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germain
2017 Jul 12
2
submitting R scripts with command_line_arguments to PBS HPC clusters
Dear all,
please could you advise me on the following : I've written a R script that
reads 3 arguments from the command line, i.e. :
" args <- commandArgs(TRUE)
TUMOR <- args[1]
GERMLINE <- args[2]
CHR <- args[3] ".
when I submit the R script to a PBS HPC scheduler, I do the following
(below), but ... I am getting an error message.
(I am not posting the error message, because the R script I wrote works
fine when it is run from a regular terminal ..)
Please may I ask,...
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
...nts are passed.
> if(length(args)==0){
> stop("no args specified")
> }
> ## Then cycle through each element of the list and evaluate the expressions.
> for(i in 1:length(args)){
> print(args[[i]])
> eval(parse(text=args[[i]]))
> }
> print(TUMOR)
> print(GERMLINE)
> print(CHR)
qsub shell script test.sh:
> #!/bin/bash
>
> #Note: the single quote '...' around the --args ... "..." "..." is important!
> R CMD BATCH --no-save --no-restore '--args TUMOR="tumor.bam" GERMLINE="germline.bam" CH...
2012 Feb 23
1
segfault when using data.table package in conjunction with foreach
...c
cat("OK\n")
}
ans
}
require(foreach)
require(doMC)
registerDoMC(cores=2)
num <- 8891
nr <- 500000000L #500 million rows at a time
MMM <- foreach(IT = 1:2) %dopar% {
require(data.table)
if (IT==1){ x <- system.time({computeAllPairSums(
paste(GERMLINE,"bc.chr22.q.20.file",sep=''),num,nr)}) } #Run it on
regular file PID 6489, 24 gb
if (IT==2){ z <- system.time({computeAllPairSums.gz(
paste(GERMLINE,"bc.chr22.q.20.gz",sep=''),num,nr)}) } #Run it on gz
file PID 6490, 24 gb
}
MY R OUTPUT/ERROR:
MMM <-...
2017 Jul 12
0
submitting R scripts with command_line_arguments to PBS HPC clusters
...017 5:25:20 PM PDT, Bogdan Tanasa <tanasa at gmail.com> wrote:
>Dear all,
>
>please could you advise me on the following : I've written a R script
>that
>reads 3 arguments from the command line, i.e. :
>
>" args <- commandArgs(TRUE)
>TUMOR <- args[1]
>GERMLINE <- args[2]
>CHR <- args[3] ".
>
>when I submit the R script to a PBS HPC scheduler, I do the following
>(below), but ... I am getting an error message.
>(I am not posting the error message, because the R script I wrote works
>fine when it is run from a regular terminal...