error: no reads in HI-C contact Matrix, java.lang.RuntimeException

[abe2016]

Hi, 

I am getting the following error when I run juicer.sh in the hic-*.err file: 

java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too hi

gh (-q) or because all reads map to the same fragment.

at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1397)

at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1168)

at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:582)

at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:313)

at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:223)

at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:98)

at juicebox.tools.HiCTools.main(HiCTools.java:77)

However, I know it is not a quality issue because in inter.txt, only about 1% of the reads fall below mapq threshold. 

I searched this forum and looks like others have gotten the same error before. I made sure that the reference genome matches with the chromosome sizes file I have as well. 

Could someone advice the best way to debug this? 

Thank you

Abe

[Muhammad Saad Shamim]

Hey Abin,

Are any of these reasons relevant?

(chromosome name / sorted input)

https://groups.google.com/forum/#!searchin/3d-genomics/No$20reads$20in$20Hi-C$20contact$20matrices|sort:relevance/3d-genomics/h14qevPLUso/6Gzeh8xtHAAJ

(different fragment numbers)

https://groups.google.com/forum/#!searchin/3d-genomics/No$20reads$20in$20Hi-C$20contact$20matrices%7Csort:relevance/3d-genomics/IlCh-dxT2_0/e3yCBNS-BgAJ

- Muhammad Saad Shamim

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