ChIA-PET2: Error: Don't have enough confident interactions to learn the model.
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Entering edit mode
13 months ago
bioinfo89 ▴ 40

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!

ChIP-Seq • 316 views
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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.
code_formatting

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Entering edit mode
12 months ago

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.

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