Java Error unable to create virtual machine

[abe2016]

Hi, 

I keep getting the following error when I get to the hic block within the juicer.sh script: 

Unrecognized option: -Xgcthreads1

Error: Could not create the Java Virtual Machine.

Error: A fatal exception has occurred. Program will exit.

This is the version of java I am running: 

java version "1.8.0_45"

Java(TM) SE Runtime Environment (build 1.8.0_45-b14)

Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

I think this might be the incorrect version of java? Could you advice? 

Thank you! 

[Neva Durand]

Hello,

The short answer is, look at the script "juicebox" and get rid of that option.

The longer answer is, I'm not sure why you're getting "Unrecognized option" because it's not obvious (from a quick web search) that this is deprecated.  You can look at this site for an explanation of the -Xgcthreads option:

http://www.ibm.com/support/knowledgecenter/SSYKE2_7.0.0/com.ibm.java.win.70.doc/diag/appendixes/cmdline/xgcthreads.html

In any case, we needed this for our SLURM cluster system, but if you don't need it, just remove it.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

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[Kyle Patrick Eagen]

Hi,

I had this problem as well on our SLURM cluster which seemed to be dependent on whether Juicer is using IBM or Oracle Java.  IBM Java uses option -Xgcthreads1 whereas Oracle uses -XX:ParallelGCThreads=1 so try changing the line within the "juicebox" script to this.

Best,

Kyle

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Kyle P. Eagen
M.D./Ph.D. Doctoral Student
Medical Scientist Training Program
Program in Biophysics
Roger Kornberg Laboratory
Department of Structural Biology
Stanford University School of Medicine
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[abe2016]

Thank you Kyle! 

I ended up removing -Xgcthreads1 and everything seems to be working. I will try your suggestion as well.