Welcome to the frequently encountered problems pages. Here we will list those problems that are often encountered by our users when running the UEA small RNA Workbench and how to solve them. Or solutions to tricky problems that have been solved by our users.
If you have encountered an issue and resolved it please inform our team so that we can post the information on this page. In addition, any issues that are solved numerous times through our comment or ticket system will be placed here.
If your problem is not listed here please feel free to contact us as usual by leaving a comment on any page.
We will continue to update these pages as more solutions are required
Version 4+ Specific:
- Display of file hierarchy may not work on the latest version of java. Workaround by right clicking and refreshing the page to make the hierarchy appear or use slightly older version of JRE (update 51 or below)
- Some differentially expressed sequences can be annotated but the actual name of the annotation may not appear. This is due to poorly formatted GFF files mostly. A fix is in progress and will appear in the next release
- Switching to plot view can often prevent the differential expression table from re-displaying. This is a fairly major issue and is currently under investigation…
No graphics displayed
This is a known issue relating to java. More specifically any version of the JRE/JDK after update 51. Every now and then it refuses to reload information entered into external JSON files (the files containing the data for plots and other graphics). A short term fix is to simply right click on the problem page and hit reload
Non local (server-client) X11 forwarding shows no graphics
This is a known problem, for some reason X11 has decided to render no interface when running from a server. However, X windows displayed directly from a linux desktop is unaffected. Investigations are ongoing…
Poor rendering performance for both the interface and graphs
OSX asks to install a legacy version of the JRE (version 6) to run the .app file from double clicking
This is due to the previous versions of Java being built by apple instead of Oracle (or Sun Microsystems at the time). DO NOT INSTALL JRE6! This will not allow the software to run. This is an issue you may encounter with any java software bundled into a .app file. To fix this, first enter this command:
sudo nano `/usr/libexec/java_home -V`/../info.plist
Then locate the lines:
<key>JVMCapabilities</key> <array> <string>CommandLine</string> </array>
And replace them with:
<key>JVMCapabilities</key> <array> <string>JNI</string> <string>BundledApp</string> <string>WebStart</string> <string>Applets</string> <string>CommandLine</string> </array>
When testing this my machine also required a restart before this took effect. After that it should load as normal using the correct JRE/JDK. Please comment below if this does not resolve your issue.
OSX Mavericks and Mountain Lion show the .app file as being damaged:
This is because of the permissions system in the new versions of OSX. All applications downloaded from the internet must be shown as trusted or signed by an official apple developer and gained from the app store. To allow the workbench to run you can either change your security permissions in the control panel or open the package up (right click and show contents) navigate to the java folder and run the sRNAWorkbenchStartup.jar file by right clicking and selecting ‘open’ then tell OSX to allow this program to run.
A new version of the .app file will be released shortly that will negate this problem and allow the software to launch as normal
Since updating OSX the terminal has defaulted to OpenJDK and the Workbench does not fully support this build:
This is because Apple no longer support java. However, assuming you have the oracle version of java on your system you can select the official build of Java using the Java Preferences program (type Java Preferences into spotlight), alternatively you must add the location of the JRE/JDK to your path variable that is found within your bash profile. Something similar to this with the version number (shown in bold) set to match whatever you have on your system:
I am quite certain that running the application from the jar or from the new launcher added in Version 3.0 will select the Oracle version if it is installed.
I am getting an error similar to the following in the console while trying to run miRCat (RESOLVED):SEVERE: WORKBENCH: MIRCAT: Message: Index: 0, Size: 0; Stack Trace: java.util.ArrayList.rangeCheck(ArrayList.java:604)
orSEVERE: WORKBENCH: java.net.ConnectException: Connection refused
This is likely due to some kind of premature close of the workbench possibly from a unrecoverable crash leaving zombie threads hanging. Until a solution presents itself in an upcoming fix, this can be resolved by ensuring all java processes related to the workbench are closed before attempting to start miRCat again.
I am having trouble using X11 forwarding through a PuTTY client on Windows 7
Install MobaXterm as X server. http://mobaxterm.mobatek.net/support/documentation.html#4_2_5 “I have an issue with an X11 remote program (Java/X11/Motif) which does not accept keyboard input: everytime I press a keyboard key, nothing is written on the text field
This problem can generally be solved easily by using X11 with a window manager instead of using X11 in “multiwindow” (transparent) mode: go to MobaXterm “Settings” window –> “X11″ tab –> select “Windowed mode with Fvwm” setting in the combo box and apply. Restart your remote program and it should take keyboard input correctly.
If you want to use the standard “multiwindow” (transparent) X11 server and occasionally use the windowed X11 server with the window manager, you can go to MobaXterm “Settings” window –> “X11″ tab –> select “Multiwindow mode” setting in the combo box and apply, then open the “tools” menu and select either “X11 tab with Dwm” or “X11 window with Fvwm2″.
(thanks to Marius Snyman for the fix)
I am getting no output from any tools on a 64bit LINUX based operating system or an error similar to:
PATMAN ERROR: Patman result file was not created:
Have you ensured the 32bit libraries are installed? An example of how to do this on the Ubuntu operating system would be:
sudo apt-get install ia32-libs
I am getting an out of memory warning from one of the tools in the workbench:
The startup program will only allocate a portion of RAM it considers as being “available” to the operating system. First you must ensure that there are no other memory hungry applications running before launching the Workbench. If you are using the system on OSX you can also run the ‘purge’ command at the terminal to free any inactive memory.
Alternatively, if you feel the workbench can use all of your available memory you can allocate RAM yourself using the -Xmx -Xms commands at the command prompt.
After navigating your terminal to the location of the workbench files you can execute the following command (where N is the amount of memory in GB you wish to use):java -XmsNg -XmxNg -jar Workbench.jar