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sanger-pathogens / iva

de novo virus assembler of Illumina paired reads
http://sanger-pathogens.github.io/iva/
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support an explicit output argument #53

Closed george-githinji closed 9 years ago

george-githinji commented 9 years ago

Support for a -o or --output_dir argument for the output folder. Currently attempting to run IVA as part of an automated pipeline and getting an error

iva --threads $T --verbose 2 -f $forwards -r $reverse $output_dir

$output_dir is a path to the output directory

I get an error iva: error: unrecognized argurments assembly/samplename

How can this be resolved?

martinghunt commented 9 years ago

The --verbose option doesn't take any values. Use it more times for more verbosity. This works for me:

iva --threads $T --verbose --verbose -f $forwards -r $reverse $output_dir

or less typing to do:

iva --threads $T -v -v -f $forwards -r $reverse $output_dir
george-githinji commented 9 years ago

OK. It was not clear from the documentation that the -v option does not take arguments. Thank you for the clarification!