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Add warning nodes not exist #73

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CarolineOhrman opened this issue Feb 27, 2025 · 0 comments
Open

Add warning nodes not exist #73

CarolineOhrman opened this issue Feb 27, 2025 · 0 comments

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@CarolineOhrman
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When updating a database with command below there will be no WARNING or error if the nodenames in genome_id_map does not match the tree_parent_child_relations file. No warnings when creating the kraken database either. I think these genomes and nodes will be skipped?! Cannot find these genomes when i dump the database (flextaxd -db mydatabse.fdb -o flextaxd_out --dump_genome_annotations --dump_genomes)

flextaxd --db mydatabase.fdb \
  --mod_file tree_parent_child_relations.tsv \
  --genomeid2taxid genome_id_map.tsv \
  --parent "${genus}" \
  --replace; \
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