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The problem is that Java, by default, only reserves 64Mb of RAM for its processes.
In your case (a very, very large library), this is not enough.
I made a correction, which will be included in the next release.
In the meantime, you should be able to run the tool if you edit the calibredbxtract.bat file, inside the bin subfolder of the directory where you installed the tool : replace the line showing set EXTRA_JVM_ARGUMENTS= with set EXTRA_JVM_ARGUMENTS=-Xmx256m
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