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aidenlab / juicer

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

dump error #167

Closed xiaowenchenjax closed 2 years ago

xiaowenchenjax commented 4 years ago

Are you sure this is a bug? If unsure, please post your question/situation to the forum first: aidenlab.org/forum.html

Describe the bug running "java -jar juicer_tools_1.19.02.jar dump observed KR inter_30.hic 1 1 BP 100000 SCI_input.txt" the error : "WARN [2020-05-12T15:04:55,107] [Globals.java:138] [main] Development mode is enabled Exception in thread "main" java.lang.NullPointerException at juicebox.tools.clt.old.Dump.extractChromosomeRegionIndices(Dump.java:454) at juicebox.tools.clt.old.Dump.readArguments(Dump.java:323) at juicebox.tools.HiCTools.main(HiCTools.java:93)" To Reproduce Steps to reproduce the behavior:

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Gonysh commented 4 years ago

I'm experiencing the same issue with juicer_tools_1.21.01, running on Ubuntu 14.04.

nchernia commented 4 years ago

@sa501428

sa501428 commented 3 years ago

@Gonysh @xiaowenchenjax can you share a link to a hic file which is failing this command?

sa501428 commented 2 years ago

I would highly recommend using https://github.com/aidenlab/straw instead of the dump command.