Exception: No mutations found in common across samples. This commonly occurs when the muation_id field does not match for mutations in the input files. Search the user group before posting a message or a bug.

[Damjan Temelkovski]

Dear All,

I tried running PyClone, and I got this error message:

"Exception: No mutations found in common across samples. This commonly occurs when the muation_id field does not match for mutations in the input files. Search the user group before posting a message or a bug."

I have 20 samples and there isn't any mutation that is shared across all 20 samples. The most frequent one is shared across 12. Is this a confounding factor for using PyClone, or am I perhaps missing a configuration parameter to allow such a case.

Here is the full stack trace:

Traceback (most recent call last):
  File "/home/damjan/miniconda2/envs/pyclone/bin/PyClone", line 11, in <module>
    load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')()
  File "/home/damjan/miniconda2/envs/pyclone/lib/python2.7/site-packages/pyclone/cli.py", line 78, in main
    args.func(args)
  File "/home/damjan/miniconda2/envs/pyclone/lib/python2.7/site-packages/pyclone/run.py", line 174, in run_analysis
    _run_analysis(args.config_file, args.seed)
  File "/home/damjan/miniconda2/envs/pyclone/lib/python2.7/site-packages/pyclone/run.py", line 199, in _run_analysis
    alpha_priors
  File "/home/damjan/miniconda2/envs/pyclone/lib/python2.7/site-packages/pyclone/pyclone_beta_binomial.py", line 29, in run_pyclone_beta_binomial_analysis
    data, sample_ids = config.load_data(config_file)
  File "/home/damjan/miniconda2/envs/pyclone/lib/python2.7/site-packages/pyclone/config.py", line 79, in load_data
    ('Search the user group before posting a message or a bug.'),
Exception: No mutations found in common across samples. This commonly occurs when the muation_id field does not match for mutations in the input files. Search the user group before posting a message or a bug.

Thank you
Damjan

[Damjan Temelkovski]

I believe this is because I should use only samples from the same patient.

Regards
Damjan

[Andrew Roth]

Hi Damjan,

Yes that would be the issue. The samples have to be related, either
from the same patient or from something like a xenograft series.

Cheers,
Andy

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