Error while visualizing contact files using juicebox

[tarak77]

Hi Tan,

I was trying to visualize one of the diploid cell contacts with and without haplotype imputation using the Juicebox tool. The haplotype-resolved .con file gives a visualization but the without haplotype resolved .con file gives me the following error:

wg-dhcp174d163d001:fraser-lab tarakshisode$ java -Xmx2g -jar juicer_tools.1.7.6_jcuda.0.8.jar pre -n ../dip-c/CDX1-413.20k/GSE117109_GSM2476407_1CDX1-413.dedup.juicer.txt.gz ../dip-c/CDX1-413.20k/1CDX1-413.dedup.hic mm9
Not including fragment map
Start preprocess
Writing header
Writing body
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$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1472)
    at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1243)
    at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:656)
    at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:378)
    at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:286)
    at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:105)
    at juicebox.tools.HiCTools.main(HiCTools.java:98)

Am I doing something wrong?

I have attached the deduce.juicer.txt.gz file, just in case GSE117109_GSM2476407_1CDX1-413.dedup.juicer.txt.gz

[tanlongzhi]

I just tested visualization on the same file; and it worked well. Please see screenshot below:

In contrast, your .juicer.txt.gz file is somehow empty. Can you provide your command and input file to generate that file?

Btw, after you generate a good .juicer.txt.gz file, you should use mm10 instead of mm9 in the juicer_tools step, because I mapped those reads to mm10 coordinates.

[tarak77]

I actually used the same command as in the repo

wg-dhcp174d163d001:dip-c tarakshisode$ ./con_to_juicer_pre_short.sh ./CDX1-413.20k/GSE117109_GSM2476407_1CDX1-413.dedup.con.gz

Ok I will use mm10

[tanlongzhi]

I just tested this command both on macOS High Sierra and on CentOS 7. Below is the .juicer.txt.gz file that I generated. You can see its content; I'm not sure what led to your empty file. GSE117109_GSM2476407_1CDX1-413.dedup.juicer.txt.gz

And below is my input file (downloaded from the GEO and renamed), in case it is different from yours. GSE117109_GSM2476407_1CDX1-413.dedup.con.gz

[tarak77]

I see now, there might be some issue when I downloaded the file. Thanks!