[R] cannot open file '--no-restore.matrix'

Sat Nov 23 22:05:42 CET 2019

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.anamarija using 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.bengtsson using 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.duncan using 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.duncan using 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.duncan using 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 <btupper using 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.anamarija using 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 <btupper using 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.anamarija using 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 using 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 using 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 using 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.