John Joe

That's weird - as far as I can tell the stream never closes itself until the program exits so output.flush() should have had the same effect. I had a similar problem a few days before you posted your issue where the file was not completely written and added output.flush() using a different method which solved it for me. The code is convoluted so I might be missing something. Well, as long as it eventually ended up working it's fine I guess.

I can't help you much with #1 since I never tried building from source myself, but for #2 make sure you still have the other necessary libraries in their proper place - your error isn't a version error but a "I can't find the stuff this program relies on error" Specifically, the file/folder layout should be (relative to Mauve.jar's directory) ./Mauve.jar ./ext/bytecode-1.9.2-SNAPSHOT.jar ./ext/commons-cli-1.2.jar ./ext/core-1.9.2-SNAPSHOT.jar ./ext/gui-1.9.2-SNAPSHOT.jar These libraries should have...

I can't help you much with #1 since I never tried building from source myself, but for #2 make sure you still have the other necessary libraries in their proper place - your error isn't a version error but a "I can't find the stuff this program relies on error" Specifically, the file/folder layout should be (relative to Mauve.jar's directory) ./Mauve.jar ./ext/bytecode-1.9.2-SNAPSHOT.jar ./ext/commons-cli-1.2.jar ./ext/core-1.9.2-SNAPSHOT.jar ./ext/gui-1.9.2-SNAPSHOT.jar

Hello, I'm not the developer, but I think I know may know what is happening: If you downloaded it directly from the website (development snapshot 2015-02-26, or really any version that is older than the latest revision r4736 (made on 2016-06-08), using the SnpExporter may result in an incomplete output file. Your choices are: 1. Build Mauve from source 2. Take the code from https://sourceforge.net/p/mauve/code/HEAD/tree//mauve/trunk/src/org/gel/mauve/analysis/SnpExporter.java, compile it, so you...