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Description
Hi
I'm trying to convert kraken2 outputs for vamb.
When I try to run this command:
taxconverter kraken2 -i ${sample_id}_kraken2.tsv -o vamb/taxconverter/${sample_id}.tsv
The kraken2 output was generate using default command:
kraken2 -threads 16 --db ${KRAKEN_DB} --output ${WD}/kraken2/${sample_id}_kraken2.tsv $contig
I get this error:
2025-06-10 20:30:35.003 | INFO | taxconverter.main:ncbi_lineage:54 - Loading NCBI lineage
Traceback (most recent call last):
File "/home/ramanujam/.local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3652, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 147, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 176, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'child_id'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ramanujam/.local/bin/taxconverter", line 8, in
sys.exit(main())
File "/home/ramanujam/.local/lib/python3.9/site-packages/taxconverter/main.py", line 282, in main
kraken_data(args.input)
File "/home/ramanujam/.local/lib/python3.9/site-packages/taxconverter/main.py", line 135, in wrapper
df = func(*arguments, **kwargs)
File "/home/ramanujam/.local/lib/python3.9/site-packages/taxconverter/main.py", line 268, in kraken_data
map_ncbi = ncbi_lineage()
File "/home/ramanujam/.local/lib/python3.9/site-packages/taxconverter/main.py", line 56, in ncbi_lineage
map_child_parent = {k: v for k, v in zip(df_ncbi[CHILD_ID].astype(str), df_ncbi[PARENT_ID].astype(str))}
File "/home/ramanujam/.local/lib/python3.9/site-packages/pandas/core/frame.py", line 3760, in getitem
indexer = self.columns.get_loc(key)
File "/home/ramanujam/.local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3654, in get_loc
raise KeyError(key) from err
KeyError: 'child_id' `
Any thoughts on fixes?
I have installed taxconverter in a fresh conda environment and manually copied over the clades.tsv file to data directory in the environment.