Entering edit mode
2.7 years ago
iamsmor
•
0
Hello I have problems that someone mentioned before too. I am trying align my trimmed data
hisat2 -q -x $RNA_REF_INDEX/genome_snp_tran -U $RNA_DATA_DIR/SRR309133.fastq.gz -S SRR133309.sam
I am using human grc38_snp_tran.gtf
for ref but I got same error
Killed (ERR): hisat2-align exited with value 137
I don't know how I can double my memory for this job. I will be grateful for any help.
How do you run the job? Local computer, server/HPC, cloud?
I am running on my local computer.
And how much memory does the machine has? Use
free -hm
to find out.Probably buying more RAM sticks is the only answer then.
my machine has this :( how much that ı require for alignment at least ?
Yeah, that is not sufficient for any serious bioinformatics analysis. These days you rarely see any machines, and be it laptops, below 8 or 16GB of RAM. You simply do not have enough RAM. So either upgrade the machine, use a more powerful workstation or familiarize yourself with cloud computing solutions, or check whether your institute operates any kind of server-based solution such as a HPC that you can use.
thank you very much ı will try to swap for temporarily solution.ı hope it will work :)