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popgenmethods / smcpp

SMC++ infers population history from whole-genome sequence data.
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RuntimeError: erroneous average coalescence time #248

Open danrans123 opened 10 months ago

danrans123 commented 10 months ago

Dear Terhorst,

While using SMC++ v1.13.0, I encountered the runtime errors: 2551 smcpp.analysis.base INFO theta: 0.000100 2551 smcpp.analysis.base INFO rho: 0.000100 2551 smcpp.data_filter INFO Loading data... 3871 smcpp.data_filter INFO 0.95 Gb of data 3893 smcpp.data_filter INFO 1 population 95252 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... 95252 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 1... 95252 smcpp.analysis.base INFO Running E-step 119367 smcpp.analysis.base INFO E-step completed 119368 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -69716330.719036 6272486 smcpp.optimize.plugins.progress_printer INFO Current model:

-1.99 -1.99 -0.47 1.53 3.23 4.00 3.50 1.88 0.90 1.99 2.28 2.06 1.70 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.62 4.64 4.64 4.64 4.64 4.64 4.64 4.64 4.64 4.64 25.33 25.33 25.33 25.33 25.33 25.33 25.33 25.33 25.33 54.33 54.33 54.33 54.33 54.33 54.33 54.33 54.33 33.27 33.27 33.27 33.27 33.27 33.27 33.27 33.27 33.27 6.55 6.55 6.55 6.55 6.55 6.55 6.55 6.55 6.55 2.47 2.47 2.47 2.47 2.47 7.34 7.34 7.34 7.34 7.34 7.34 7.34 7.34 7.34 7.34 7.34 7.34 9.76 9.76 9.76 9.76 9.76 9.76 9.76 7.84 7.84 7.84 7.84 7.84 5.48 6272497 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model:

1e+06 ++--+-----+--+-+---+-----+--++----+-----+--++---+-----+--+-+---+++

6272527 smcpp.data_filter INFO Loading data... 6274013 smcpp.data_filter INFO 0.95 Gb of data 6274019 smcpp.data_filter INFO 1 population Traceback (most recent call last): File "/gss1/App_dir/anaconda3/envs/smcpp/bin/smc++", line 11, in load_entry_point('smcpp==1.15.3', 'console_scripts', 'smc++')() File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/frontend/console.py", line 26, in main cmds[args.command].main(args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/commands/estimate.py", line 47, in main analysis = Analysis(args.data, args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/analysis.py", line 88, in init self._init_regularization(args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/analysis.py", line 121, in _init_regularization self._penalty = abs(self.Q()) * (10 ** -args.regularization_penalty) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/base.py", line 124, in Q qq = [self._ims[pop].Q(separate=True) for pop in self._ims] File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/base.py", line 124, in qq = [self._ims[pop].Q(separate=True) for pop in self._ims] File "smcpp/_smcpp.pyx", line 285, in smcpp._smcpp._PyInferenceManager.Q File "smcpp/_smcpp.pyx", line 280, in smcpp._smcpp._PyInferenceManager.Q RuntimeError: erroneous average coalescence time 7019 smcpp.analysis.base INFO theta: 0.000100 7020 smcpp.analysis.base INFO rho: 0.000100 7020 smcpp.data_filter INFO Loading data... 8288 smcpp.data_filter INFO 0.95 Gb of data 8315 smcpp.data_filter INFO 1 population 29431 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... 29432 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 1... 29432 smcpp.analysis.base INFO Running E-step 52930 smcpp.analysis.base INFO E-step completed 52932 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -69716201.969917 13166211 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model:

1e+06 ++--+-----+--++---+-----+-+-+---+----+--+-+---+----+--++----+---++

13166222 smcpp.optimize.plugins.progress_printer INFO Current model:

