Hi, I'm trying to run SINTAX taxonomy assignment against a custom database, but only the "phylum level" is assigned. example output (seq deleted for readability):

ASV_ID	Phylum	Class	Order	Family	Genus	Species	confidence	sequence
00054979a8794ad8c02788626a779480	Bacteria						1.00	TCGT...CGG
000a9b5947d04ec2eab4762ddbc28bdf	Bacteria						1.00    TGAT...CGG
002b0c3fc99d5c0a53617ecbdd969dc5	Archaea						    1.00	TCAT...CGG
022b761540eec657f5d7fe0cd5c3a6ca	Bacteria						1.00    CTTT...CGG

My sintax formated reference file looks like the following:

>GQ347297.1.1347;tax=d:Bacteria;p:Proteobacteria;c:Gammaproteobacteria;o:Methylococcales;f:Methylomonadaceae;g:Milano-WF1B-03;s:uncultured_gamma proteobacterium
<SEQUENCE>
...

My run has the following options:

# tried with:
# --sintax_assign_taxlevels "Phylum,Class,Order,Family,Genus,Species"
# and with
# --sintax_assign_taxlevels Phylum,Class,Order,Family,Genus,Species

nextflow run nf-core/ampliseq \
	-profile docker \
	--input samplesheet.tsv \
	--metadata metadata.tsv \
	--skip_fastqc \
	--outdir run_20260416 \
	--sintax_ref_tax_custom /local/databases/ampliseq_alternative_database/dna-sequences-sintax.fasta.gz \
	--sintax_assign_taxlevels "Phylum,Class,Order,Family,Genus,Species" \
	--vsearch_cluster \
	--qiime_ref_tax_custom /local/databases/ampliseq_alternative_database/alternative_ref_db.tar.gz \
	--FW_primer GTGYCAGCMGCCGCGGTAA \
	--RV_primer GGACTACNVGGGTWTCTAAT \
	--ignore_empty_input_files \
	--skip_diversity_indices \
	--skip_alpha_rarefaction \
	--max_cpus 32 \
	-resume \
	-c config.conf

What could be wrong?

Difficult to say. Have you tried the same fasta file that you provide for Sintax with any other tool, e.g. the DADA2

assignTaxonomy

(i.e. provide your custom file -- correctly formatted -- to

--dada_ref_tax_custom

)? Did that fare better?