Looking at the https://github.com/eleporcu/TWMR/blob/master/README.txt, it looks like you should pass a single argument when you call the MR.R script and it should be the name of a gene, e.g. 'ENSG00000154803'. You are passing two arguments and they look like filenames.
Update the script, because it should really use commandArgs(TRUE), to: cmd_args <- commandArgs(TRUE) if (length(cmd_args) == 0L) stop("No arguments specified.") print(cmd_args) gene<-cmd_args[length(cmd_args)] ## Last argument is the 'gene' Ngwas<-239087 N_eQTLs<-32000 out<-c("gene","alpha","SE","P","Nsnps","Ngene") file<-paste(gene,"matrix",sep=".") if (!file.exists(file)) stop("File not found: ", file) filecluster<-read.table(file,header=T,sep=" ",dec=".") ... The call the script from the command line as: $ Rscript MR.R ENSG00000154803 That should do it /Henrik On Sat, Nov 23, 2019 at 12:24 PM Ana Marija <sokovic.anamar...@gmail.com> wrote: > > it is confusing because in documentation they say this is how you run > the script: > https://github.com/eleporcu/TWMR > > I tried changing this on the script: > > cmd_args=commandArgs(TRUE) > print(cmd_args) > gene<-cmd_args[3] > Ngwas<-239087 > N_eQTLs<-32000 > out<-c("gene","alpha","SE","P","Nsnps","Ngene") > > file<-paste(gene,"matrix",sep=".") > if (!file.exists(file)) stop("File not found: ", file) > filecluster<-read.table(file,header=T,sep=" ",dec=".") > #file<-paste(gene,"matrix",sep=".") > #filecluster<-read.table(file,header=T,sep=".",dec=" ") > beta<-as.matrix(filecluster[,2:(length(filecluster[1,])-1)]) > > and I run it: > Rscript< MR.R --no-save ENSG00000154803.ld ENSG00000154803.matrix > Error: unexpected numeric constant in "1.000 0.089" > Execution halted > > > I also tried this: > Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > [1] "ENSG00000154803.ld" "ENSG00000154803.matrix" > Error: File not found: NA.matrix > Execution halted > > > Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > [1] "ENSG00000154803.ld" "ENSG00000154803.matrix" > Error: File not found: NA.matrix > Execution halted > > On Sat, Nov 23, 2019 at 2:08 PM Henrik Bengtsson > <henrik.bengts...@gmail.com> wrote: > > > > Maybe it would help to add: > > > > file<-paste(gene,"matrix",sep=".") > > if (!file.exists(file)) stop("File not found: ", file) > > filecluster<-read.table(file,header=T,sep=" ",dec=".") > > > > /Henrik > > > > On Sat, Nov 23, 2019 at 11:55 AM Duncan Murdoch > > <murdoch.dun...@gmail.com> wrote: > > > > > > On 23/11/2019 1:21 p.m., Ana Marija wrote: > > > > Hi Duncan, > > > > > > > > thanks, I just did, > > > > Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > > > > [1] "ENSG00000154803.ld" "ENSG00000154803.matrix" > > > > Error in file(file, "rt") : cannot open the connection > > > > Calls: read.table -> file > > > > In addition: Warning message: > > > > In file(file, "rt") : > > > > cannot open file 'NA.matrix': No such file or directory > > > > Execution halted > > > > > > > Your script works with the third element in the list of arguments, and > > > there are only two. > > > > > > Duncan Murdoch > > > > > > > > > > > Please advise > > > > > > > > On Sat, Nov 23, 2019 at 12:13 PM Duncan Murdoch > > > > <murdoch.dun...