error when running the example

[symnina]

Hi,
I'm wondering if anyone could help me resolve the following issue. When I ran the example, it showed an error as follows:

Error in getopt_options(object, args) :
Error in getopt(spec = spec, opt = args) :
"phenofile=“../testWAS/data/phenotypes.csv”" is not a valid option, or does not support an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted

And here's my codes:
cd WAS
Rscript phenomeScan.r
--phenofile=“../testWAS/data/phenotypes.csv”
--traitofinterestfile=“../testWAS/data/exposure.csv”
--variablelistfile=“../variable-info/outcome-info.tsv”
--datacodingfile=“../variable-info/data-coding-ordinal-info.csv”
--traitofinterest=“exposure”
--resDir=“../results2/“
--userId=“userId”
--sensitivity
--genetic=FALSE
--partIdx=1
--numParts=20
Error in getopt_options(object, args) :
Error in getopt(spec = spec, opt = args) :
"phenofile=“../testWAS/data/phenotypes.csv”" is not a valid option, or does not support an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted

[Louise]

The commands to run the test example are here: https://github.com/MRCIEU/PHESANT/tree/master/testWAS

Note that testWAS has its own variable info files, where as the variablelistfile and datacodingfile arguments you have are using the main phesant ones in the variable-info directory.

In the command you supplied the quotes are ” rather than ".

Here is your command, adapted so that it works:
Rscript phenomeScan.r
--phenofile="../testWAS/data/phenotypes.csv"
--traitofinterestfile="../testWAS/data/exposure.csv"
--variablelistfile="../testWAS/variable-lists/outcome-info.tsv"
--datacodingfile="../testWAS/variable-lists/data-coding-ordinal-info.txt"
--traitofinterest="exposure"
--resDir="../results2/"
--userId="userId"
--sensitivity
--genetic=FALSE