hisat2 :Killed (ERR): hisat2-align exited with value 137

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2.9 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.

RNA-seq alignment hisat2 • 3.7k views

ADD COMMENT • link updated 15 months ago by Ram 44k • written 2.9 years ago by iamsmor • 0

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

ADD REPLY • link 2.9 years ago by ATpoint 85k

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I am running on my local computer.

ADD REPLY • link 2.9 years ago by iamsmor • 0

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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.

ADD REPLY • link 2.9 years ago by ATpoint 85k

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

ADD REPLY • link 2.9 years ago by iamsmor • 0

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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.

ADD REPLY • link 2.9 years ago by ATpoint 85k

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

ADD REPLY • link 2.9 years ago by iamsmor • 0

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