR35463766' could not be found
  ls: cannot access 'SRR35463766': No such file or directory

I am doing the template update right now. I was just wondering whether there is a reason behind the file structure in workflows? If not, I would suggest to include the code in workflows/sra/main.nf directly in workflows/fetchngs.nf.

Hello, I'm trying to run fetchngs for the first time but both my custom accessions and the test profile seem to not progress at all at the SRA_IDS_TO_RUNINFO stage. Is this an ENA API endpoint issue?

I am running

nextflow run nf-core/fetchngs --input SRR_Acc_List.txt -resume -profile biowulf --outdir na_rna_fastq

but I am getting the following error: How Do I fix this?

!! 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>
------------------------------------------------------
WARN: The following invalid input values have been detected:

* --igenomes_base: /fdb/igenomes_nf/


ERROR ~ Could not derive file type from /asm/t2tMap/bam_fixed_rg/SRR_Acc_List.txt. Please specify the file extension (CSV, TSV, YML and YAML are supported).

 -- Check script '/data/okendojo/.nextflow/25.10.0/assets/nf-core/fetchngs/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf' at line: 57 or see '.nextflow.log' file for more details

I have a researcher trying to download using info from here: https://nf-co.re/fetchngs/1.12.0/docs/usage/ I'm a firewall engineer and we've had to block web downloads because our instiutions IP gets block by NIH for too many hits. I would like to educate users how to use FTP or other ways other than web downloads via a script. Can anyone help me with FTP URLs or IPs that I can allow on the firewall? Many thanks, this has been an issue for years

I'm seeing odd behaviour when running fetchngs in combination with my institutional config file. Somehow, some of the config params are being recognised as pipeline params, and this causes fetchngs to stop:

WARN: The following invalid input values have been detected:

* --vsc_calcua_scratchdir: /scratch/antwerpen/203/vsc20380
* --vsc_calcua_apptainer_tmpdir: /scratch/antwerpen/203/vsc20380/apptainer/tmp
* --vsc_calcua_apptainer_cachedir: /scratch/antwerpen/203/vsc20380/apptainer/cache
* --vsc_calcua_nxf_apptainer_cachedir: /scratch/antwerpen/203/vsc20380/apptainer/nextflow_cache
* --vsc_calcua_partition: zen2
* --vsc_calcua_slurm_scheduling: true

This is the config in question: https://nf-co.re/configs/vsc_calcua/ Oddly enough, I don't see this problem in my own pipeline nor for nf-core/rnaseq. I'm using

NXF_SYNTAX_PARSER=v1 NXF_VER=26.04.4

. Any ideas?

I'm trying to use fetchngs in part of a reproducibility refactor, and I'm encountering issues with just retrieving the data through fetchngs. There are around 3000 accessions, and most come back with information from the SRA however there are some that come back without it. The SRA_IDS_TO_RUNINFO succeeds, but the tsv only has the header line, and then when it gets to SRA_RUNINFO_TO_FTP it errors because the 2nd tsv file isn't written out even though the python script "succeeds". Checking these accessions, there is information in both ENA and SRA on them, but the pipeline isn't populating the runinfo.tsv. What action should I take?

@Cameron Lloyd @Mahesh Binzer-Panchal @Evangelos Karatzas I know all of us have a shared interest into having a release soon. I do think we are close, for me the only real blocker is https://github.com/nf-core/fetchngs/pull/387, which is currently under review. About to merge the subway map update PR from Cameron. And I think we are real close to this release. Please shout out if you think I missed anything. Anyone else is free to join in on the fun as well.

small follow-up PR

Are we updating github.com/nf-core/fetchngs/tree/dev#… now that there are more pipelines

I'd also like to get github.com/nf-core/modules/pull/12909 merged and update the

fastq-dl

module in the pipeline before release if possible (I cross-posted in request-review)

I added a changelog entry in github.com/nf-core/fetchngs/pull/389

I decided to update the docs: github.com/nf-core/fetchngs/pull/391

@Maxime Garcia do you have a dark-mode fetchngs logo?

✅ fetchngs/test_full completed successfully! 🎉 Run Name chaotic_lichterman Duration 21m 22s Status ✅ Success Tasks Completed: 25 Sep 11, 2026 at 9:23 AM

✅ fetchngs/test_full completed successfully! 🎉 Run Name curious_hamilton Duration 39m 3s Status ✅ Success Tasks Completed: 25, Failed: 1 Sep 14, 2026 at 2:06 PM

We have a release 🚀 https://github.com/nf-core/fetchngs/releases/tag/1.13.0 I know the last one was 2 years ago, so this one was most likely awaited by many people. TL,DR 🤔 • If your HPC compute nodes lack outbound internet,

--download_method aspera

will fail. Switch to

ftp

,

sratools

, or

fastq-dl

. • No changes to input/output schemas or parameter defaults. Existing workflows run without modification. We have new pipelines: 🧰 fetchngs now generates samplesheets for ampliseq, mag, metatdenovo, and sarek, alongside the existing atcseq, rnaseq, taxprofiler, and viralrecon support. new download method: fastq-dl 🚄 Aspera was updated, resulting in some fixes, and some breaking changes 🌩️ • The

ascp

binary is no longer bundled. So use

ftp

,

sratools

, or

fastq-dl

if it fails instead. • DSA deprecation was handled More fixes 🐛💥🔨 •

wget

container updated to 1.25.0, fixing DNS resolution failures •

sratools/prefetch

updated for reliable download integrity checks •

multiqc_mappings_config

fixed stray quote and comma handling in CSV parsing •

sra_fastq_ftp

stub blocks now work (gzip was missing from conda environment) • ENA metadata fields with spaces no longer cause word-splitting errors Thanks 🙏🙇 @Adam Talbot, @Adrian Janucik, @Cameron Lloyd, @Maxime Borry, @Sebastian Uhrig, @Tabea Attig, @Venkat Malladi, @Evangelos Karatzas

✅ fetchngs/test_full completed successfully! 🎉 Run Name shrivelled_jepsen Duration 22m 28s Status ✅ Success Tasks Completed: 25 Sep 15, 2026 at 8:42 AM

filed this issue:github.com/nf-core/fetchngs/issues/401 the group column for the mag samplesheet cannot be empty

similar to this detaxizer issue: github.com/nf-core/detaxizer/issues/100

Hello all -- would it be worth adding support for https/ftp protocol switching in the pipeline? I note

fastq-dl

already supports this via

--protocol

although it isn't exposed in the pipeline parameters. We're having recurring issues with ftp on our system, so an https option would be very appreciated. happy to draft a PR for this if it sounds sensible. Thanks!