calculate LCA with MEGAN UE command line mode for multiple bast files
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6 months ago

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.

LCA line MEGAN6 command • 201 views
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