Unrecognized Option

[SoumenMaity922]

Hi, I am new to this application. In the following link https://choishingwan.github.io/PRSice/command_detail/ they have mentioned some commands for plotting purposes like --bar-col-high, --bar-col-low, and few more. But When i write the command like PRSice --base Height.QC.gz --target EUR.QC --binary-target F --pheno EUR.height --cov EUR.covariate --base-maf MAF:0.01 --base-info INFO:0.8 --stat OR --or --out EUR --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5 --bar-col-high "firebrick" --bar-col-low "dodgerblue" It shows an error like Unrecognized option '--bar-col-high'. Why this is happening?? Any help??

[choishingwan]

Same answer to your previous question:

You need to use the PRSice R script in addition to the executable.

On Wed, Sep 20, 2023, 4:14 PM Soumen Maity @.***> wrote:

Hi, I am new to this application. In the following link https://choishingwan.github.io/PRSice/command_detail/ they have mentioned some commands for plotting purposes like --bar-col-high, --bar-col-low, and few more. But When i write the command like PRSice --base Height.QC.gz --target EUR.QC --binary-target F --pheno EUR.height --cov EUR.covariate --base-maf MAF:0.01 --base-info INFO:0.8 --stat OR --or --out EUR --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5 --bar-col-high "firebrick" --bar-col-low "dodgerblue" It shows an error like Unrecognized option '--bar-col-high'. Why this is happening?? Any help??

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[SoumenMaity922]

But sir, I am writing the above command in the HPC environment. I have downloaded the PRSice_linux zip file since mobaxterm works as a Linux distribution and upload that into the working directory of mobaxterm and run the following code Rscript PRSice.R PRSice --base Height.QC.gz --target EUR.QC --binary-target F --pheno EUR.height --cov EUR.covariate --base-maf MAF:0.01 --base-info INFO:0.8 --stat OR --or --out EUR --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5 Again it throws an error like Trying to install ggplot2 in ./lib Trying to install data.table in ./lib Trying to install optparse in ./lib Usage: PRSice.R [options]

PRSice.R: error: Error in getopt(spec = spec, opt = args) : "PRSice" is not a valid option, or does not support an argument . So I removed that PRSice option and modify the code in the following way Rscript PRSice.R --base Height.QC.gz --target EUR.QC --binary-target F --pheno EUR.height --cov EUR.covariate --base-maf MAF:0.01 --base-info INFO:0.8 --stat OR --or --out EUR --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5 It also gives an error like Error: Cannot run PRSice without the PRSice binary file Execution halted After this again i add an argument '--prsice PRSice_linux' (which was included in the downloaded linux distribution zip file), then it shows an error that sh: ./PRSice_linux: Permission denied Error: Execution halted. Please help. It will be very helpful.

[choishingwan]

I'd refer you to our documentation

https://choishingwan.github.io/PRSice/quick_start/

Am currently away in a conference

Sam

On Wed, Sep 20, 2023, 4:48 PM Soumen Maity @.***> wrote:

But sir, I am writing the above command in the HPC environment. Truly speaking, I don't understand what are you trying to say. I am really new in this domain. Can you please tell me in a more elaborate and what I have to do exactly? It will be very helpful. Thanks in advance.

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[SoumenMaity922]

Thanks sir. Now it works properly.