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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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hicpro2juicer.sh issue: no output #443

Closed Paladin258 closed 3 years ago

Paladin258 commented 3 years ago

Hello,

I'm running hicpro2juicer.sh to make hic file for visualization with I don't get any output files. Here is my command:

/HiC-Pro-3.0.0/3.0.0/bin/utils/hicpro2juicebox.sh -i HiC_1.allValidPairs \ -j /juice_box/Juicebox-master/out/artifacts/juicer_tools_jar/juicer_tools.jar \ -r RE_file -g hg38_size -o out_files

the log below seems to indicate the job finished but I don't see any output. Any help will be appreciated.

HiC-Pro format > 2.7.5 detected ... Generating Juicebox input files ... Running Juicebox ... WARN [2021-05-25T23:17:48,249] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) 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 !

nservant commented 3 years ago

Hi, Which Juicer version are you using please ? Would you have any files in the temporary folder ? Thanks

Paladin258 commented 3 years ago

Hello,

Thank you for your response. I'm currently using their most recent juicer version 1.5. There were some files in the tpm folder when I monitored the job but no files saved anywhere when it's done.

Paladin258 commented 3 years ago

Hi,

Sorry for your time. I was able to resolve the issues.