-1.99 -1.99 -1.99 -1.12 0.24 1.68 2.84 3.64 4.01 4.01 3.36 1.93 0.74 1.29 2.52 3.16 2.96 2.11 1.07 0.10 -0.87 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.33 0.33 0.33 0.33 0.33 0.33 1.27 1.27 1.27 1.27 1.27 5.34 5.34 5.34 5.34 5.34 17.19 17.19 17.19 17.19 17.19 17.19 37.97 37.97 37.97 37.97 37.97 54.97 54.97 54.97 54.97 54.97 54.97 54.97 54.97 54.97 54.97 54.97 28.91 28.91 28.91 28.91 28.91 6.88 6.88 6.88 6.88 6.88 2.10 3.63 3.63 3.63 3.63 3.63 3.63 3.63 3.63 3.63 3.63 3.63 12.42 12.42 12.42 12.42 12.42 23.63 23.63 23.63 23.63 19.27 19.27 19.27 8.25 8.25 8.25 8.25 2.91 2.91 2.91 1.11 1.11 1.11 1.11 0.42 13166230 smcpp.data_filter INFO Loading data... 13167709 smcpp.data_filter INFO 0.95 Gb of data 13167716 smcpp.data_filter INFO 1 population Traceback (most recent call last): File "/gss1/App_dir/anaconda3/envs/smcpp/bin/smc++", line 11, in load_entry_point('smcpp==1.15.3', 'console_scripts', 'smc++')() File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/frontend/console.py", line 26, in main cmds[args.command].main(args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/commands/estimate.py", line 47, in main analysis = Analysis(args.data, args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/analysis.py", line 88, in init self._init_regularization(args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/analysis.py", line 121, in _init_regularization self._penalty = abs(self.Q()) * (10 ** -args.regularization_penalty) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/base.py", line 124, in Q qq = [self._ims[pop].Q(separate=True) for pop in self._ims] File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/base.py", line 124, in qq = [self._ims[pop].Q(separate=True) for pop in self._ims] File "smcpp/_smcpp.pyx", line 285, in smcpp._smcpp._PyInferenceManager.Q File "smcpp/_smcpp.pyx", line 280, in smcpp._smcpp._PyInferenceManager.Q RuntimeError: erroneous average coalescence time 7776 smcpp.analysis.base INFO theta: 0.000100 7776 smcpp.analysis.base INFO rho: 0.000100 7777 smcpp.data_filter INFO Loading data... 9028 smcpp.data_filter INFO 0.95 Gb of data 9048 smcpp.data_filter INFO 1 population 27481 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... 27481 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 1... 27481 smcpp.analysis.base INFO Running E-step 52560 smcpp.analysis.base INFO E-step completed 52571 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -69716979.687712 2419015 smcpp.optimize.plugins.progress_printer INFO Current model:

1.40 4.01 3.72 0.91 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 4.07 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 54.96 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 41.24 2.48 2419047 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model:

1e+06 ++-------+------+-----+----+---+--+--+--+-----------------+-----++

2419060 smcpp.data_filter INFO Loading data... 2420694 smcpp.data_filter INFO 0.95 Gb of data 2420701 smcpp.data_filter INFO 1 population Traceback (most recent call last): File "/gss1/App_dir/anaconda3/envs/smcpp/bin/smc++", line 11, in load_entry_point('smcpp==1.15.3', 'console_scripts', 'smc++')() File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/frontend/console.py", line 26, in main cmds[args.command].main(args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/commands/estimate.py", line 47, in main analysis = Analysis(args.data, args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/analysis.py", line 88, in init self._init_regularization(args) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/analysis.py", line 121, in _init_regularization self._penalty = abs(self.Q()) * (10 ** -args.regularization_penalty) File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/base.py", line 124, in Q qq = [self._ims[pop].Q(separate=True) for pop in self._ims] File "/gss1/App_dir/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/analysis/base.py", line 124, in qq = [self._ims[pop].Q(separate=True) for pop in self._ims] File "smcpp/_smcpp.pyx", line 285, in smcpp._smcpp._PyInferenceManager.Q File "smcpp/_smcpp.pyx", line 280, in smcpp._smcpp._PyInferenceManager.Q RuntimeError: erroneous average coalescence time

my estimation command: smc++ estimate --cores 2 --timepoints 10 20000 -o ./result/model_time 6.1e-9 ./out/.smc.gz smc++ estimate --cores 2 --timepoints 10 20000 -o ./result/model_knots --knots 15 6.1e-9 ./out/.smc.gz smc++ estimate --cores 2 -o ./result/model 6.1e-9 ./out/*.smc.gz

Is there any problem with my command line?

Thank you!