@gmail.com> wrote: > > > >> > > > >> On 23/11/2019 11:05 a.m., Ana Marija wrote: > > > >>> Hi Ben, > > > >>> > > > >>> I am not sure what you mean when you say to print, is it this? > > > >>> > > > >>>> cmd_args=commandArgs(TRUE) > > > >>>> print(cmd_args) > > > >>> character(0) > > > >>>> cmd_args=commandArgs() > > > >>>> print(cmd_args) > > > >>> [1] "/software/linux-el7-x86_64/compilers/r-3.6.1/lib64/R/bin/exec/R" > > > >>> > > > >>> I changed in the first line of this script: > > > >>> https://github.com/eleporcu/TWMR/blob/master/MR.R > > > >>> > > > >>> cmd_args=commandArgs() to be cmd_args=commandArgs(TRUE) > > > >>> > > > >>> but again I get the same error: > > > >>> > > > >>> Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > > > >>> Error in file(file, "rt") : cannot open the connection > > > >>> Calls: read.table -> file > > > >>> In addition: Warning message: > > > >>> In file(file, "rt") : > > > >>> cannot open file 'NA.matrix': No such file or directory > > > >>> Execution halted > > > >> > > > >> You didn't put the print(cmd_args) into the script. > > > >> > > > >> Duncan Murdoch > > > >>> > > > >>> > > > >>> Please advise, > > > >>> Ana > > > >>> > > > >>> On Sat, Nov 23, 2019 at 9:44 AM Duncan Murdoch > > > >>> <murdoch.dun...@gmail.com> wrote: > > > >>>> > > > >>>> On 23/11/2019 10:26 a.m., Ana Marija wrote: > > > >>>>> HI Ben, > > > >>>>> > > > >>>>> I tried it but it doesn't work: > > > >>>>> > > > >>>>> Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > > > >>>>> Error in file(file, "rt") : cannot open the connection > > > >>>>> Calls: read.table -> file > > > >>>>> In addition: Warning message: > > > >>>>> In file(file, "rt") : > > > >>>>> cannot open file '--no-restore.matrix': No such file or > > > >>>>> directory > > > >>>>> Execution halted > > > >>>>> > > > >>>> > > > >>>> You should print the cmd_args variable that is set on the first line > > > >>>> of > > > >>>> that script. When I run a script that prints it using your command > > > >>>> line, this is what it looks like: > > > >>>> > > > >>>> $ Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > > > >>>> [1] "/Library/Frameworks/R.framework/Resources/bin/exec/R" > > > >>>> [2] "--slave" > > > >>>> [3] "--no-restore" > > > >>>> [4] "--no-save" > > > >>>> [5] "--file=MR.R" > > > >>>> [6] "--args" > > > >>>> [7] "ENSG00000154803.ld" > > > >>>> [8] "ENSG00000154803.matrix" > > > >>>> > > > >>>> The next line > > > >>>> > > > >>>> gene <- cmd_args[3] > > > >>>> > > > >>>> is obviously wrong for my system, because it would set gene to > > > >>>> "--no-restore". Your results will probably be somewhat different, > > > >>>> but > > > >>>> it might be clear what you should use instead of the third element. > > > >>>> > > > >>>> By the way, changing the first line > > > >>>> > > > >>>> cmd_args=commandArgs() > > > >>>> > > > >>>> to > > > >>>> > > > >>>> cmd_args <- commandArgs(TRUE) > > > >>>> > > > >>>> makes a lot of sense in most cases. I haven't read your whole > > > >>>> script so > > > >>>> I don't know it it makes sense for you. > > > >>>> > > > >>>> Duncan Murdoch > > > >>>> > > > >>>> > > > >>>>> Please advise, > > > >>>>> Ana > > > >>>>> > > > >>>>> On Sat, Nov 23, 2019 at 4:16 AM Ben Tupper <btup...@bigelow.org> > > > >>>>> wrote: > > > >>>>>> > > > >>>>>> Hi, > > > >>>>>> > > > >>>>>> I think you want this order... > > > >>>>>> > > > >>>>>> Rscript [options for R] script_file.R argument_1 argument_2 ... > > > >>>>>> > > > >>>>>> So, like this ... > > > >>>>>> > > > >>>>>> Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix > > > >>>>>> > > > >>>>>> Cheers, > > > >>>>>> Ben > > > >>>>>> > > > >>>>>> On Fri, Nov 22, 2019 at 8:59 PM Ana Marija > > > >>>>>> <sokovic.anamar...