Can't save Comparison.megan file


We’re running into an odd issue with the latest MEGAN release (Ultimate Edition, v6.8.15), via Linux. We have a very large number of samples (68), and have been able to all of them if we bump the memory up enough for comparison. What is unusual is that the ‘Comparison.megan’ file cannot be saved (the ‘Save as…’ is greyed out). This worked in past releases.

I have also tested this on Mac with the same version and have the same issue, even with smaller samples. Any reason this was disabled, or is it a bug?


@cjfields I’m also finding this error with the new update. A solution would be greatly appreciated!


68 isn’t very large, I am working with a dataset containing 1280 samples… :wink:

Yes, this indeed appears to be a newly introduced bug and I will upload a fix today.


@cjfields I am also trying to compare lots of samples, not as many as 1280 as I only have 115 samples but it’s still challenging to load all 115 RMA6 files for comparison. @Daniel Is there’s a command option to create such comparison.megan file? Thanks!


Managed to create a comparison file for two RMA6 MEGAN files using the command-line as follows:

$ /Applications/MEGAN_Ultimate-Edition/ -g -E < CompareSamples.txt

where CompareSamples.txt contains the following commands:

compare mode=RELATIVE meganfile=’/path/to/file1.rma6’ ‘/path/to/file2.rma6’;
save file=’/path/to/comparing-two-files.megan’

Now, the question would be whether there’s a more elegant/optimum way to specify a large number of file names in the “compare” command, specifically in the meganfile= parameter. Right now I can only think to add the names individually to my CompareSamples.txt file. A more optimum way could be something like reading a list from a file or opening all RMA6 files in a specific directory. Not sure if MEGAN command line supports this kind of interactions?

Any thoughts regarding this?

Thank you very much :smiley:


I have just implemented code that does checks whether a given name is a directory and if it is, it recursively collects and lists all suitable files found in that directory. This will be available in the next update.


Thanks a lot for this! :smiley: Looking forward to the next update :wink:


Just uploaded it a few hours ago, if you run into problems, then please let me know


Excellent!! thanks a lot for this! :slight_smile: