How to combine .rma6 file


#1

Hi there,

I’m working with the MEGAN command line mode.
I want to know how to combine multiple .rma6 files created by blast2rma script.
When I simplly concatenate .rma6 files (using bash cat command) it doesn’t work because .rma6 files contain binary.

Here is my commands

./blast2rma -i ~ -o out1.rma6 -a2kegg ~ -f ~ -bm ~ -c false
./blast2rma -i ~ -o out2.rma6 -a2kegg ~ -f ~ -bm ~ -c false

cat out1.rma6 out2.rma6 > out_concat.rma6

then I open out_concat.rma6 using MEGAN, the error below occurs.

Thanks a lot for your help!
Best,
Marina


#2

Hi Marina.

rma files can’t be concatenated. You can open two or more .rma files and then use menu items of the Sample Viewer to combined into a “total biome” file that represents the union of all the files


#3

Thank you for your reply, Daniel.

I want to use commandFile option, how can I do that using command line mode?

$ ./MEGAN -g -c

Best,
Marina


#4

Do something like this:

-g -c ~/script -E

However, please note that this is only available in MEGAN UE

If you are using MEGAN CE, then use one of the command line programs in the tools directory