Unable to open NCBI map


I recently updated to MEGAN CE 16.7.0 (under Windows 10) and now MEGAN steadily refuses to load the NCBI map - it gets stuck at this point. After terminating the process, MEGAN tells me that it might help to increase the memory - but I adjusted this already to 14GB. Older versions of MEGAN do not work either now.
I assume that there is some incompatibility with my Windows configuration or there might be some issues with different JAVA versions on my computer. Did anybody have similar experiences and does maybe have some hints what the reason for this problem might be?

Thank you,


Do you mean MEGAN CE 6.17.0?

Dear Ralf,

I just tried this on Windows10 and MEGAN CE 16.7.0 doesn’t get stuck for me.
What is contained in this file?

/Volumes/[C] Windows 10.hidden/Program Files/Megan6CE/MEGAN.vmoptions

It should be this (and not -Xmx14M or something invalid):


On the other hand, if older versions don’t work either, then that suggests that there might be something toxic in the preferences file .Megan.def, located here:

/Volumes/[C] Windows 10.hidden/Users/<your-user-name>/.Megan.def

You can delete that file (or move it away) and then try starting the program.


@cheryl: yes, of course I meant version 6.17.0 - sorry!

@Daniel: thank you for the tips but unfortunately the loading of the ncbi files still stops at some point. Sometimes the loading process goes up to 502 Mb (of around 530 Mb or so) of the ncbi.map until it stops, in some rare cases ncbi.map seems to be fully loaded and then the loading gets stuck at the attempt to load ncbi.tre.

It can’t be a Java incompatibility because MEGAN uses its own bundled JRE.

So you deleted the .Megan.def file and verified that the .vmoptions file contains -Xmx14000M.

What it the content of the message window?
After terminating the program, what is contained in the error.log file (located in the installation directory).