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!