Error while reading graphs file: java.io.FileNotFoundException: /master/kristina_leem/hi_c/juicer/work/HIC003/aligned/inter_hists.m (No such file or directory)

[임도경]

Hello,

I am having problems with running juicer.sh on the HIC003 fastqs provided on the juicer github page. The files up to bwa alignment is built succesfully, but it seems to run into errors when creating the hist.m files. Since the hist.m files are not created, empty/incorrect .hic files and contact & loop directories are created at the end. I will attach a screenshot of the slurm-output file with the error messages, my scripts/common/ directory my aligned output directory. It would be greate if you guys can help me out. 

Sincerely,

Kristina Leem

[Wenjun Yan]

Hi

I'm using juicer_tools.2.20.00.jar and I'm having the same issue, no inter_hists.m or merged1_index.txt files were generated in the aligned folder. And error message ( Error while reading graphs file: java.io.FileNotFoundException:xxx/aligned/inter_hists.m (No such file or directory)) was reported in the hic-xxx.err file. Since .hic files were generated, I wonder if it's necessary to generate the inter_hists.m file? The Juicer Pre wiki page says that "-g <graphs file> Add the text graphs file to the Hi-C file header", but I'm not sure how the header could affect downstream analysis. If it's indeed required, not do I generate it?  How do I generate it? Any suggestion is appreciated.

Best,

Wenjun