Rike Hanssen
02/17/2026, 9:55 AMtest_full profile in an effort to make sure all pipelines have the full size test results displayed on the website and am running into:
/usr/local/lib/python3.12/site-packages/freyja/utils.py:63: UserWarning: Missing parents found:
Child 'QL.1.1' missing parent 'QL.1'
Using default lineage hierarchy yml for SARS-CoV-2
warnings.warn(warning_msg, UserWarning)
Validating the lineage hierarchy yaml ...
Traceback (most recent call last):
Please check your lineage yaml file.
File "/usr/local/bin/freyja", line 10, in <module>
Lineage hierarchy file is likely behind the selected barcode file. Try updating the hierarchy file.
sys.exit(cli())
^^^^^
File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1442, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1363, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/click/core.py", line 794, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/freyja/_cli.py", line 168, in demix
df_barcodes = collapse_barcodes(df_barcodes, df_depth, depthcutoff,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/freyja/utils.py", line 1103, in collapse_barcodes
set([alias.split('.')[0] for alias in pango_aliases])) > 1
^^^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'pango_aliases' where it is not associated with a value
for
freyja \
demix \
--depthcutoff 1 \
--output SAMPLE_22.tsv \
--barcodes usher_barcodes.feather \
--meta curated_lineages.json \
SAMPLE_22.variants.tsv \
SAMPLE_22.depth.tsv
cat <<-END_VERSIONS > versions.yml
"NFCORE_VIRALRECON:VIRALRECON:BAM_VARIANT_DEMIX_BOOT_FREYJA:FREYJA_DEMIX":
freyja: $(echo $(freyja --version 2>&1) | sed 's/^.*version //' )
END_VERSIONS
does anyone know why? Is this a known issue?