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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
399 stars 181 forks source link

Why does not run with res: 40000 to produce results #305

Closed songxh1996 closed 1 year ago

songxh1996 commented 1 year ago

I encountered the following error, please help me, thank you

java -jar $juicer_tool hiccups --cpu --threads 40 --ignore-sparsity -m 1024 -k KR -p 4,2 -r 25000,40000 -t 0.02,1.5,1.75,2 ${path}/juicer/buffalo_clean.allValidPairs.hic ${path}/loop2

WARN [2023-02-11T21:15:08,162] [Globals.java:138] [main] Development mode is enabled Reading file: /home/songxh/cres/H/zm/longmiss/juicer/buffalo_clean.allValidPairs.hic Resolution 40000 not available. Discarding invalid configuration: Config res: 25000 peak: 4 window: 3 fdr: 10% radius: 50000 No valid configurations specified, using default settings WARNING - You are using the CPU version of HiCCUPS. The GPU version of HiCCUPS is the official version and has been tested extensively. The CPU version only searches for loops within 8MB (by default) of the diagonal and is still experimental. Using 40 CPU thread(s) Warning Hi-C map is too sparse to find many loops via HiCCUPS. Default settings for 5kb, 10kb, and 25kb being used Running HiCCUPS for resolution 5000 4% 9% ...

sa501428 commented 1 year ago

Hi, please use the forum for general questions. This has been answered here: https://groups.google.com/g/3d-genomics/c/h5WG8JuKajM/m/2XVARYoqDAAJ