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
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No assignment in MEGAN6 output
written by nisrinalulu •
MEGAN has its own user forum which is pretty good, I would also try there: http://megan.informatik.uni-tuebingen.de
I think with the --function argument, it is expecting you to say what you are after
E.g. something like
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