Problem running MEGAN v6.10.3 on Ubuntu 16.04.3 LTS

User Questions
1

Hello!

I have been having problems with running MEGAN6 on my local machine and I would really really appreciate some help to make this work.

  • I have downloaded the .sh file here (http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html) for version 6.10.3 (Community Edition)
  • I have installed it (simple chmod and following the steps)
  • I have generated a text file for commands (megan6_commands.txt) and inside of it:
    import blastfile = ‘/home/administrator/storage/pipelines_mcgr/multi-metagenome/info_extraction/assembly.orfs.hmm.blast.xml’ meganfile=’/home/administrator/storage/pipelines_mcgr/multi-metagenome/info_extr
    action/temp.rma’;
    recompute topPercent=5;
    recompute minSupport=1;
    update;
    collapse rank=Species;
    update;
    select nodes=all;
    export what=CSV format=read
    name_taxonpath separator=tab file=’/home/administrator/storage/pipelines_mcgr/multi-metagenome/info_extraction/assembly.orfs.hmm.blast.tax.txt’;
    update;
    quit;
  • now I am trying to run the following command:
    $ MEGAN -g -E < megan6_commands.txt

and I get the following on my error.log:
Version MEGAN Community Edition (version 6.10.3, built 9 Nov 2017)
Copyright © 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
This is free software, licensed under the terms of the GNU General Public License, Version 3.
MEGAN fatal error:
jloda.util.UsageException: Invalid, unknown or duplicate option: -g -E
, use option ‘-h’ for help
Invalid, unknown or duplicate option: -g -E
, use option ‘-h’ for help

Can somebody please help me with this? I would deeply appreciate.

Thanks a lot!
Rodolfo Toscan

2

Hi,
try running via xvfb-run, e.g.:

xvfb-run ./MEGAN -g -c tmp_megan_cmd.txt

3

Thanks Ania for the help and sorry for the late reply, I was regenerating the input data.

Anyway, the command still doesn’t work.

My command:
xvfb-run /home/administrator/Documents/softwares/megan/MEGAN -g -c megan6_commands.txt

my command file ( megan6_commands.txt):
import blastfile = ‘/home/administrator/storage/pipelines_mcgr/multi-metagenome/info_extraction/assembly.orfs.hmm.blast.xml’ meganfile=’/home/administrator/storage/pipelines_mcgr/multi-metagenome/info_extraction/temp.rma’;
recompute topPercent=5;
recompute minSupport=1;
update;
collapse rank=Species;
update;
select nodes=all;
export what=CSV format=read
name_taxonpath separator=tab file=’/home/administrator/storage/pipelines_mcgr/multi-metagenome/info_extraction/assembly.orfs.hmm.blast.tax.txt’;
update;
quit;

My error.log inside the megan folder:
Version MEGAN Community Edition (version 6.10.3, built 9 Nov 2017)
Copyright © 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
This is free software, licensed under the terms of the GNU General Public License, Version 3.
MEGAN fatal error:
jloda.util.UsageException: Invalid, unknown or duplicate option: -g -c megan6_commands.txt
, use option ‘-h’ for help
Invalid, unknown or duplicate option: -g -c megan6_commands.txt
, use option ‘-h’ for help

Do you have any idea of what kind of problem this is? Again, I thank you deeply for the attention.

Rodolfo

4

Dear Rodolfo,

The community edition does not have a command line mode. Please explore the tools in the megan/tools directory, then can be used to do the kind of stuff that you are trying to do.