Index 3 out of bounds for length 2 Error

[Dario Copetti]

Hello,

I am running juicer pre to generate a .hic file from CiFi data but I get the following error:

Starting Post-Processing for UROCH...
Filtration Statistics:
Total pairs processed: 12241419
Passed pairs: 3505587
Failed due to unmapped: 4839491
Failed due to not paired: 262553
Failed due to low MAPQ: 3896341
Failed due to mate not found: 0
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-12-18T18:30:08,780]  [Globals.java:138] [main]  Development mode is enabled
Using 16 CPU thread(s) for primary task
Using 10 CPU thread(s) for secondary task
No mndIndex provided
Using single threaded preprocessor
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.ArrayIndexOutOfBoundsException: Index 3 out of bounds for length 2
        at juicebox.tools.utils.original.mnditerator.ComplexLineParser.generateBasicPair(ComplexLineParser.java:56)
        at juicebox.tools.utils.original.mnditerator.MNDFileParser.parseDCICFormat(MNDFileParser.java:118)
        at juicebox.tools.utils.original.mnditerator.MNDFileParser.parse(MNDFileParser.java:83)
        at juicebox.tools.utils.original.mnditerator.GenericPairIterator.advance(GenericPairIterator.java:56)
        at juicebox.tools.utils.original.mnditerator.GenericPairIterator.next(GenericPairIterator.java:46)
        at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:603)
        at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:690)
        at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:452)
        at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:176)
        at juicebox.tools.HiCTools.main(HiCTools.java:97)
srun: error: n010: task 0: Exited with exit code 56
__ Post-processing failed!

the command is 

java -jar /opt/nextflow_assets/juicer_tools.2.20.00.jar pre -t /tmp -j 16 DOR364n.bam2pairs.bsorted.pairs.gz output.hic sizes.genome

and the pairs.gz file was generated with this pipeline

https://github.com/mydennislab/CiFi

I get an empty .hic file, but a colleague was able to generate one that has data. I was able to upload that file on Juicebox, but I can't edit the matrix - clicking on a section, I just zoom in. There are no green and blue lines on the matrix as well.

How do I resolve the out of bounds error and how can I edit the map?
Thanks,

Dario