Troubleshooting

Connection issues

Many Gopher functions depend on an active internet connection including (obviously) the downloads. The visualization of viewpoints is implemented with a call to the UCSC genome browser. Therefore, you must be onlne for Gopher to work correctly, and if you receive an error message or if a blank page is shown for the visualization of viewpoints, you should check your internet connection.

Proxy

If you are behind a proxy server, then you will need to enter the HTTP proxy and port with

the Edit|Set proxy menu item.

Java version

GOPHER requires a Java runtime environment (JRE) of 1.8 or higher to run. If one attempts to start Java with an older JRE, an error message such as the following may appear:

Unsupported major.minor version 52.0

Please consult the Java download page <https://java.com/en/>_ for more information. To determine the Java version on your computer, open a terminal window and enter

$ java -version

You should then seen a response such as

java version "1.8.0_181"
Java(TM) SE Runtime Environment (build 1.8.0_181-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.181-b13, mixed mode)

The version in this example is thus 1.8.0_181.

Memory errors

We recommend starting GOPHER with at least 2 GB memory. The amount of memory required by GOPHER will depend on the size of the panel and GOPHER may require more memory with very large panels. GOPHER will display an error dialog stating Out of Memory Error if it runs out of memory. In this case, you will need to close the program, adjust the memry settings, and restart GOPHER.

There are several ways to adjust the amount of memory that the Java Virtual Machine provides to Java apps. When starting an app such as GOPHER from the command line, you can determine the amount of Minimum and Maximum memory provided to the app as follows.

$ java -Xms2g -Xmx6g -jar GOPHER.jar

This command will start GOPHER with at least 2 gigabytes of RAM (-Xms2g) and allow GOPHER to use up to 6 gigabytes of RAM (-Xmx6g).

Logging

By default, GOPHER will only write messages to its log file if an error occurs. If you run into difficulties using GOPHER, you can set the logging level to TRACE (in the Help menu). This will cause GOPHER to write detailed messages to its log file that you can see with the Show log entry in the Help menu. You can contact us and if you like can send us the log file (which will be stored in your GOPHER user directory (.gopher in linux and Mac, and gopher in Windows).