[R] cannot open file '--no-restore.matrix'
Henrik Bengtsson
henr|k@bengt@@on @end|ng |rom gm@||@com
Sat Nov 23 21:08:03 CET 2019
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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