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supertree-toolkit / stk

Supertree Toolkit is a GUI, CLI and Python module for processing data ready for analysis
http://supertreetoolkit.org/
GNU General Public License v3.0
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Error in carrying out autosubs #6

Open cjnaylor opened 5 years ago

cjnaylor commented 5 years ago

***Error: failed to carry out auto subs due to unknown error. File a bug report, please! https://github.com/supertree-toolkit/stk/issues Traceback (most recent call last): File "/home/stk/supertree_toolkit.py", line 1648, in autoprocess phyml = generate_species_level_data(phyml,taxonomy,verbose=verbose) File "/home/stk/supertree_toolkit.py", line 770, in generate_species_level_data if ('species' in taxonomy[taxon]): KeyError: 'Acangaobitermes krishnai'

jhill1 commented 5 years ago

Looks like the key "Acangaobitermes krishnai" is missing the (i.e. should be a "" not a space). Have a look at the taonxomy file generated in the previous step (in Excel or similar) and check the OTU column has _ not spaces. Then look around line 770 in supertreetoolkit.py and check where the taxa list comes from, i.e. there'll be a line that is: taxa = stk.get...blah There might need to be a line in the loop that goes over taxa to do a replace: `taxon = taxon.replace(" ","")` at the start of that loop.