Hello! I am running the `test_full` profile in an ...
# viralrecon
r
Hello! I am running the
test_full
profile in an effort to make sure all pipelines have the full size test results displayed on the website and am running into:
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/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
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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?