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rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
http://rrwick.github.io/Bandage/
GNU General Public License v3.0
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Bandage crashes when trying to load/view large/eukaryote assemblies #78

Open crysclitheroe opened 5 years ago

crysclitheroe commented 5 years ago

Good day

I Installed Bandage on my iMac desktop (Intel core i5, 8GB ram, AMD Radeon HD 6970M 1024 MB), and it worked fine for viewing bacterial/mitochondrial genome assemblies. The problem is when I load eukaryote assemblies (~1.3Gb), the program takes a very long time to load and eventually fails and hangs.

Im running/viewing bandage on a local machine but loading the assemblies from a server. Could this be the reason for the hang or is it a problem with my own machine?

Thanks and kind regards Crystal

rec3141 commented 5 years ago

I've loaded assemblies of that size on a mac with 128Gb RAM but they do take a while, you can change some of the parameters, like decreasing the number of iterations, that might make it faster. If there are a lot more edges than nodes you probably just have a huge hairball due to numerous repeats, which will not be very enlightening to look at anyway. You might try to limit your view by selecting nodes of interest, or by excluding high-coverage nodes from the visualization using the depth Scope.