HISAT2 alignment out of memory

0

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4.8 years ago

psschlogl ▴ 50

Hi guys I was trying to using hisat2 for align one rna_seq but looks like my pc is not prepared for. I have 32GB of memory and a AMD Ryzen 5 2600 Six-Core Processor cpu. And I was trying to finish this tut:

https://bioinformatics-core-shared-training.github.io/CRUK_CI_RNAseq_course/Supplementary_Materials/S1_Getting_raw_reads_from_SRA.html

But I got this message:
$ Ran out of memory; automatically trying more memory-economical parameters.

The command I used was:

hisat2-build referenceData/fasta/Mus_musculus.GRCm
38.dna_sm.primary_assembly.fa --ss referenceData/hisat2_index/splice_sites.txt --exon referenceData/hisat2_index/exons.txt referenceData/hisat2_index/GRCm38.hisat2

I probably have no machine for that right? I am not vinculated at any institution so I cant have access to any super machine. Do you have any cheap solution or suggestion?

next-gen alignment Assembly RNA-Seq • 2.0k views

ADD COMMENT • link 4.8 years ago by psschlogl ▴ 50

2

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This command requires ( if memory serves ) hundreds of Gb. There are premade indices at the hisat2 website.

ADD REPLY • link 4.8 years ago by ATpoint 81k

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