Thanks - someone else noticed this too and made a pull request and I wrote there as well. See https://github.com/theaidenlab/juicer/pull/26

[Djangodu]

          Thanks - someone else noticed this too and made a pull request and I wrote there as well.  See https://github.com/theaidenlab/juicer/pull/26

We're keeping this structure for now and you should soft-link, see https://github.com/theaidenlab/juicer/wiki/Installation#quick-start

Originally posted by @theaidenlab in #30 (comment)

[Djangodu]

Dear,
It is twice I make genome assembly work with juicer.sh, the first time I finish it very well, but this time I also miss this Path issue for CPU script execution problem.
As you last suggestion, the first time I did the sort-link, also this time, but it didn't work with this operation. I don't know why it happened, and I just use the first time conda enviroment and the same juicer.sh version, the same juicer work file with the same soft-link, but didn't work.

at the begining, will found that:

/public/home/swun-duzhany/chromosome_assemble_annotation/JL-sheep_6.12.24/juicer/scripts/juicer.sh: line 358: /opt/juicer/scripts/common/countligations.sh: No such file or directory

and will end with like this：

***! Failure during chimera handling of /gpfs/gibbs/pi/ycga/mane/at2253/wangSung/20221019_HiC/AS-FB_HiC//splits/AS-FB-HiC_AHV5HHDSX3_L001_001.fastq.gz

I am try many times, and make soft-link, and download new version, but didn't work any more.

please help me, it is a little disappointed with this problem.