Problem in juicebox48g (Java program)

[Zhong Wang]

I tested the juicer.sh in SLURM environment on stampede.tacc.xsede.org and changed the codes to help it run normally. But the .hic file generated by juicebox48g looks like weird. The file attached in this post includes genome path, statistics information, variables(graphs A, B,D, x) in text format. Do you think it follows the Hi-C file format (version 8)?

I checked the debug file, one error happened in the java program, I am not sure whether the ,hic results is affected by this error. What do you think?

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.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1390)
    at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1161)
    at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:575)
    at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:306)
    at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:216)
    at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:94)
    at juicebox.tools.HiCTools.main(HiCTools.java:79)

I also have one suggestion. Because the pipeline maybe runs on the HPC environment and the results can not be visualized at same environment, please give a option to select the different genome path with the hic file in JuicerBox parogram. Now the genome path is included in .hic file, I didn't find to use the different one in JuicerBox.

Thanks,

Zhong Wang

[Neva Durand]

Hello Zhong Wang,

The error you got: "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."

means that no contact matrices were created.  What does your input file look like?  Does it have any reads in it?  Do all the reads map to the same fragment or have low mapping quality?

As to your suggestion: there is already an option in Juicer and in the "pre" command of the Juicebox command line tools to use your own genome.  If you use your own genome, the chromosome information is stored within the .hic file and Juicebox can read and display it.  If you look at the README.md here, you can see how to call Juicer with your own genome:

https://github.com/theaidenlab/juicer  

For Juicebox command line tools, it suffices to send in the appropriate chrom.sizes file instead of genomeID.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Zhong Wang]

My problem has been solved.

Because I used the wrong file for the parameter '-p' (chromosome size file), the pipeline stopped with this error message and outputted a head part of HIC result, which was very small (only has 15KB).

Thanks,

Zhong Wang

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