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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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Form a combined .hic file #350

Open narzouni opened 1 month ago

narzouni commented 1 month ago

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)