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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
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precompiled Aptasuite 0.9.4 #87

Closed mengops closed 4 years ago

mengops commented 4 years ago

I am running aptasuite from the precompiled .jar file. When trying to start a new experiment the window opens up fine but the content does not fit. Therefore some parts of the windows are not visible. I tried to use tab and the pointers to move around or even scrolling but nothing happened. As it is, I can't launch any experiment on any of the platforms. Is there a way to fix it or should I just give up and use the command line option?

this is the only warning the code shows :

(java:72904): Gtk-WARNING **: 12:02:32.266: Unable to locate theme engine in module_path: "pixm
Gtk-Message: 12:02:32.272: Failed to load module "canberra-gtk-module"

Many thanks in advance for your help

drivenbyentropy commented 4 years ago

Thank you for the report. Could you attach a screenshot of the issue you are facing?

What is the current screen resolution of your system? Thanks!

mengops commented 4 years ago

aptasuite

The screenshot is attached and the resolution is 800x600.

many thanks for yout help and quick reply

drivenbyentropy commented 4 years ago

Thanks. AptaSuite requires a resolution of at least 1024x768 to fit all its content. Please try to adjust the resolution of your OS and see if that solves the issue.

mengops commented 4 years ago

Hi that solved the issue! Many thanks! May I ask advice on another issue? I tried launching the analysis and the job failed. The window closed and the cmd shows the following error

May 07, 2020 4:34:38 PM javafx.fxml.FXMLLoader$ValueElement processValue WARNING: Loading FXML document with JavaFX API of version 9 by JavaFX runtime of version 8.0.121 Reading configuration from file. Error invoking construtor of AptamerPool backend java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at lib.aptamer.datastructures.Experiment.<init>(Experiment.java:147) at gui.wizards.newexperiment.Wizard2Controller$1.call(Wizard2Controller.java:155) at gui.wizards.newexperiment.Wizard2Controller$1.call(Wizard2Controller.java:141) at javafx.concurrent.Task$TaskCallable.call(Task.java:1423) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.OutOfMemoryError: Java heap space at java.util.BitSet.initWords(BitSet.java:166) at java.util.BitSet.<init>(BitSet.java:161) at orestes.bloomfilter.memory.BloomFilterMemory.<init>(BloomFilterMemory.java:15) at orestes.bloomfilter.FilterBuilder.buildBloomFilter(FilterBuilder.java:313) at lib.aptamer.datastructures.MapDBAptamerPool.<init>(MapDBAptamerPool.java:98) ... 10 more Error invoking AptamerPool backen

attached you have the log file log_2020-05-07_16-34-38.txt

Could you advise me on how to solve this?

drivenbyentropy commented 4 years ago

Caused by: java.lang.OutOfMemoryError: Java heap space at java.util.BitSet.initWords(BitSet.java:166) at java.util.BitSet.<init>(BitSet.java:161) at orestes.bloomfilter.memory.BloomFilterMemory.<init>(BloomFilterMemory.java:15)

You are running out of memory. If this is a virtual machine, try increasing the memory available to it and also make sure that AptaSuite can use it by setting the maximum allowed memory for Java. See the FAQ for more information.