STAR mapping crashes with Killed:9 even with sufficient memory

[Chahat Upreti]

Hi,

I have a system with 48 GB memory, and I am trying to run STAR on about 25 samples, but it crashes with Killed: 9 error everytime and restarts the system (Mac). The log file of one of the failed files is attached. I am trying to run STAR on all of them using this loop - 

for i in $(ls /Volumes/bam/DRG/fastq_50/PhenoInfoAvailable/unzipped); do  

 STAR --runThreadN 3  --genomeDir /Users/chahat/Documents/DRG/STAR-master/genome --readFilesIn /Volumes/bam/DRG/fastq_50/PhenoInfoAvailable/unzipped/$i --outFileNamePrefix /Volumes/bam/DRG/results/2020_02_04/STAR_rerun_for_GATK/$i --outSAMtype BAM Unsorted --twopassMode Basic ; done

My system has 4 cores.

I am not sure why this is happening. Is it because I am not using the shared genome-loading option, and it has to load the genome to the memory every time (if so, what command would you recommend)? Or is it something else?

Thank you!

[Alexander Dobin]

Hi Chahat,

nothing suspicious in the Log.out file, and 48GB should be enough. What is the output of

ulimit -a

Maybe the the RAM limits are too small?

Cheers

Alex

[Chahat Upreti]

Hi Alex,

The output of `ulimit -a` is - 

| => ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 256
pipe size (512 bytes, -p) 1
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4256
virtual memory (kbytes, -v) unlimited

[Alexander Dobin]

Hi Chahat,

it looks unlimited. Can you check how much RAM is used by other processes? 
Also, it would be good to try the latest release, 2.7.3a.

Cheers

Alex