Error when trying to run IGV on server

Question

[kristina.mahan]

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.

1. Can igv be used on a server
2. How do you launch igv once it is installed on a server
3. What are these errors?

Any help would be appreciated

[steve]

I am pretty sure that igvtools is not the same thing as IGV.

[GenoMax]

Command line version of IGV includes igvtools. That package requires Java 11.

[GenoMax]

IGV can be used on a server. Do you have java installed on this server? IGV needs Java. Local installs require Java 11.

[kristina.mahan]

(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?

[steve]

I am guessing that 1.7 is based on Java 7? If thats the case you will need to update this.

Answer 1

[kvshamsudheen]

If any one looking for the fix, install the latest openjdk using conda by conda install -c conda-forge openjdk and it works.

[Michal Nevo]

I did this and I got :

:# All requested packages already installed.

But still I get an error that igv cannot load my sam file..

[GenoMax]

Is your sam file sorted and indexed? Do you get this error when browsing in IGV GUI to select the file you are trying to view?

[Michal Nevo]

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.