Hi Community,
I am trying to use the software MEGAN6 UE in command line mode to calculate LCA from my blastn results of multiple samples. I am new to using megan this way and so fare unsuccessful.
I have tried to run this from the directory of my blastn files:
megan/MEGAN -g -E -c megantest.txt
where megantest.txt says:
load mapFile='/mnt/Data/databases/silvamod128v2_megan/silvamod128v2_megan.map';
load treeFile='/mnt/Data/databases/silvamod128v2_megan/silvamod128v2_megan.tre';
for i in *.blastn; do
import blastFile=$i meganFile=$i.rma;
done;
But nothing really happens, no error messages and no files are generated, Megan seems to open in a split second but disappears again. The terminal just gives me a new line. I am not very skilled in writing these type of scripts, so any feedback would be greatly appreciated!
I have also posted this in the MEGAN community forum here
But it is so frustrating being stuck at this point that I take the liberty to post the question here as well and hope some of you are doing a similar thing and can help me.
