I am using the latest release -r 1.0.1

@Joon Klaps Thanks for developing this pipeline! I am trying to use this pipeline and I have some questions. 1. I tried running it on aquatic viral metagenomes, and I followed your suggestion earlier on Github to use mmSeqs instead of cdhit for clustering and it worked. However, when it came to

extract_cluster.py

, it couldn’t finish running the script with the 2-day period I assigned. I assume it was because there were too many clusters. Do you have a suggestion to solve it? 2. I also used your pipeline to assemble isolates, since in this case I only have concentrated DNA of one/two distinct isolates in one well, considering them as a metagenome will yield one/two circular whole genomes with high coverage, and some short fragments with very low coverage. The isolate assemblies were satisfactory for me (--skip_read_classification --skip_polishing), but I don’t know so much about the details of the pipeline. Do you think the work-frame of your pipeline suits this usage?

Is there any way to force the pipeline to use pre-downloaded files and function mostly offline?

I added a dev branch back. not sure how it disappeared tbh

Hi I am facing this error

ERROR ~ Error executing process > 'NFCORE_VIRALMETAGENOME:VIRALMETAGENOME:FASTA_CONTIG_CLUST:FASTA_FASTQ_CLUST:CDHIT_CDHITEST (sample2_taxid0)'

Caused by:
  Process exceeded running time limit (8h)

Command executed:

  cd-hit-est \
      -d 50 -c 0.85 -mask rRyYkKsSwWmMbBdDhHvVnN \
      -i sample2_taxid0.fa \
      -o sample2_taxid0_cdhit.fa \
      -M 29491 \
      -T 6
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_VIRALMETAGENOME:VIRALMETAGENOME:FASTA_CONTIG_CLUST:FASTA_FASTQ_CLUST:CDHIT_CDHITEST":
      cdhit: $(cd-hit-est -h | head -n 1 | sed 's/^.*====== CD-HIT version //;s/ (built on .*) ======//' )
  END_VERSIONS

Is it normal for the cd-hit-est to run out of running time? how could I config a longer time if this is normal?

Is there a way to configure viralmetagenome to use a pre-built BLAST database? We are interested in using the pipeline with our local version of BLASTN.

CONGRATS @Joon Klaps!!!

Quick question about Bracken. I noticed it's mentioned under 3. Metagenomic diversity mapping in the Introduction page, but no where else. I don't see any output from my run either. I guess it is either depreciated or aspirational? If I want to run it manually from the Kraken2 output, where is the Kraken2 DB to specify? https://github.com/jenniferlu717/Bracken# Thanks in advance!

set the channel description: Everything you need for eukaryotic virus genome reconstruction. Read more about the pipeline in it’s [publication](https://doi.org/10.1093/bioinformatics/btag187) or the [docs](https://nf-co.re/viralmetagenome/)

set the channel description: Everything you need for eukaryotic virus genome reconstruction. Read more about the pipeline in it’s publication (https://doi.org/10.1093/bioinformatics/btag187) or the docs (https://nf-co.re/viralmetagenome/)

I’ve been struggling a ton with an

ERROR ~ Cannot load from object array because "this.keys" is null

error, anyone else?

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name admiring_montalcini Duration 23m 52s Status ✅ Success Tasks Completed: 481 Jun 1, 2026 at 3:07 AM

New patch release is out 🎉

v1.1.2 - Blush Bunting

🎉 with an important bug fix to allow thread safety for different meta maps! Thanks to the reviewers and @André Soares and @Nick Minor for their contributions

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name determined_noether Duration 21m 55s Status ✅ Success Tasks Completed: 481 Jun 3, 2026 at 8:59 AM

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name stoic_fermi Duration 17m 35s Status ✅ Success Tasks Completed: 481 Jun 3, 2026 at 9:00 AM

