bwa mem2 index genome - chipseq analysis
1
0
Entering edit mode
Maka • 0
@54d5a2c1
Last seen 8 months ago
Germany

I am trying to index my reference genome using bwa-mem2 (latest version). I downloaded GRCm39.primary_assembly.genome.fa from https://www.gencodegenes.org/mouse/release_M27.html 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
Killed

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

-cpu
          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
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.2k
@atpoint-13662
Last seen 1 minute ago
Germany

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

A quick search for indexing memory requirements reveals https://github.com/bwa-mem2/bwa-mem2/issues/118 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.

ADD COMMENT

Login before adding your answer.

Traffic: 622 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6