@gmail.com> wrote: > > > >>>>>>> > > > >>>>>>> HI Ben, > > > >>>>>>> > > > >>>>>>> thank you so much , I did this: > > > >>>>>>> > > > >>>>>>> Rscript --no-save ENSG00000154803.ld ENSG00000154803.matrix MR.R > > > >>>>>>> Error: unexpected numeric constant in "1.000 0.089" > > > >>>>>>> Execution halted > > > >>>>>>> > > > >>>>>>> I made ENSG00000154803.ld with: > > > >>>>>>> library(MASS) > > > >>>>>>> write.matrix(ENSG00000154803.ld, file="ENSG00000154803.ld") > > > >>>>>>> > > > >>>>>>> and it looks like this: > > > >>>>>>> > > > >>>>>>> 1.000 0.089 0.006 0.038 0.012 0.014 0.003 0.001 0.005 0.015 0.013 > > > >>>>>>> 0.000 0.000 0.000 0.001 0.003 0.000 > > > >>>>>>> 0.089 1.000 0.002 0.007 0.005 0.001 0.004 0.005 0.000 0.003 0.014 > > > >>>>>>> 0.001 0.012 0.005 0.000 0.004 0.004 > > > >>>>>>> 0.006 0.002 1.000 0.004 0.008 0.029 0.040 0.001 0.001 0.006 0.013 > > > >>>>>>> 0.054 0.006 0.002 0.010 0.001 0.000 > > > >>>>>>> 0.038 0.007 0.004 1.000 0.460 0.044 0.008 0.022 0.010 0.229 0.095 > > > >>>>>>> 0.066 0.010 0.030 0.001 0.003 0.000 > > > >>>>>>> 0.012 0.005 0.008 0.460 1.000 0.151 0.018 0.047 0.021 0.272 0.185 > > > >>>>>>> 0.002 0.003 0.066 0.006 0.004 0.004 > > > >>>>>>> 0.014 0.001 0.029 0.044 0.151 1.000 0.007 0.018 0.218 0.010 0.023 > > > >>>>>>> 0.016 0.000 0.025 0.000 0.005 0.000 > > > >>>>>>> 0.003 0.004 0.040 0.008 0.018 0.007 1.000 0.003 0.002 0.020 0.031 > > > >>>>>>> 0.128 0.019 0.005 0.030 0.002 0.016 > > > >>>>>>> 0.001 0.005 0.001 0.022 0.047 0.018 0.003 1.000 0.004 0.014 0.004 > > > >>>>>>> 0.098 0.010 0.012 0.001 0.006 0.003 > > > >>>>>>> 0.005 0.000 0.001 0.010 0.021 0.218 0.002 0.004 1.000 0.004 0.000 > > > >>>>>>> 0.012 0.000 0.006 0.018 0.004 0.013 > > > >>>>>>> 0.015 0.003 0.006 0.229 0.272 0.010 0.020 0.014 0.004 1.000 0.466 > > > >>>>>>> 0.001 0.091 0.057 0.062 0.002 0.005 > > > >>>>>>> 0.013 0.014 0.013 0.095 0.185 0.023 0.031 0.004 0.000 0.466 1.000 > > > >>>>>>> 0.238 0.180 0.073 0.058 0.000 0.006 > > > >>>>>>> 0.000 0.001 0.054 0.066 0.002 0.016 0.128 0.098 0.012 0.001 0.238 > > > >>>>>>> 1.000 0.158 0.006 0.044 0.006 0.001 > > > >>>>>>> 0.000 0.012 0.006 0.010 0.003 0.000 0.019 0.010 0.000 0.091 0.180 > > > >>>>>>> 0.158 1.000 0.077 0.237 0.009 0.000 > > > >>>>>>> 0.000 0.005 0.002 0.030 0.066 0.025 0.005 0.012 0.006 0.057 0.073 > > > >>>>>>> 0.006 0.077 1.000 0.056 0.000 0.004 > > > >>>>>>> 0.001 0.000 0.010 0.001 0.006 0.000 0.030 0.001 0.018 0.062 0.058 > > > >>>>>>> 0.044 0.237 0.056 1.000 0.000 0.003 > > > >>>>>>> 0.003 0.004 0.001 0.003 0.004 0.005 0.002 0.006 0.004 0.002 0.000 > > > >>>>>>> 0.006 0.009 0.000 0.000 1.000 0.002 > > > >>>>>>> 0.000 0.004 0.000 0.000 0.004 0.000 0.016 0.003 0.013 0.005 0.006 > > > >>>>>>> 0.001 0.000 0.004 0.003 0.002 1.000 > > > >>>>>>> > > > >>>>>>> the other file (ENSG00000154803.matrix) looks like this: > > > >>>>>>> > > > >>>>>>> GENES ENSG00000154803 BETA_GWAS > > > >>>>>>> rs12601631 -0.320577 -0.0160778 > > > >>>>>>> rs1708623 0.708706 0.0717719 > > > >>>>>>> rs1708628 -0.645996 -0.0973019 > > > >>>>>>> rs17804843 -0.78984 0.0059607 > > > >>>>>>> rs4078062 -0.340732 -0.0716837 > > > >>>>>>> rs4316813 -0.721137 -0.00502219 > > > >>>>>>> rs7217764 -0.61641 0.16997 > > > >>>>>>> rs7221842 -0.377727 -0.00184011 > > > >>>>>>> rs12602831 -0.397059 0.0154625 > > > >>>>>>> rs138437542 -0.590669 0.0145733 > > > >>>>>>> rs2174369 -0.167913 -0.0268728 > > > >>>>>>> rs242252 0.20184 0.0161709 > > > >>>>>>> rs34121330 0.328602 0.0753894 > > > >>>>>>> rs4792798 -0.303601 0.00227314 > > > >>>>>>> rs7222311 -0.367686 -0.0419168 > > > >>>>>>> rs74369938 0.687555 -0.223105 > > > >>>>>>> rs8075751 -0.261916 -0.0313484 > > > >>>>>>> > > > >>>>>>> On Fri, Nov 22, 2019 at 7:44 PM Ben Tupper <btup...