The bioBakery help forum

Plot_tree_graphlan.py error!

Dear all,

I tried to follow up the tutorial in https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0 after installing with conda and tried to plot in graphlan here is what I run:

plot_tree_graphlan.py --ifn_tree output/RAxML_bestTree.s__Bacteroides_caccae.StrainPhlAn3.tre.metadata --colorized_metadata subjectID

I got an error of :
Traceback (most recent call last):

  • File “/home/ubelix/dbmr/terziev/anaconda2/bin/plot_tree_graphlan.py”, line 176, in *
  • main(args)*
  • File “/home/ubelix/dbmr/terziev/anaconda2/bin/plot_tree_graphlan.py”, line 103, in main*
  • nodestr = node.get_node_str().strip("’")*
    AttributeError: ‘Node’ object has no attribute ‘get_node_str’

I am not so sure what is wrong and honestly I can run the exact command as in tutorial which is

plot_tree_graphlan.py -t output/RAxML_bestTree.s__Bacteroides_caccae.StrainPhlAn3.tre.metadata -m subjectID

It doesn’t accept -t and -m options. So weird!
Anyone can guide me what’s happening?
Thank you so much.
Best wishes,
Bahti