Nura7177
commented
8 months ago I have resolved this issue with adding --gtdbtk_classification_file, which turned out to be a summary.tsv file ([prefix].[domain].summary.tsv i.e. in my case - ./GTDB-tk_output/gtdbtk.bac120.summary.tsv
Hello, I run decorate on my tree of 300+ genomes from NCBI and get this issue: how to resolve it? [2024-03-12 15:35:05] INFO: GTDB-Tk v2.3.2 [2024-03-12 15:35:05] INFO: gtdbtk decorate --input_tree /nfs/ashilova/genomes/THR_out/gtdbtk.unrooted.tree --output_tree /nfs/ashilova/genomes/THR_out/decorated_tree [2024-03-12 15:35:05] INFO: Using GTDB-Tk reference data version r214: /nfs/lisagrig/gtdb_toolkit [2024-03-12 15:35:05] INFO: Reading GTDB taxonomy for representative genomes. [2024-03-12 15:35:05] INFO: Read taxonomy for 85,205 genomes. [2024-03-12 15:35:05] INFO: Reading tree. [2024-03-12 15:35:05] INFO: Removing any previous internal node labels. [2024-03-12 15:35:05] INFO: Calculating F-measure statistic for each taxa. [2024-03-12 15:35:05] INFO: Calculating taxa within each lineage. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Domain rank. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Phylum rank. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Class rank. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Order rank. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Family rank. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Genus rank. [2024-03-12 15:35:05] INFO: Processing 0 taxa at Species rank. [2024-03-12 15:35:05] INFO: Placing labels on tree. [2024-03-12 15:35:05] INFO: Writing out statistics for taxa. [2024-03-12 15:35:05] INFO: Writing out inferred taxonomy for each genome. [2024-03-12 15:35:05] ERROR: Uncontrolled exit resulting from an unexpected error.
================================================================================ EXCEPTION: IndexError MESSAGE: list index out of range
Traceback (most recent call last): File "/home/ashilova/anaconda3/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/main.py", line 102, in main gt_parser.parse_options(args) File "/home/ashilova/anaconda3/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/main.py", line 1209, in parse_options self.decorate(options) File "/home/ashilova/anaconda3/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/main.py", line 815, in decorate reports = d.run(options.input_tree, File "/home/ashilova/anaconda3/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/decorate.py", line 379, in run self._write_taxonomy(tree, out_taxonomy) File "/home/ashilova/anaconda3/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/decorate.py", line 314, in _write_taxonomy taxa = self._leaf_taxa(leaf) File "/home/ashilova/anaconda3/envs/gtdbtk-2.3.2/lib/python3.8/site-packages/gtdbtk/decorate.py", line 295, in _leaf_taxa last_rank = ordered_taxa[-1][0:3] IndexError: list index out of range
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