@bigelow.org> > > > >>>>>>> wrote: > > > >>>>>>>> > > > >>>>>>>> Hi, > > > >>>>>>>> > > > >>>>>>>> You might check the order of your arguments. Options come > > > >>>>>>>> before the > > > >>>>>>>> script filename. See the details here... > > > >>>>>>>> > > > >>>>>>>> https://www.rdocumentation.org/packages/utils/versions/3.6.1/topics/Rscript > > > >>>>>>>> > > > >>>>>>>> Ben > > > >>>>>>>> > > > >>>>>>>> On Fri, Nov 22, 2019 at 8:17 PM Ana Marija > > > >>>>>>>> <sokovic.anamar...@gmail.com> wrote: > > > >>>>>>>>> > > > >>>>>>>>> Hello, > > > >>>>>>>>> > > > >>>>>>>>> I am trying to run this code: > > > >>>>>>>>> https://github.com/eleporcu/TWMR/blob/master/MR.R > > > >>>>>>>>> > > > >>>>>>>>> with r-3.6.1 > > > >>>>>>>>> > > > >>>>>>>>> via: > > > >>>>>>>>> > > > >>>>>>>>> Rscript MR.R --no-save ENSG00000154803 > > > >>>>>>>>> > > > >>>>>>>>> in the current directory I have saved: ENSG00000154803.ld and > > > >>>>>>>>> ENSG00000154803.matrix as the software requires > > > >>>>>>>>> > > > >>>>>>>>> but I am getting this error: > > > >>>>>>>>> > > > >>>>>>>>> Error in file(file, "rt") : cannot open the connection > > > >>>>>>>>> Calls: read.table -> file > > > >>>>>>>>> In addition: Warning message: > > > >>>>>>>>> In file(file, "rt") : > > > >>>>>>>>> cannot open file '--no-restore.matrix': No such file or > > > >>>>>>>>> directory > > > >>>>>>>>> Execution halted > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> Please advise, > > > >>>>>>>>> > > > >>>>>>>>> Thanks > > > >>>>>>>>> Ana > > > >>>>>>>>> > > > >>>>>>>>> ______________________________________________ > > > >>>>>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, > > > >>>>>>>>> see > > > >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help > > > >>>>>>>>> PLEASE do read the posting guide > > > >>>>>>>>> http://www.R-project.org/posting-guide.html > > > >>>>>>>>> and provide commented, minimal, self-contained, reproducible > > > >>>>>>>>> code. > > > >>>>>>>> > > > >>>>>>>> > > > >>>>>>>> > > > >>>>>>>> -- > > > >>>>>>>> Ben Tupper > > > >>>>>>>> Bigelow Laboratory for Ocean Science > > > >>>>>>>> West Boothbay Harbor, Maine > > > >>>>>>>> http://www.bigelow.org/ > > > >>>>>>>> https://eco.bigelow.org > > > >>>>>> > > > >>>>>> > > > >>>>>> > > > >>>>>> -- > > > >>>>>> Ben Tupper > > > >>>>>> Bigelow Laboratory for Ocean Science > > > >>>>>> West Boothbay Harbor, Maine > > > >>>>>> http://www.bigelow.org/ > > > >>>>>> https://eco.bigelow.org > > > >>>>> > > > >>>>> ______________________________________________ > > > >>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > > >>>>> https://stat.ethz.ch/mailman/listinfo/r-help > > > >>>>> PLEASE do read the posting guide > > > >>>>> http://www.R-project.org/posting-guide.html > > > >>>>> and provide commented, minimal, self-contained, reproducible code. > > > >>>>> > > > >>>> > > > >> > > > > > > ______________________________________________ > > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > > https://stat.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting guide > > > http://www.R-project.org/posting-guide.html > > > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.