R version: /usr/local/share/applications/R-3.4.3/bin/R
homo: Aesc_assa_HG013_c98.Aesc_assa_HG013_c98.homo dir: Aesc_assa_HG013_c98.Aesc_assa_HG013_c98 cds1: Aesc_assa_HG013_c98.cds cds2: Aesc_assa_HG013_c98.cds sp1: Aesc_assa_HG013_c98 sp2: Aesc_assa_HG013_c98
2020-05-13 06:55:56: INFO	
2020-05-13 06:55:56: INFO	codeml found
2020-05-13 06:55:56: INFO	
2020-05-13 06:55:56: INFO	
2020-05-13 06:55:57: INFO	Translating CDS file
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2020-05-13 06:56:14: WARNING	There were 0 warnings during translation
2020-05-13 06:56:14: INFO	Started whole paranome Ks analysis
2020-05-13 06:56:14: WARNING	Filtered out the 2 largest gene families because n*(n-1)/2 > `max_pairwise`
2020-05-13 06:56:14: WARNING	If you want to analyse these large families anyhow, please raise the `max_pairwise` parameter. 
2020-05-13 06:56:14: INFO	Started analysis in parallel (n_threads = 1)
2020-05-13 06:56:14: INFO	Performing analysis on gene family GF_000003
2020-05-13 06:56:36: INFO	Performing analysis on gene family GF_000004
2020-05-13 06:56:43: INFO	Performing analysis on gene family GF_000005
2020-05-13 06:57:50: INFO	Performing analysis on gene family GF_000006
2020-05-13 06:58:07: INFO	Performing analysis on gene family GF_000007
2020-05-13 06:58:34: INFO	Performing analysis on gene family GF_000008
2020-05-13 06:59:13: INFO	Performing analysis on gene family GF_000009
2020-05-13 06:59:18: INFO	Performing analysis on gene family GF_000010
2020-05-13 06:59:40: INFO	Performing analysis on gene family GF_000011
2020-05-13 06:59:55: INFO	Performing analysis on gene family GF_000012
2020-05-13 06:59:57: INFO	Performing analysis on gene family GF_000013
2020-05-13 07:00:03: INFO	Performing analysis on gene family GF_000014
2020-05-13 07:00:10: INFO	Performing analysis on gene family GF_000015
2020-05-13 07:00:12: INFO	Performing analysis on gene family GF_000016
2020-05-13 07:00:29: INFO	Performing analysis on gene family GF_000017
2020-05-13 07:00:36: INFO	Performing analysis on gene family GF_000018
2020-05-13 07:00:38: INFO	Performing analysis on gene family GF_000019
2020-05-13 07:00:42: INFO	Performing analysis on gene family GF_000020
2020-05-13 07:00:47: INFO	Performing analysis on gene family GF_000021
2020-05-13 07:00:53: INFO	Performing analysis on gene family GF_000022
2020-05-13 07:01:04: WARNING	No Ks value for Aesc_assa_c98.83532 - Aesc_assa_c98.10806!
2020-05-13 07:01:04: WARNING	No Ka value for Aesc_assa_c98.83532 - Aesc_assa_c98.10806!
2020-05-13 07:01:04: WARNING	No ω value for Aesc_assa_c98.83532 - Aesc_assa_c98.10806!
Traceback (most recent call last):
  File "/home/kuokuo/anaconda3/envs/python36/bin/wgd", line 8, in <module>
    sys.exit(cli())
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/wgd_cli.py", line 632, in ksd
    max_pairwise=max_pairwise
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/wgd_cli.py", line 773, in ksd_
    max_pairwise=max_pairwise,
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/wgd/ks_distribution.py", line 645, in ks_analysis_paranome
    ) for family in sorted_families)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/parallel.py", line 779, in __call__
    while self.dispatch_one_batch(iterator):
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/parallel.py", line 625, in dispatch_one_batch
    self._dispatch(tasks)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/parallel.py", line 588, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 111, in apply_async
    result = ImmediateResult(func)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 332, in __init__
    self.results = batch()
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/parallel.py", line 131, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/joblib/parallel.py", line 131, in <listcomp>
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/wgd/ks_distribution.py", line 305, in analyse_family
    results_dict, msa=msa_path_protein, method=method)
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/wgd/ks_distribution.py", line 98, in _weighting
    tree_path, pairwise_estimates['Ks'])
  File "/home/kuokuo/anaconda3/envs/python36/lib/python3.6/site-packages/wgd/phy.py", line 138, in phylogenetic_tree_to_cluster_format
    node.name = id_map[node.name]
KeyError: 'Aesc_assa_c98.54211'