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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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hicpro2juicebox.sh #446

Open Paladin258 opened 3 years ago

Paladin258 commented 3 years ago

Hello,

I used to use hicpro2juicebox.sh to convert hicpro valid pairs to hic for Juicebox with 2 steps: step 1: use hicpro2juicebox.sh with Juicebox.jar to make pre hic files step 2: juicer_tools.jar with pre command on pre_sorted from step 1 to make hic

Years later, I installed new version Hicpro 3.0 and new juicer tools. From all the threads I've read, it seems hicpro2juicebox.sh now uses juicer_tools.jar instead of Juicebox.jar with 1 step to make hic files. Correct me if I'm wrong on that. I'm still a little confused. So I tried and it does not seem to work. My hic file appears small (66M instead of 1-2 GB) and it does not work on Juicebox software. Please any help will be appreciated.

nservant commented 3 years ago

Hi Yes, it uses the Juicer command line, and not Juicebox. Do you have any messages, something, to validate that there is an issue with your file ? N

Paladin258 commented 3 years ago

Hi,

Here is the log:

HiC-Pro format > 2.7.5 detected ... Generating Juicebox input files ... Running Juicebox ... WARN [2021-05-26T14:02:03,096] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/math3/stat/descriptive/DescriptiveStatistics at juicebox.tools.utils.original.MatrixZoomDataPP.computeStats(MatrixZoomDataPP.java:675) at juicebox.tools.utils.original.MatrixZoomDataPP.mergeAndWriteBlocks(MatrixZoomDataPP.java:482) at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:1038) at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:675) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:434) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:161) at juicebox.tools.HiCTools.main(HiCTools.java:94) Caused by: java.lang.ClassNotFoundException: org.apache.commons.math3.stat.descriptive.DescriptiveStatistics at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ... 7 more done !

I'm not sure if it could relate to memory issues. It says using 1 CPU thread(s). I did assign 48 cores for the task.

raquelsofi commented 2 years ago

Hi i'm having similar issue, could you identify which jar file works to run the hicpro2juicebox.sh utility? On my situation it creates the Temp folder and then crashes with issue with the jar file.

Thank you, Raquel