search

GuipengLi / ChIA-PET2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data
GNU General Public License v3.0
33 stars 19 forks source link

error when run MICC.R #19

Open liencau opened 5 years ago

liencau commented 5 years ago

my code: ~/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 3 6 1e-10

Output for running MICC.R: Loading required package: VGAM Loading required package: methods Loading required package: stats4 Loading required package: splines Running MICC... Intra data: seedling_H3K4me3_interactions.intra.bedpe Inter data: seedling_H3K4me3_interactions.inter.bedpe Output file: miccOUT PET count cutoff: 3 Minimun Confident PET count: 6 reltol: 1e-10 Loading intra data... Loading inter data... Cacluating... Intra: 24481 Inter: 27511 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 Execution halted

GuipengLi commented 5 years ago

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

ykai16 commented 5 years ago

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

liencau commented 5 years ago

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

GuipengLi commented 5 years ago

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

ykai16 commented 5 years ago

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

ag-abhishek commented 3 years ago

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

sun-huimin commented 3 years ago

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

myliu221 commented 3 years ago

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