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graftm tree decorate not working when given undecorated tree? #227

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wwood opened this issue Sep 23, 2016 · 0 comments
Open

graftm tree decorate not working when given undecorated tree? #227

wwood opened this issue Sep 23, 2016 · 0 comments
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@wwood
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wwood commented Sep 23, 2016

This is on my https://github.com/wwood/graftM/tree/final_skbio_removal branch, which seems otherwise OK.

The idea is that I've annotated most tips of this tree, and I want to propagate these annotations to the rest of the tree.

/srv/projects/abisko/aterrible_bins/12_assembly73_individuals_flat20160115/gtdb/tree_bacterial_set$ ~/git/graftM/bin/graftM tree --decorate --rooted_tree decorated.rerooted.tree --input_greengenes_taxonomy /srv/projects/abisko/annotation/18_aterrible12_prokka_to_KO/aterrible12_s5_graftm.autotaxonomy2 --output_tree decorated.rerooted.autotaxonomy_decorated.tree --output_taxonomy decorated.rerooted.autotaxonomy_decorated.taxonomy 

                             GraftM 0.9.5
09/23/2016 03:02:11 PM INFO: Reading in taxonomy
09/23/2016 03:02:11 PM INFO: Reading Greengenes style taxonomy
09/23/2016 03:02:11 PM INFO: Decorating tree
Traceback (most recent call last):
  File "/home/ben/git/graftM/bin/graftM", line 419, in <module>
    Run(args).main()
  File "/home/ben/git/graftM/bin/../graftm/run.py", line 733, in main
    self.args.no_unique_tax, self.args.decorate, None) 
  File "/home/ben/git/graftM/bin/../graftm/decorator.py", line 80, in main
    td.decorate(output_tree, output_tax, no_unique_tax)
  File "/home/ben/git/graftM/bin/../graftm/tree_decorator.py", line 181, in decorate
    if tip.taxon.label.replace(' ', '_') in self.taxonomy])
ValueError: max() arg is an empty sequence

Is there no unit tests for graftM tree? I couldn't see any immediately.

Any ideas?

@geronimp geronimp added the bug label Jul 12, 2017
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