search for: germlin

Displaying 4 results from an estimated 4 matches for "germlin".

Did you mean: 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...