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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

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RuntimeWarning using multievolve.py

gengyuncong opened this issue · comments

commented

Hi,
When I run multievolve.py, I encountered the following problem after all MCMCs are done:

multievolve.py:235: RuntimeWarning: invalid value encountered in less
  assert np.all(logSumLHs < 0)
Traceback (most recent call last):
  File "multievolve.py", line 323, in <module>
    main()
  File "multievolve.py", line 319, in main
    included_chains, excluded_chains = determine_chains_to_merge(chain_dirs, args['chain_inclusion_factor'])
  File "multievolve.py", line 235, in determine_chains_to_merge
    assert np.all(logSumLHs < 0)
AssertionError
commented

I found some error in ssm.txt where total read count is smaller than the reference read count at some site. I have fixed that problem and the error has disappeared.