Errors while Parameter Estimation
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Chuan Fu Yap
Mar 25, 2015, 5:38:11 PM3/25/15
to copasi-u...@googlegroups.com
Dear All,
I am attempting to run the parameter estimation using Copasi for a Mini Model I have constructed, however I get the following warnings after the estimation is complete. What does these errors mean? Does it mean the estimation has failed and is unable to find the right fit? I have attached the copasi file for my model. I have also attached the txt file which contains the synthetic data for the estimation. I have set the Species with boundary condition "true" and enzymes of the reaction to be independent variable (initial concentration), while those species with boundary condition false to be dependent variable (transient concentration) and the reactions V1-V9 to be dependent variable (fluxes of their respective reaction).
Please advice on how I rectify the problem.
Regards,
Chuan Fu Yap
I am attempting to run the parameter estimation using Copasi for a Mini Model I have constructed, however I get the following warnings after the estimation is complete. What does these errors mean? Does it mean the estimation has failed and is unable to find the right fit? I have attached the copasi file for my model. I have also attached the txt file which contains the synthetic data for the estimation. I have set the Species with boundary condition "true" and enzymes of the reaction to be independent variable (initial concentration), while those species with boundary condition false to be dependent variable (transient concentration) and the reactions V1-V9 to be dependent variable (fluxes of their respective reaction).
Please advice on how I rectify the problem.
Regards,
Chuan Fu Yap
>EXCEPTION 2015-03-25 19:52:17<
CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.17717e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.17717e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.17717e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.17717e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-4.35435e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-4.35435e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-4.35435e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.84038e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.84038e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.065241', R2 = '-2.84038e-19'
DLSODA- Above warning has been issued I1 times.
It will not be issued again for this problem.
In above message, I1 = '10'
DLSODA- At current T (=R1), MXSTEP (=I1) steps
taken on this call before reaching TOUT
In above message, I1 = '10000'
In above message, R1 = '-0.065241'
Please see result for indications of numerical instability
>EXCEPTION 2015-03-25 19:52:18<
CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0772318', R2 = '4.95417e-18'
DLSODA- Above warning has been issued I1 times.
It will not be issued again for this problem.
In above message, I1 = '10'
DLSODA- At current T (=R1), MXSTEP (=I1) steps
taken on this call before reaching TOUT
In above message, I1 = '10000'
In above message, R1 = '0.0772319'
Please see result for indications of numerical instability
>EXCEPTION 2015-03-25 19:52:23<
CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '2.71829e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '2.71829e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '2.71829e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '4.99589e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '4.99589e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '4.99589e-19'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '2.54347e-20'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '5.08693e-20'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '5.08693e-20'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '0.0102', R2 = '5.08693e-19'
DLSODA- Above warning has been issued I1 times.
It will not be issued again for this problem.
In above message, I1 = '10'
DLSODA- At current T (=R1), MXSTEP (=I1) steps
taken on this call before reaching TOUT
In above message, I1 = '10000'
In above message, R1 = '0.0102'
Please see result for indications of numerical instability
>EXCEPTION 2015-03-25 19:52:25<
CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-3.61387e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-3.61387e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-3.61387e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-3.61387e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-2.25677e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-2.25677e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-2.25677e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-2.25677e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-2.25677e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.120546', R2 = '-2.25677e-18'
DLSODA- Above warning has been issued I1 times.
It will not be issued again for this problem.
In above message, I1 = '10'
DLSODA- At current T (=R1), MXSTEP (=I1) steps
taken on this call before reaching TOUT
In above message, I1 = '10000'
In above message, R1 = '-0.120546'
Please see result for indications of numerical instability
>EXCEPTION 2015-03-25 19:52:29<
CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.228384', R2 = '-1.10783e-18'
DLSODA- Above warning has been issued I1 times.
It will not be issued again for this problem.
In above message, I1 = '10'
DLSODA- At current T (=R1), MXSTEP (=I1) steps
taken on this call before reaching TOUT
In above message, I1 = '10000'
In above message, R1 = '-0.228384'
Please see result for indications of numerical instability
>EXCEPTION 2015-03-25 19:52:30<
CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = '-0.141683', R2 = '-4.81436e-18'
DLSODA- Above warning has been issued I1 times.
It will not be issued again for this problem.
In above message, I1 = '10'
DLSODA- At current T (=R1), MXSTEP (=I1) steps
taken on this call before reaching TOUT
In above message, I1 = '10000'
In above message, R1 = '-0.141683'
Please see result for indications of numerical instability
>WARNING 2015-03-25 19:57:33<
CFitting (12): The Fisher information matrix is singular. Therefore, the correlation matrix can not be calculated.
>WARNING 2015-03-25 19:57:57<
Optimization (8): '828' Function Evaluations out of '3814' failed.
Stefan Hoops
Mar 25, 2015, 9:16:41 PM3/25/15
to copasi-u...@googlegroups.com
Hello Chuan,
The warning below says that about 20% of your tested parameters failed.
A certain number of failures is expected but above 10% COPASI will give
a warning since this indicates that your parameter range may be
unphysical. The DLSODA warnings are just more detailed information what
went wrong. In principle they tell you when (T) and the step size (H)
under which the integration did not continue.
The final result is nevertheless OK you just tried only 3000 parameter
sets successfully.
Thanks,
Stefan
On Wed, 25 Mar 2015 14:38:11 -0700 (PDT)
Chuan Fu Yap <yapch...@gmail.com> wrote:
> >WARNING 2015-03-25 19:57:57<
> Optimization (8): '828' Function Evaluations out of '3814' failed.
--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute
Virginia Tech
1015 Life Science Circle (0477)
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
Email: sho...@vbi.vt.edu
The warning below says that about 20% of your tested parameters failed.
A certain number of failures is expected but above 10% COPASI will give
a warning since this indicates that your parameter range may be
unphysical. The DLSODA warnings are just more detailed information what
went wrong. In principle they tell you when (T) and the step size (H)
under which the integration did not continue.
The final result is nevertheless OK you just tried only 3000 parameter
sets successfully.
Thanks,
Stefan
On Wed, 25 Mar 2015 14:38:11 -0700 (PDT)
Chuan Fu Yap <yapch...@gmail.com> wrote:
> >WARNING 2015-03-25 19:57:57<
> Optimization (8): '828' Function Evaluations out of '3814' failed.
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute
Virginia Tech
1015 Life Science Circle (0477)
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
Email: sho...@vbi.vt.edu
Message has been deleted
Chuan Fu Yap
Mar 26, 2015, 3:43:23 PM3/26/15
to copasi-u...@googlegroups.com
Dear Stefan,
Thank you for your response, it is much appreciated.
I have reduced the parameter range and that has stopped the warning of " x function evaluations out of x failed", but i still get DLSODA warnings, is there anything I can do to stop that from appearing as well?
What about this warning?
Thank you for your response, it is much appreciated.
I have reduced the parameter range and that has stopped the warning of " x function evaluations out of x failed", but i still get DLSODA warnings, is there anything I can do to stop that from appearing as well?
What about this warning?
>WARNING 2015-03-25 19:57:33<
CFitting (12): The Fisher information matrix is singular. Therefore, the correlation matrix can not be calculated.
Regards,
Chuan Fu
Chuan Fu
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