Plot_tree_graphlan.py error!

Infrastructure and utilities GraPhlAn
1

Dear all,

I tried to follow up the tutorial in Home · biobakery/MetaPhlAn Wiki · GitHub 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

1 Like
2

I am having the same issue. I’ve installed graphlan into a conda environment running python 2.7 and then metaphlan into the same environment.

This error pops up when I try to run the commands from the tutorial:
plot_tree_graphlan.py --ifn_tree RAxML_bestTree.s__Eubacterium_rectale.StrainPhlAn3.tre.metadata --colorized_metadata Country --leaf_marker_size 60 --legend_marker_size 60

1 Like
3

Same problem here!
Could you resolve this issue? Anyone?