augur lbi CalledProcessError: returned non-zero exit status 1

Help and Getting Started
1

Hi, Community members

My Goal
interpret the local branching index (fitness) of H7 avian influenza virus

Current Behavior
an error was met when interpreting the LBI: CalledProcessError: returned non-zero exit status 1

the error details I met:

Traceback (most recent call last):
  File "/home/yzu/miniconda3/envs/nst/bin/augur", line 10, in <module>
    sys.exit(main())
  File "/home/yzu/miniconda3/envs/nst/lib/python3.8/site-packages/augur/__main__.py", line 10, in main
    return augur.run( argv[1:] )
  File "/home/yzu/miniconda3/envs/nst/lib/python3.8/site-packages/augur/__init__.py", line 75, in run
    return args.__command__.run(args)
  File "/home/yzu/miniconda3/envs/nst/lib/python3.8/site-packages/augur/lbi.py", line 102, in run
    node.attr = branch_lengths["nodes"][node.name]
KeyError: None
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
/tmp/ipykernel_1471/351339975.py in <module>
----> 1 get_ipython().run_cell_magic('bash', '', 'augur lbi \\\n--tree H7_HA/h7n9_ha_03_iqtree_rename.tree \\\n--branch-lengths H7_HA/h7_ha_05_node_data.json \\\n--output H7_HA/h7_ha_06_lbi.json \\\n--attribute-names lbi \\\n--tau 0.25 \\\n--window 0.75\n')

~/miniconda3/envs/nst/lib/python3.8/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
   2401             with self.builtin_trap:
   2402                 args = (magic_arg_s, cell)
-> 2403                 result = fn(*args, **kwargs)
   2404             return result
   2405 

~/miniconda3/envs/nst/lib/python3.8/site-packages/IPython/core/magics/script.py in named_script_magic(line, cell)
    140             else:
    141                 line = script
--> 142             return self.shebang(line, cell)
    143 
    144         # write a basic docstring:

<decorator-gen-103> in shebang(self, line, cell)

~/miniconda3/envs/nst/lib/python3.8/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

~/miniconda3/envs/nst/lib/python3.8/site-packages/IPython/core/magics/script.py in shebang(self, line, cell)
    243             sys.stderr.flush()
    244         if args.raise_error and p.returncode!=0:
--> 245             raise CalledProcessError(p.returncode, cell, output=out, stderr=err)
    246 
    247     def _run_script(self, p, cell, to_close):

CalledProcessError: Command 'b'augur lbi \\\n--tree H7_HA/h7n9_ha_03_iqtree_rename.tree \\\n--branch-lengths H7_HA/h7_ha_05_node_data.json \\\n--output H7_HA/h7_ha_06_lbi.json \\\n--attribute-names lbi \\\n--tau 0.25 \\\n--window 0.75\n'' returned non-zero exit status 1.

how did I get the h7_ha_05_node_data.json file

%%bash
augur refine \
-a H7_HA/h7_ha_02_align.fasta \
-t H7_HA/h7n9_ha_03_iqtree_rename.tree \
--metadata H7_HA/h7_ha_metadate.tsv \
--timetree \
--output-tree H7_HA/h7_ha_05_refine_tree.nwk \
--output-node-data H7_HA/h7_ha_05_node_data.json \
--branch-length-inference auto

how the h7_ha_05_node_data.json looks like

image
image890×1063 61.7 KB

Expected behavior
a json file

image
image1083×609 39.9 KB

How to reproduce
Steps to reproduce the current behavior:

  1. Open / run jupyter-lab
  2. augur refine to get the json file meet the demand --branch-lengths
  3. augur lbi, see the detail below
%%bash
augur lbi \
--tree H7_HA/h7_ha_05_refine_tree.nwk \
--branch-lengths H7_HA/h7_ha_05_node_data.json \
--output H7_HA/h7_ha_06_lbi.json \
--attribute-names lbi \
--tau 0.25 \
--window 0.75
  1. See error

Your environment: if running Nextstrain locally

  • Operating system: Ubuntu 20.04.2 LTS
  • Browser: Chrome Version 91
  • Version: augur 12.0.0

Any help would be greatly appreciated!
Yang

2

Hi, in augur lbi use the tree.nwk obtained from the --output-tree option in augur refine.

I just tried and I got the same error

node.attr = branch_lengths["nodes"][node.name] line 102 of lbi.py

when using the tree_raw.nwk from augur tree, while it worked when using the tree.nwk from augur refine.

3

Hi, babarlelephant
Thanks for your reply.
It’s worked since I build the tree with nextstrain rather than import the tree from another program.

Thank you very much.

4

glad you could solve it. augur refine labels all nodes and such that later steps have a common set of node names to refer to. That is why the “refined” tree is necessary.