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aidenlab / Juicebox

Visualization and analysis software for Hi-C data -
https://aidenlab.org/juicebox
MIT License
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Error loading basic annotation #160

Closed mhoeger closed 8 years ago

mhoeger commented 9 years ago

Can't load a few of the basic annotations (RepeatMasker > LINE, RepeatMasker > SINE, RepeatMasker > DNA). Juicebox shows the Loading glass pane and does nothing from there (no error message, etc.). The only error I've gotten is a timeout error if I leave it loading. I haven't tried all of the RepeatMasker elements, but I know that Satellite does load.

nchernia commented 9 years ago

Which genome?

Check code and see if url loads

On Friday, July 24, 2015, mhoeger notifications@github.com wrote:

Can't load a few of the basic annotations (RepeatMasker > LINE, RepeatMasker > SINE, RepeatMasker > DNA). Juicebox shows the Loading glass pane and does nothing from there (no error message, etc.). The only error I've gotten is a timeout error if I leave it loading. I haven't tried all of the RepeatMasker elements, but I know that Satellite does load.

— Reply to this email directly or view it on GitHub https://github.com/theaidenlab/Juicebox/issues/160.

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

mhoeger commented 9 years ago

GM12878, and nothing gets printed when I try to load it

sa501428 commented 9 years ago

If you download the file (43.5 MB gzipped) and then try loading locally: 2015-07-24 11:51:18.640 java[57195:4458434] Metadata.framework [Error]: couldn't get the client port Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded at java.awt.EventQueue.postEvent(EventQueue.java:317) at java.awt.EventQueue.postEventPrivate(EventQueue.java:278) at java.awt.EventQueue.postEvent(EventQueue.java:250) at sun.awt.PostEventQueue.flush(SunToolkit.java:2133) at sun.awt.SunToolkit.flushPendingEvents(SunToolkit.java:544) at java.awt.EventQueue.getNextEvent(EventQueue.java:534) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:170) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

nchernia commented 9 years ago

try in IGV, that's where they come from

On Fri, Jul 24, 2015 at 12:54 PM, Muhammad Saad Shamim < notifications@github.com> wrote:

If you download the file (43.5 MB gzipped) and then try loading locally: 2015-07-24 11:51:18.640 java[57195:4458434] Metadata.framework [Error]: couldn't get the client port Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded at java.awt.EventQueue.postEvent(EventQueue.java:317) at java.awt.EventQueue.postEventPrivate(EventQueue.java:278) at java.awt.EventQueue.postEvent(EventQueue.java:250) at sun.awt.PostEventQueue.flush(SunToolkit.java:2133) at sun.awt.SunToolkit.flushPendingEvents(SunToolkit.java:544) at java.awt.EventQueue.getNextEvent(EventQueue.java:534) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:170) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

— Reply to this email directly or view it on GitHub https://github.com/theaidenlab/Juicebox/issues/160#issuecomment-124577896 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

sa501428 commented 9 years ago

Some lag, but ultimately works fine on IGV no error.

imachol commented 8 years ago

This problem does not replicate on my setup, it might have been resolved by latest buffer settings.

nchernia commented 8 years ago

At some point I put our own repeatmasker tracks up so this might have fixed it

On Fri, Dec 18, 2015 at 11:53 AM, imachol notifications@github.com wrote:

This problem does not replicate on my setup, it might have been resolved by latest buffer settings.

— Reply to this email directly or view it on GitHub https://github.com/theaidenlab/Juicebox/issues/160#issuecomment-165836441 .

Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org