error when run MICC.R about chia-pet2 HOT 8 OPEN

How many interactions that with at least 6 PETs supported does the dataset have ? Coud this error be repeatable if you try the below command?

~/software/executable_file/R-3.4.3/bin/Rscript /public1/home/pg3152/lien/software/ChIA-PET2-master/bin/MICC2.R seedling_H3K4me3_interactions.intra.bedpe seedling_H3K4me3_interactions.inter.bedpe miccOUT 2 5 1e-10

from chia-pet2.

Has this problem been resolved? I have encountered exactly the same problem. Would be appreciated a lot if any solutions/suggestions can be posted.

Here is the log:

Rscript /homes6/ykai/bin/MICC2.R P1_interaction.out.bedpe.intra.bedpe P1_interaction.out.bedpe.inter.bedpe miccOUT 1 1 1e-2
Loading required package: stats4
Loading required package: splines
Running MICC...
Intra data: P1_interaction.intra.bedpe
Inter data: P1_interaction.inter.bedpe
Output file: P1
PET count cutoff: 1
Minimun Confident PET count: 1
reltol: 0.01
Loading intra data...
Loading inter data...
Cacluating...
Intra: 101627 Inter: 49322
Error in optim(InitialValue, fn = Loglik.theta12.params, gr = D1.Loglik.theta12.params, :
L-BFGS-B needs finite values of 'fn'
Calls: MICCoutput2 ... Estimate.Theta12.params -> Solve.Theta12.params -> optim
In addition: Warning messages:
1: In zeta(theta) : value out of range in 'gammafn'
2: In log(ZetaTruncated(theta)) : NaNs produced
3: In zeta(theta) : value out of range in 'gammafn'
4: In log(ZetaTruncated(theta)) : NaNs produced
Execution halted

from chia-pet2.

I have tried the command you suggested, and this error was repeatable.

from chia-pet2.

@liencau @ykai16
Could you provide the test dataset ? so I can work on this

from chia-pet2.

@GuipengLi , I just sent my data to your gmail box. Thank you.

from chia-pet2.

Hi ,
I am encoutring the same issue , is there any update for this issue ?
This issue have been raised from many days , @GuipengLi it is my humble request to mark your comment on this issue.
Thank you.

#CMD# :

Rscript /home/abhishek/bin/ChIA-PET2_0.9.3/bin/MICC2.R
/mnt/raid/abhishek/ChIA-PET_gm12878/step_5/interaction.out.bedpe.intra.bedpe
/mnt/raid/abhishek/ChIA-PET_gm12878/step_5/interaction.out.bedpe.inter.bedpe
/mnt/raid/abhishek/ChIA-PET_gm12878/step_6 2 5 1e-10

#OUTPUT# :

Loading required package: VGAM
Loading required package: methods
Loading required package: stats4
Loading required package: splines
Running MICC...
Intra data: /mnt/raid/abhishek/ChIA-PET_gm12878/step_5/interaction.out.bedpe.intra.bedpe
Inter data: /mnt/raid/abhishek/ChIA-PET_gm12878/step_5/interaction.out.bedpe.inter.bedpe
Output file: /mnt/raid/abhishek/ChIA-PET_gm12878/step_6
PET count cutoff: 2
Minimun Confident PET count: 5
reltol: 1e-10
Loading intra data...
Loading inter data...
Cacluating...
Intra: 27042 Inter: 14412
Error in optim(InitialValue, fn = Loglik.theta12.params, gr = D1.Loglik.theta12.params, :
L-BFGS-B needs finite values of 'fn'
Calls: MICCoutput2 ... MICCMainLearn -> EMIter -> Solve.Theta12.params -> optim
In addition: Warning messages:
1: In dhyper(cAB, cA, 2 * N - cA, cB, log = TRUE) : NaNs produced
2: In dhyper(0, cA, 2 * N - cA, cB) : NaNs produced
Execution halted

from chia-pet2.

Hi ,
I am encoutring the same issue , is there any update for this issue ?

[07-26 03:06:04] Running Step 7: MICC ...

Rscript /usr/bin/MICC2.R OUTdir7/index-1.interactions.intra.bedpe OUTdir7/index-1.interactions.inter.bedpe OUTdir7/index-1.interactions.MICC 2
载入需要的程辑包：VGAM
载入需要的程辑包：stats4
载入需要的程辑包：splines
Running MICC...
Intra data: OUTdir7/index-1.interactions.intra.bedpe
Inter data: OUTdir7/index-1.interactions.inter.bedpe
Output file: OUTdir7/index-1.interactions.MICC
PET count cutoff: 2
Minimun Confident PET count: 5
reltol: 1e-08
Loading intra data...
Loading inter data...
Cacluating...
Intra: 421 Inter: 11
Error in optim(InitialValue, fn = Loglik.theta12.params, gr = D1.Loglik.theta12.params, :
L-BFGS-B不能有'fn'的无限值
Calls: MICCoutput2 ... MICCMainLearn -> EMIter -> Solve.Theta12.params -> optim
此外: Warning messages:
1: In dhyper(cAB, cA, 2 * N - cA, cB, log = TRUE) : 产生了NaNs
2: In dhyper(0, cA, 2 * N - cA, cB) : 产生了NaNs
停止执行

from chia-pet2.

Hi,

I got same errors when in the MICC step. Is this problem correlated with R version?

Loading required package: ggplot2
Loading required package: scales
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Error in optim(InitialValue, fn = Loglik.theta12.params, gr = D1.Loglik.theta12.params, :
L-BFGS-B needs finite values of 'fn'
Calls: MICCoutput2 ... MICCMainLearn -> EMIter -> Solve.Theta12.params -> optim
In addition: Warning messages:
1: In dhyper(cAB, cA, 2 * N - cA, cB, log = TRUE) : NaNs produced
2: In dhyper(0, cA, 2 * N - cA, cB) : NaNs produced
Execution halted

Best,
Thanks

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