Closed mkellom closed 2 years ago
Same problem here...
23-03-2022 05:29:50: Found 18 marker genes, placing them in the tree using epa-ng
Traceback (most recent call last):
File "/home/thackl/software/anaconda3/envs/eukcc/bin/eukcc", line 10, in <module>
sys.exit(main())
File "/home/thackl/software/anaconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/__main__.py", line 416, in main
run_eukcc(args)
File "/home/thackl/software/anaconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/__main__.py", line 74, in run_eukcc
clade = E.determine_subdb()
File "/home/thackl/software/anaconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/eukcc.py", line 359, in determine_subdb
lng = tax_LCA(tree, info, places)
File "/home/thackl/software/anaconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/treehandler.py", line 138, in tax_LCA
info = load_tax_info(taxinfo)
File "/home/thackl/software/anaconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/base.py", line 60, in load_tax_info
d[row[1]] = [str(x) for x in ncbi.get_lineage(row[0])]
File "/home/thackl/software/anaconda3/envs/eukcc/lib/python3.9/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 241, in get_lineage
raise ValueError("%s taxid not found" %taxid)
ValueError: 2478750 taxid not found
This seems to be related with issues in ETE, so I assume providing a ete database will solve this issues for everyone. So I will set this higher on my todo list.
Thank you for reporting.
In the meantime this might be solved by updating the NCBI taxid database as outline here: http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html
This is not an error produced by EukCC, but I guess it should handle it more gracefully.
Please see this comment for a solution: https://github.com/Finn-Lab/EukCC/issues/30#issuecomment-1086230673
I am testing a new release with a ete database provided by me
What could be causing this error? Here is the log output, thank you:
09-03-2022 12:18:52: EukCC version 2.0 09-03-2022 12:18:52: Found 182 bins 09-03-2022 12:39:44: Searching for marker genes in base database 09-03-2022 12:39:45: No placement marker genes found. 09-03-2022 12:39:45: Searching for marker genes in base database 09-03-2022 12:39:46: No placement marker genes found. 09-03-2022 12:39:46: Searching for marker genes in base database 09-03-2022 12:39:47: Found 4 marker genes, placing them in the tree using epa-ng Traceback (most recent call last): File "/global/homes/m/mkellom/.conda/envs/assemble/bin/eukcc", line 10, in
sys.exit(main())
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/main.py", line 413, in main
eukcc_folder(args)
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/refine.py", line 65, in eukcc_folder
refine(state)
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/refine.py", line 153, in refine
bins.append(bin(state, wd, path, protein=True))
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/bin.py", line 22, in init
self.run_eukcc()
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/bin.py", line 42, in run_eukcc
clade = E.determine_subdb()
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/eukcc.py", line 359, in determine_subdb
lng = tax_LCA(tree, info, places)
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/treehandler.py", line 138, in tax_LCA
info = load_tax_info(taxinfo)
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/eukcc/base.py", line 60, in load_tax_info
d[row[1]] = [str(x) for x in ncbi.get_lineage(row[0])]
File "/global/homes/m/mkellom/.conda/envs/assemble/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 238, in get_lineage
raise ValueError("%s taxid not found" %taxid)
ValueError: 13349 taxid not found