pulling the latest studies from the phylesystem shards
Already up-to-date.
/Users/karen/Documents/opentreeoflife/data/phylesystem-prod/shards
pulling the latest collections from the collections shards
Already up-to-date.
/Users/karen/Documents/opentreeoflife/data/phylesystem-prod/shards
Logs will show up in the ../opentree8.0/logs directory (in the event that something fails, check there).
cleaning previous outputs...
Building the supertree
cleaning the inputs...
creating the supertree...
annotating the supertree...
make extra...
running the assessments of the tree...
creating documentation of the outputs...
2016-11-29 13:33:32,504 INFO  [default] reading "../opentree8.0/labelled_supertree/labelled_supertree.tre"...
2131472 leaves
230046 non-leaf nodes (internals including the root)
156658 non-leaf nodes with out-degree > 1 (internals including the root)
2361518 total nodes
Traceback (most recent call last):
  File "./bin/document_outputs.py", line 490, in <module>
    dg = DocGen(propinquity_dir, prefix_dir, args.config)
  File "./bin/document_outputs.py", line 292, in __init__
    self.broken_taxa = self.read_broken_taxa()
AttributeError: 'DocGen' object has no attribute 'read_broken_taxa'
make: *** [html-output] Error 1
Failed building of html step