Comments (8)
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
from chia-pet2.
Related Issues (20)
- Unable to start CPT2 HOT 10
- Download ChIA-PET2.tar.gz Url HOT 5
- enough confident interactions to learn the model HOT 3
- stopped at 4th stage HOT 3
- std::bad_alloc error HOT 4
- extend parameter not used? HOT 2
- BWA issue
- bug in trimLinker -h HOT 3
- MayBe error for the main bedpe2Phased HOT 2
- How can we get the significant Interactions? HOT 4
- Runnung Error in Step2,input error HOT 1
- need remove -sorted in the latest version of bedtools
- ERROR: The input file is neither a BAM file nor a SAM file.
- Solution to ld missing -lz during make
- Truncated .tag.sort file error: rmdup.bedpe.tag.sorted has 3 fields, but 6 were expected. HOT 1
- MICC error: there is no package called 'VGAM' HOT 4
- Sam file is not written HOT 2
- bedpe2Interaction core dumped HOT 2
- macs2 callpeaks
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from chia-pet2.