Hi all, This is probably not specific to facets but i am struggling to run facets.R in an HPC (linux).
Rscript --vanilla facets.R -i $PATIENT_ID -f $INPUT -o $OUTPUT -c $CVAL
Loading required package: pctGCdata Taking input= as a system command ('gunzip -c /exports/igmm/eddie/WGS/variants/cnv/facets/pileups/E13.csv.gz') and a variable has been used in the expression passed to input=. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Error: cannot allocate vector of size 2.3 Gb Execution halted
I've give the job 32Gb of ram through the cluster setting but it keeps giving off this error. Is there a way around it? How do you increase RAM use for R scripts run through Rscript?
I've tried ulimit but the same error was obtained.