ChIA-PET2: Error: Don't have enough confident interactions to learn the model.

Question

[bioinfo89]

Hi All,

I am currently getting the following error when I use ChIA-PET2:

Running MICC...
Intra data:  ChIAPET_rawdata/rep1_ChIAPET.interactions.intra.bedpe 
Inter data:  ChIAPET_rawdata/rep1_ChIAPET.interactions.inter.bedpe 
Output file:  ChIAPET_rawdata/rep1_ChIAPET.interactions.MICC 
PET count cutoff:  2 
Minimun Confident PET count:  5 
reltol:  1e-08 
Loading intra data...
Loading inter data...
Cacluating...
Intra:  252     Inter: 59 
Error: Don't have enough confident interactions to learn the model.
Execution halted

I checked for adaptor contamination using FastQC and also confirmed the Linker sequences as mentioned in your above suggestions to solve the error. But I still get the same error.

I am using the following command:

ChIA-PET_tools/ChIA-PET2-0.9.3/bin/ChIA-PET2 -t 4 -d 1 -Q 20 -g /hg19/hg19.fa -b /hg19/hg19.chrom.sizes -f rep1_R1_combined.fastq.gz -r rep1_R2_combined.fastq.gz -A GTTGGATAAG -B GTTGGAATGT -o ChIAPET_rawdata -n rep1_ChIAPET

Attached is my QC_plot file: rep1_ChIAPET.QCplot.pdf

And I am using the following data for analysis (Replicate 1): https://www.encodeproject.org/experiments/ENCSR672RHL/

I am not sure what exactly in my case is causing this error. Any help from your end would be appreciated. Thank you!

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[lakhujanivijay]

Hi bioinfo89

The best way to troubleshoot such errors is to look at the source code. The error is thrown from these lines of this R script

And, this is not a new issue, someone has reported similar one here. See if you can find any clue. Sounds like it is related to either trimming or high level of duplication.