MEGAN_community_unix_6.5.10: daa2rma error "invalid. unknown or duplicate option" for functional classification

Question

[sal028]

Hi everyone!

I am trying to analyze some dataset from shotgun metagenome sequencing with Illumina HiSeq. In particular, I want to convert the output obtained after running blastp with the software DIAMOND (output file in daa-format) into a "rma" file in order to further visualize it with MEGANv6.5.10. My computer is not powerful enough and I have to use a computer server so it has to be done in a command-line environment. I run both "daa2rma" or "daa-meganizer" scripts available in the MEGAN package for this purpose, using KEGG, SEED, EggNOG databases for functional annotation.

For that I run the following string:

./daa2rma --in my_input_file.daa --out my_output_file.rma --function --acc2taxa prot-acc2taxid-August2016.abin --acc2eggnog acc2eggnog-June2016X.abin --gi2kegg gi2kegg-Feb2015X.bin --gi2seed gi2seed-May2015X.bin

obtaining:

Version MEGAN Community Edition (version 6.5.10, built 13 Oct 2016) Author(s) Daniel H. Huson Copyright (C) 2016 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY. Caught: jloda.util.UsageException:

Invalid, unknown or duplicate option: --acc2eggnog acc2eggnog-June2016X.abin --gi2kegg gi2kegg-Feb2015X.bin --gi2seed gi2seed-May2015X.bin

, use option '-h' for help at jloda.util.ArgsOptions.done(ArgsOptions.java:210) at megan.tools.DAA2RMA6.run(DAA2RMA6.java:150) at megan.tools.DAA2RMA6.main(DAA2RMA6.java:63)**

The same happened with "daa.meganizer". I also omitted the "--function" option with no difference.

Any thoughts?

Thank you so much in advanced!

Alex

[Tonor]

MEGAN has its own user forum which is pretty good, I would also try there: http://megan.informatik.uni-tuebingen.de

[Tonor]

I think with the --function argument, it is expecting you to say what you are after

 Functional classification:
    -fun, --function [string(s)]         Function assignments (any of EGGNOG INTERPRO2GO KEGG SEED).

[Tonor]

E.g. something like

./daa2rma --in my_input_file.daa --out my_output_file.rma --acc2taxa prot-acc2taxid-August2016.abin --function EGGNOG KEGG SEED --acc2eggnog acc2eggnog-June2016X.abin --gi2kegg gi2kegg-Feb2015X.bin --gi2seed gi2seed-May2015X.bin

[sal028]

Hello Tonor,

Firstly, thank you so much for the quick reply. I've just tried what you suggested and it seems to work perfectly!!

Thank you again for your help XD