I want to use IGV on a server so I don't have to download bam files to my local machine. I used conda to install igvtools. When I type igvtools in the command line I get this error:
Using system JDK. Unrecognized option: --module-path=/home/kmmahan/miniconda3/envs/igv/share/igvtools-2.5.3-0/lib Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
Any help would be appreciated
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kristina.mahan
If any one looking for the fix, install the latest openjdk using conda by conda install -c conda-forge openjdk and it works.
I did this and I got :
:# All requested packages already installed.
But still I get an error that igv cannot load my sam file..
Yes , my sam file was sorted and indexed ,I fixed the problem by uploading the correct reference genome. I didnt know that the default refseq is the human genome. thats was my problem.
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IGV can be used on a server. Do you have
javainstalled on this server? IGV needs Java. Local installs requireJava 11.(igv) [kmmahan@blogin4 analysis]$ java -version openjdk version "1.7.0_91" OpenJDK Runtime Environment (Zulu 7.12.0.3-linux64) (build 1.7.0_91-b15) OpenJDK 64-Bit Server VM (Zulu 7.12.0.3-linux64) (build 24.91-b15, mixed mode)
So it is using JDK instead of JVM?
I am guessing that 1.7 is based on Java 7? If thats the case you will need to update this.
I am pretty sure that
igvtoolsis not the same thing as IGV.Command line version of IGV includes igvtools. That package requires
Java 11.