Hi everyone, I have been using nf-core/viralmetagenomics for several months to analyze acute febrile illness samples. I am running the pipeline with host read removal and the Broad Institute Kraken2 database, and overall, the pipeline has completed successfully for multiple batches. However, I have noticed something that I am struggling to understand and validate. For several viral taxa detected by Kraken2, when I extract the reads assigned to a given virus and perform independent BLAST searches (both nucleotide and translated searches), I often obtain either no significant hits or hits that do not support the original viral classification. Similarly, when I take contigs reported by the pipeline and re-run BLAST analyses manually (e.g., using NCBI BLAST), the results can be substantially different from the BLAST assignments reported by the pipeline. This has made it difficult for me to independently validate some of the viral findings. I would like to ask: 1. Has anyone observed similar discrepancies between Kraken2 classifications, pipeline-reported BLAST results, and independent BLAST validation? 2. Could differences in database composition explain these observations? 3. Are there recommended QC or validation steps to assess whether these classifications are likely true positives versus spurious assignments? 4. For low-abundance viral detections, what is the recommended approach to confirm the findings (read extraction, remapping to references, assembly validation, alternative classifiers, etc.)? 5. Are there any known issues with Broad Kraken2 database classifications that could generate false-positive viral assignments after host removal? Any suggestions on how to systematically investigate these discrepancies would be greatly appreciated. Thank you!

The pipeline is failing right now because RVDB is currently inaccessible ERROR ~ No such file or directory: rvdb.dbi.udel.edu/download/C-RVDBvCurrent.fasta.gz The link goes to 404 | NOT FOUND. Seems like this issue came up previously too: github.com/nf-core/viralmetagenome/issues/213 The .fasta.tar.gz link does work though rvdb.dbi.udel.edu/download/C-RVDBvCurrent.fasta.tar.gz

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name nice_avogadro Duration 20m 58s Status ✅ Success Tasks Completed: 481 Jul 2, 2026 at 1:59 AM

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name thirsty_curie Duration 20m 31s Status ✅ Success Tasks Completed: 481 Jul 2, 2026 at 8:16 AM

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name nice_venter Duration 26m 41s Status ✅ Success Tasks Completed: 495 Sep 15, 2026 at 5:39 PM

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name pedantic_swirles Duration 20m 44s Status ✅ Success Tasks Completed: 495 Sep 16, 2026 at 8:02 AM

New release is out 🎉

v1.2.0 - Damson Dove

— a feature-packed minor release! Highlights: opt-in

--keep_unmapped

to control unmapped read handling,

--normalise_reads

for digital normalisation with BBNorm before assembly,

--annotation_metadata

to supply consensus annotations from a table, a new “Contig Taxonomy” + genome-completeness MultiQC chart, and

--use_host_filtered_reads

for routing host-filtered reads into refinement/variant-calling. Plus a

params

-passing refactor for cleaner subworkflows, updated modules/subworkflows, and several release/CI fixes. Thanks to everyone who reviewed and tested this cycle! 🙏 extreme teamwork

✅ viralmetagenome/test_full completed successfully! 🎉 Run Name stoic_hodgkin Duration 26m 47s Status ✅ Success Tasks Completed: 495 Sep 16, 2026 at 2:16 PM

Not sure if you have seen these two long reads (nanopore) assembly tools: myloasm and metaMDBG. The latest version of

metaMDBG

has integrated the

nanoMDBG

method.

Hey Joon, I am running viralmetagenome on default settings/databases with a clinical sample extracted twice (one with and without IC, the only difference). At the kraken step, in both samples, the pipeline identified the suspected virus. But only in one sample (non-IC) did it assembly the genome of the virus. Any idea why? The total reads in kraken2 was plenty for assembly: 12k and 60k.

As I write this, I think I realised something... it did assemble the virus but only a tiny region. Either the sample has high duplication rate or only a tiny fragment was sequenced.

Just a quick question, are all of the default parameters suitable for Nanopore sequences?

Hey there! depictio loading We built a dashboard for viralmetagenome, and we would love your eyes on it @Joon Klaps 🙂 Depictio (open source, from EMBL) turns the output of a workflow run into an interactive dashboard you can share, so nobody has to write a Shiny or Streamlit app for each project. Point a template at any run of a pipeline and you get the same dashboard, which you can edit (UI & YAML), version and comment. 🦠 The viralmetagenome dashboard template shows the MultiQC report, the samples, the de novo contigs, the consensus genomes, the mapping coverage and the variants each genome carries. 🙌 Could you have a look? Tell us what is useful, what is misleading and what is missing, in #C0AFS06G9HR (all templates and details there) or in the viralmetagenome GitHub discussion. Even one line helps, thank you!