This is a test version of Biostars. For the public version, visit https://www.biostars.org.
hisat2 :Killed (ERR): hisat2-align exited with value 137

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.

rna-seq alignment hisat2
• 5,285 views • link
updated by Ram Ram • written by iamsmor • iamsmor

How do you run the job? Local computer, server/HPC, cloud?

• 0 views • link
written by ATpoint ATpoint

I am running on my local computer.

• 0 views • link
written by iamsmor • iamsmor

And how much memory does the machine has? Use free -hm to find out.

ı dont know how ı can double my memory for this jop?

Probably buying more RAM sticks is the only answer then.

• 0 views • link
written by ATpoint ATpoint

enter image description here

my machine has this :( how much that ı require for alignment at least ?

• 0 views • link
written by iamsmor • iamsmor

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.

• 0 views • link
written by ATpoint ATpoint

thank you very much ı will try to swap for temporarily solution.ı hope it will work :)

• 0 views • link
written by iamsmor • iamsmor

0 answers

No answers yet.

Log in to answer this question.

More posts like this