Juicebox .jar file not found. Exit

[lifan2022]

Hello,
Thank you for providing this powerful software！
I'm having some problems with the hicpro2juicebox.sh.

> /home/lifan/software/hicpro/HiC-Pro-3.1.0/bin/utils/hicpro2juicebox.sh \
> -i /home/lifan/lixiang/result/hic/XX-1/hic_result/data/XX-1/XX-1.allValidPairs \
> -g /home/lifan/index/mouse_GRCm39_ensembl/genome.sizes \
> -j /home/lifan/software/juicer/juicer/scripts/common/juicer_tools.2.20.00.jar \
> -o /home/lifan/lixiang/result/hic/XX-1/hic_result/data/XX-1/result/ \
> -r /home/lifan/lixiang/result/hic/XX-1/hic.bed
> Juicebox .jar file not found. Exit

An error message is displayed: "Juicebox .jar file not found. Exit". But my juicer_tools.2.20.00.jar is working.

1. java -jar /home/lifan/software/juicer/juicer/scripts/common/juicer_tools.2.20.00.jar WARN [2024-12-22T16:39:50,575] [Globals.java:138] [main] Development mode is enabled Juicer Tools Version 2.20.00 Usage: dump <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize> [outfile] dump <norm/expected> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile] dump <loops/domains> <hicFile URL> [outfile] pre [options] <infile> <outfile> <genomeID> addNorm <input_HiC_file> [input_vector_file] pearsons [-p] <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile] eigenvector -p <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile] apa <hicFile(s)> <PeaksFile> <SaveFolder> arrowhead <hicFile(s)> <output_file> hiccups <hicFile> <outputDirectory> hiccupsdiff <firstHicFile> <secondHicFile> <firstLoopList> <secondLoopList> <outputDirectory> validate <hicFile> -h, --help print help -v, --verbose verbose mode -V, --version print version Type juicer_tools <commandName> for more detailed usage instructions

I've also tried other versions of juicer_tools.jar or Juicebox.jar but I'm getting the same issue.Hope you can help me.

[hrk110]

I'm unfamiliar with HiC-Pro, but your jar file is 'juicer_tools.2.20.00.jar', which is not 'juicebox.jar'. (I think this isn't very clear)
You can download juicebox.jar from the JuiceboxGUI repo: https://github.com/aidenlab/JuiceboxGUI/releases/tag/v3.1.4
Hope this helps!

[lifan2022]

Thanks for your help. But based on some of the tutorials I read, hicpro2juicebox.sh now uses juicer_tools.jar instead of Juicebox.jar to make hic files. I've tried using juicebox.jar but I'm still getting the same error.

I'm unfamiliar with HiC-Pro, but your jar file is 'juicer_tools.2.20.00.jar', which is not 'juicebox.jar'. (I think this isn't very clear) You can download juicebox.jar from the JuiceboxGUI repo: https://github.com/aidenlab/JuiceboxGUI/releases/tag/v3.1.4 Hope this helps!