bwa mem2 index genome - chipseq analysis
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Maka • 0
Last seen 8 months ago

I am trying to index my reference genome using bwa-mem2 (latest version). I downloaded GRCm39.primary_assembly.genome.fa from and run the following

bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index /media/jay/Data/reference_genome/GRCm39.primary_assembly.genome.fa

I got this output

[bwa_index] Pack FASTA... 7.03 sec
init ticks = 216871092051
ref seq len = 5456444902
binary seq ticks = 176853625961
build index ticks = 4277710586226
ref_seq_len = 5456444902
count = 0, 1585357357, 2728222451, 3871087545, 5456444902
BWT[2307856305] = 4
CP_SHIFT = 5, CP_MASK = 31
sizeof CP_OCC = 64

I read that might be a problem of memory so I checked my mem and swap

free -hm
              total        used        free      shared  buff/cache   available
Mem:            62G        1,2G         59G        520M        1,9G         60G
Swap:          2,0G        1,4G        650M

and I am working with

No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.6 LTS
Release:    18.04
Codename:   bionic

and my pc specs

          product: Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz

Could you please help me out? is there a way to implement the memory usage by using bwa-mem2 index command?

If the memory is not enough, could you suggest me another way to create an index to proceed with my Chipseq analysis?

Thank you a lot.

Genome bwamem ChIPSeqData index • 2.0k views
Entering edit mode
ATpoint ★ 4.2k
Last seen 1 minute ago

It's not related to Bioconductor, in the future please ask at

A quick search for indexing memory requirements reveals so you're most likely out of RAM. Either use 'normal' bwa-mem, it produces identical outputs without these absurd memory requirements of the new version (bwa-mem2) of that tool or use bwa-mem2 and build the index on a big memory machine to eventually bebefit from the speed enhancements of mem2. If you need more help please post elsewhere.


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