###STDERR:<< Exception in thread "main" java.lang.NullPointerException at juicebox.tools.clt.old.Dump.extractChromosomeRegionIndices(Dump.java:467) at juicebox.tools.clt.old.Dump.readArguments(Dump.java:364) at juicebox.tools.HiCTools.main(HiCTools.java:85) >>

[LaForever]

Hello, recently I encountered the same error when running Centromics on different servers. My command is ：
centromics -l hifi.clean.fasta.gz -g nogap_verkkofilling_Chr1_12.fasta -pre hifihic -hic merged_nodups.hic -tmpdir hifihic.tmp -ncpu 20
Here is the error message：
24-03-12 10:01:54 [INFO] run CMD: java -jar /public/home/zhaojiale/software/yes/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE merged_nodups.hic Chr2 Chr9 BP 100000 /public/home/zhaojiale/KLF/centromics/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr9.100000.mat
24-03-12 10:01:55 [WARNING] exit code 1 for CMD java -jar /public/home/zhaojiale/software/yes/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE merged_nodups.hic Chr2 Chr6 BP 100000 /public/home/zhaojiale/KLF/centromics/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr6.100000.mat:
24-03-12 10:01:55 [WARNING]
###STDOUT:<< HiC file version: 8

###STDERR:<< Exception in thread "main" java.lang.NullPointerException
at juicebox.tools.clt.old.Dump.extractChromosomeRegionIndices(Dump.java:467)
at juicebox.tools.clt.old.Dump.readArguments(Dump.java:364)
at juicebox.tools.HiCTools.main(HiCTools.java:85)

I'm not sure if this is a problem with the Java version, but the error I encountered is the same on both servers.

[zhangrengang]

I have no sense about the error. You can just run the command java -jar /public/home/zhaojiale/software/yes/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE merged_nodups.hic Chr2 Chr6 BP 100000 /public/home/zhaojiale/KLF/centromics/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr6.100000.mat to debug, or try new version of juicebox_tools (https://github.com/aidenlab/juicer/).