I'm getting the out of memory error too on several pdf files. I tried increasing the Java heap size by adding the -Xmx1500m command to Java but that didn't do anything.

20160727 18:01:36 [Scanner thread] ERROR com.ubooquity.Ubooquity - Uncaught exception on thread: Scanner thread
java.lang.OutOfMemoryError: Java heap space
    at java.awt.image.DataBufferInt.<init>(Unknown Source) ~[na:1.8.0_101]
    at java.awt.image.Raster.createPackedRaster(Unknown Source) ~[na:1.8.0_101]
    at java.awt.image.DirectColorModel.createCompatibleWritableRaster(Unknown Source) ~[na:1.8.0_101]
    at java.awt.image.BufferedImage.<init>(Unknown Source) ~[na:1.8.0_101]
    at sun.java2d.pipe.DrawImage.makeBufferedImage(Unknown Source) ~[na:1.8.0_101]
    at sun.java2d.pipe.DrawImage.renderImageXform(Unknown Source) ~[na:1.8.0_101]
    at sun.java2d.pipe.DrawImage.transformImage(Unknown Source) ~[na:1.8.0_101]
    at sun.java2d.pipe.DrawImage.transformImage(Unknown Source) ~[na:1.8.0_101]
    at sun.java2d.pipe.DrawImage.transformImage(Unknown Source) ~[na:1.8.0_101]
    at sun.java2d.SunGraphics2D.drawImage(Unknown Source) ~[na:1.8.0_101]
    at org.apache.pdfbox.rendering.PageDrawer.drawBufferedImage(PageDrawer.java:823) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.rendering.PageDrawer.drawImage(PageDrawer.java:781) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.contentstream.operator.graphics.DrawObject.process(DrawObject.java:62) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.contentstream.PDFStreamEngine.processOperator(PDFStreamEngine.java:815) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.contentstream.PDFStreamEngine.processStreamOperators(PDFStreamEngine.java:472) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.contentstream.PDFStreamEngine.processStream(PDFStreamEngine.java:446) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.contentstream.PDFStreamEngine.processPage(PDFStreamEngine.java:149) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.rendering.PageDrawer.drawPage(PageDrawer.java:189) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.rendering.PDFRenderer.renderPage(PDFRenderer.java:208) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.rendering.PDFRenderer.renderImage(PDFRenderer.java:139) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at org.apache.pdfbox.rendering.PDFRenderer.renderImageWithDPI(PDFRenderer.java:94) ~[pdfbox-2.0.0.jar.8466586005085621666.tmp:2.0.0]
    at com.ubooquity.fileformat.pdf.b.a(SourceFile:71) ~[Ubooquity.jar:1.10.1]
    at com.ubooquity.fileformat.pdf.b.a(SourceFile:44) ~[Ubooquity.jar:1.10.1]
    at com.ubooquity.data.feeder.a.b(SourceFile:382) ~[Ubooquity.jar:1.10.1]
    at com.ubooquity.data.feeder.a.a(SourceFile:212) ~[Ubooquity.jar:1.10.1]
    at com.ubooquity.data.feeder.a.b(SourceFile:316) ~[Ubooquity.jar:1.10.1]
    at com.ubooquity.data.feeder.a.a(SourceFile:35) ~[Ubooquity.jar:1.10.1]
    at com.ubooquity.data.feeder.a$1.run(SourceFile:116) ~[Ubooquity.jar:1.10.1]
    at java.lang.Thread.run(Unknown Source) ~[na:1.8.0_101]

Here is one of the pdf files if you need it for testing. https://www.dropbox.com/s/ffzl0yu9mhl01qt/Crimson%20Skies%20-%20Aircraft%20Manual.pdf?dl=0