Issues

• Correct genome size value for asm.size.txt when generating .hic file for large diploid assembly

  aidenlab/juicer#395 · Filter by author FAndresReyes opened on Jun 24, 2026

• Juicer SLURM Submission Error: Invalid Time Limit / Dependency Problem

  aidenlab/juicer#393 · Filter by author IrinaVKuznetsova opened on Apr 15, 2026
  1

• Which version is the official release for juicer_tools

  aidenlab/juicer#392 · Filter by author cassidy-a-johnson opened on Feb 4, 2026
  1

• does not create merged_nodups.txt

  bug
  aidenlab/juicer#391 · Filter by author cip25 opened on Feb 3, 2026

• Intra-chromosomal interactions and Long Range are less

  aidenlab/juicer#390 · Filter by author Nitin123-4 opened on Jan 9, 2026

• Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics

  bug
  aidenlab/juicer#389 · Filter by author Renshengjie opened on Dec 31, 2025

• Incorrect support of 4DN DCIC format (pairs) in recent Pre versions (worked in 1.22.01 but fails in 2.16.00 and later)

  bug
  aidenlab/juicer#387 · Filter by author tanlongzhi opened on Nov 17, 2025
  2

• Unable to find All-All or All-All

  aidenlab/juicer#386 · Filter by author HHan-ZJU opened on Nov 16, 2025

• juicer merged_nodups.txt > cool ?

  aidenlab/juicer#385 · Filter by author Zheng19w opened on Nov 11, 2025

• "juicer_tools: Permission denied" error

  aidenlab/juicer#384 · Filter by author wen10-git opened on Nov 2, 2025
  1

• Run too longtime

  bug
  aidenlab/juicer#383 · Filter by author ucsfpan opened on Sep 30, 2025
  4

• not able to run the juicer tool

  aidenlab/juicer#382 · Filter by author Ram-Nagar opened on Sep 28, 2025

• identify chromatin loops

  aidenlab/juicer#381 · Filter by author qixin271 opened on Sep 6, 2025

• generate_site_positions.py

  bug
  aidenlab/juicer#379 · Filter by author SeqMaster opened on Aug 7, 2025

• addNorm -w flag not work

  bug
  aidenlab/juicer#378 · Filter by author Miracle-Yao opened on Jul 18, 2025

• how to generate combined analysis

  aidenlab/juicer#377 · Filter by author GenomeArch opened on Jun 30, 2025

• SLURM/juicer.sh wrong account submitting job

  bug
  aidenlab/juicer#375 · Filter by author zapell opened on Jun 6, 2025
  2

• Failure to generate .hic file

  aidenlab/juicer#373 · Filter by author qixin271 opened on May 8, 2025

• Failure in converting merged_nodups.txt to a .hic matrix.

  aidenlab/juicer#370 · Filter by author qixin271 opened on Apr 28, 2025
  2

• juicer.sh is not compatible with iso TIME_STYLE

  bug
  aidenlab/juicer#369 · Filter by author Fan-iX opened on Apr 28, 2025
  1

• Attempt to run on Colab CPU - .bam files missing!

  aidenlab/juicer#365 · Filter by author nickkolok opened on Jan 28, 2025

• Wrong reference genome indicated in the juicer.log

  bug
  aidenlab/juicer#364 · Filter by author Audald opened on Dec 28, 2024
  5

• Increase usablity on other systems by updating (SLURM)/scripts/juicer.sh

  aidenlab/juicer#363 · Filter by author bclaremar opened on Dec 12, 2024
  7

• Errors in the run log

  bug
  aidenlab/juicer#361 · Filter by author Hlc813 opened on Oct 26, 2024

• How can I generate a .hic contact matrix at the fragment level using Micro-C data?

  aidenlab/juicer#359 · Filter by author hanshanmengqi opened on Oct 4, 2024