`-g` argument not getting passed to `juicer_postprocessing.sh`

[agilly]

This is hopefully the last issue I post!

After upgrading to Juicer Tools 2.13.07 (Juicer was pulled from github using git clone), I successfully manage to pick up my process and run all steps until the very last. However, after writing norms, postprocessing fails. It seems -p hg38 is not getting translated to juicer_postprocessing.sh -g hg38.

$> ./opt/scripts/juicer.sh -S final -D $(readlink -f opt) -z $(pwd)/opt/references/hg38.p13.fa.gz -d $(pwd)/L79851_Track-123454/ -p hg38 -t 32
Finished writing norms

real    123m24.622s
user    714m45.769s
sys     18m23.893s
Juicer/opt/scripts/common/juicer_postprocessing.sh: option requires an argument -- g
Usage: Juicer/opt/scripts/common/juicer_postprocessing.sh [-h] -j <juicer_tools_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>

[sa501428]

Hey @agilly! Which file are you seeing this bug in? It seems like it's getting passed here: https://github.com/aidenlab/juicer/blob/main/CPU/juicer.sh#L758

[Norbittner]

Hi @sa501428

I'm part of agilly's team who intitiated the issue and i'm also working on implementing the juicer piepline in our lab. I want to add a new finding to the bug issue he raised which might help in resolving the issue.

I rerun his command with adding -g h38 manually and then the postprocessing starts without any problem and the pipeline is running fine.

Still the function of giving the genome id with the -z command is not working when giving the path as agilly did in his code posted (the reference directory he is pointing to has all the bwa index files)

I also did a rerun with giving the argument -z hg38 which also didn't resolve the problem.