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nick-youngblut / gtdb_to_taxdump

Convert GTDB taxonomy to NCBI taxdump format
MIT License
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lineage2taxid error (module 'gtdb_to_taxdump' has no attribute 'Dmp') #14

Closed emaxortiz closed 1 year ago

emaxortiz commented 2 years ago

Hi Nick. Thanks for developing this tool. I'm trying to get the taxid using the GTDB-tk lineage output for the MAGs I recovered. No matter what I try in my command, I'm getting the same error:

$ lineage2taxid.py gtdbtk.ar122.summary.tsv /ncbi_taxdump/names.dmp /ncbi_taxdump/nodes.dmp

Traceback (most recent call last):   File "/home/eortiz/.local/bin/lineage2taxid.py", line 125, in     main(args)   File "/home/eortiz/.local/bin/lineage2taxid.py", line 116, in main     G = gtdb2td.Dmp.load_dmp(args.names_dmp, args.nodes_dmp) AttributeError: module 'gtdb_to_taxdump' has no attribute 'Dmp'

Any guidance about how to solve this? Thank you. Max

nick-youngblut commented 2 years ago

How did you install gtdb_to_taxdump? It seems that something is messed up with your PYTHONPATH

nick-youngblut commented 1 year ago

I'm closing this issue due to a lack of activity