Hi everyone, I was wondering if anyone might know why my taxprofiler execution is not working for my long-read 16S gene data. What basically happens is that the pipeline runs, but the Kraken step is skipped. I went through the workflow step by step and can’t figure out where the problem is. The log looks like this:

executor >  local (4)
[9b/499c22] NFCORE_TAXPROFILER:taxprofiler:UNTAR (SILVA_138_2_k2db.tar.gz) [100%] 1 of 1 ✔
[7a/a1b12f] NFCORE_TAXPROFILER:taxprofiler:FASTQC (bc22)                   [100%] 2 of 2 ✔
[-        ] NFCORE_TAXPROFILER:taxprofiler:PROFILING:KRAKEN2_KRAKEN2       -
[-        ] NFCORE_TAXPROFILER:taxprofiler:PROFILING:BRACKEN_BRACKEN       -
[9f/670dcd] NFCORE_TAXPROFILER:taxprofiler:MULTIQC                         [100%] 1 of 1 ✔
-[nf-core/taxprofiler] Pipeline completed successfully-
Completed at: 10-Feb-2026 14:12:39
Duration    : 4m 46s
CPU hours   : 0.8
Succeeded   : 4

The command I used:

nextflow run nf-core/taxprofiler \
  -profile conda \
  --input ${path_output}/samplesheet.csv \
  --databases 16S_databases.csv \
  --outdir ${path_output}/kraken_output \
  --longread_qc_skipadaptertrim \
  --run_kraken2

The input FASTQ files DO exist, as FastQC is executed successfully. The 16S databases CSV looks like this: tool,db_name,db_params,db_type,db_path kraken2,silva138_2,--quick,long,/home/povp/scripts/Metagenomics_workflow/taxonomic_profiling/kraken_dbs/SILVA_138_2_k2db.tar.gz

My group is using this pipeline for 16s nanopore data analysis https://github.com/genomic-medicine-sweden/TRANA and this nf-core pipeline https://github.com/nf-core/proposals/issues/104 is also under development. Is it nanopore data? Pacbio is supported in nf-core/ampliseq

I have data from PacBio, and I specifically wanted to try Kraken (for some internal reasons). I managed to run Kraken so far; there was a mistake in the database CSV, which caused the Kraken step not to be executed initially. However, I would also like to perform host removal, since I know there is minor contamination in the data. Unfortunately, I am facing the same issue as before: the step is not executed. My question is therefore mainly about debugging Nextflow: is there a way to track why a particular step is not executed? How can I determine what is missing or misconfigured when a specific module is skipped? Thanks!

Could you share your

.nextflow.log

file @User? Typically the reason why a module doesn't execute in nf-core tapxrofiler: • Is either a typo in a parameter (although looks OK to me here), • Name of the tool in the

database.csv

is wrong (So taxprofiler can't send the right database) • The module did not recieve a required file (for whatever reason)