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jfy133 / rma-tabuliser

Bash wrapper script to generate count/taxon/OTU tables from RMA6 files (wrapper to MEGAN6 rma2info)
MIT License
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Invalid, unknown or duplicate option: -V #1

Closed ivelsko closed 3 years ago

ivelsko commented 3 years ago

I ran ./rma-tabuliser -d ./eager2/metagenomic_classification/malt/ -c Taxonomy -n -r 'P' -s -t 4 -V

and get this error repeated several times

Version   MEGAN Community Edition (version 6.21.7, built 23 Jun 2021)
Author(s) Daniel H. Huson
Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Caught:
jloda.util.UsageException: Invalid, unknown or duplicate option: -V
, use option '-h' for help
    at jloda/jloda.swing.util.ArgsOptions.done(ArgsOptions.java:203)
    at megan/megan.tools.RMA2Info.run(RMA2Info.java:110)
    at megan/megan.tools.RMA2Info.main(RMA2Info.java:63)

Then it creates a count_table.tsv with only the headers, no entries.

It runs fine and creates a complete count_table.tsv when I remove -V

jfy133 commented 3 years ago

Fixed with https://github.com/jfy133/rma-tabuliser/commit/079a8135462638d57e635b4b774a03da977fdb04