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

Ana Marija @okov|c@@n@m@r|j@ @end|ng |rom gm@||@com
Sat Nov 23 21:25:47 CET 2019


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.



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