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It looks like Muscle is running out of memory, I dont think it is limited by AliView memory setting. Muscle is started as a separate process. Maybe you are giving Aliview to much memory, and nothing is left to Muscle?
Im having similar problems, I increased the memory and it refuses so start the program. The only things that get the program to work is reinstalling it.
Error when i start it after i change memory and even when i change it to default.
-Xmx20024m
in ' .ini' file has no effect and alignments crash due to lack of memory
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