I'm running STAR to map RNAseq reads to the mouse genome. I've run this command plenty in the past, but it is not working now for some reason. It's saying I don't have enough RAM, but my machine has 64GB of RAM, so it should be plenty.

STAR --genomeDir Fullstar --readFilesIn samples/2_Forward.fq samples/2_Reverse.fq --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --runThreadN 16 --outFileNamePrefix "2_star/"

Dec 21 15:19:57 ..... started STAR run
Dec 21 15:19:57 ..... loading genome

EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc

Possible cause 1: not enough RAM. Check if you have enough RAM 28193309652 bytes

Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v 28193309652

Dec 21 15:19:57 ...... FATAL ERROR, exiting

ulimit -v

unlimited

ulimit -a

core file size (blocks, -c) 0

data seg size (kbytes, -d) unlimited

scheduling priority (-e) 0

file size (blocks, -f) unlimited

pending signals (-i) 257011

max locked memory (kbytes, -l) 16384

max memory size (kbytes, -m) unlimited

open files (-n) 1024

pipe size (512 bytes, -p) 8

POSIX message queues (bytes, -q) 819200

real-time priority (-r) 0

stack size (kbytes, -s) 8192

cpu time (seconds, -t) unlimited

max user processes (-u) 257011

virtual memory (kbytes, -v) 28193309652

file locks (-x) unlimited

Let me know other info you need to help me solve this problem



Source link