Form a combined .hic file

[narzouni]

Hello All,
I am trying to merge two hic maps, but I received some errors. I hope someone can give a helpful suggestion. I am using the following:

1- I combined two nodups pairs files as follows which generated the merged_1A1B.pairs file without any errors:

    sort -m -k2,2d -k6,6d Lib1_Sample1A_Mapped.pairs.gz  Lib2_Sample1B_Mapped.pairs.gz > merged_1A1B.pairs

2- if I try to generate the .hic file for the merged file, it gives an error. The command I am using is:

       java -Xmx48000m  -Djava.awt.headless=true -jar juicertools.jar pre --threads 16 merged_1A1B.pairs Merged_1A1B.hic mm39.genome

and the error is the following:

java.io.IOException: Unexpected column count. Check file format
at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:167)
at juicebox.tools.utils.original.AsciiPairIterator.(AsciiPairIterator.java:74)
at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:565)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:658)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:425)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:139)
at juicebox.tools.HiCTools.main(HiCTools.java:94)
java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
at juicebox.tools.utils.original.MatrixZoomDataPP.mergeAndWriteBlocks(MatrixZoomDataPP.java:276)
at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:970)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:659)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:425)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:139)
at juicebox.tools.HiCTools.main(HiCTools.java:94)