wtdbg2: out of memory error

Question

[Maliha]

I am doing a whole genome assembly of a chicken that has been sequenced using a Pacbio SMRT long-read sequencer.

The genome size is 60g. I am using wtdbg2 tool to do the assembly. I used this following command:

wtdbg2 -x sq -g 60g -t 40 -i SRR10161541.fastq -f -o /home/u1001/asil

And I got this error:

--
-- total memory      131753908.0 kB
-- available         117124396.0 kB
-- 32 cores
-- Starting program: wtdbg2 -x sq -g 60g -t 40 -i SRR10161541.fastq -f -o /home/zsiddiki/Asil_WGS_project
-- pid                    935954
-- date         Mon Jan  2 11:46:25 2023
--[Mon Jan  2 11:46:25 2023] loading reads
1990000 -- Out of memory, try to allocate 8053063680 bytes, old size 7784628224, in encap_basebank -- dna.h:537 --
wtdbg2(+0x5704)[0x55deb3195704]
wtdbg2(+0xd102)[0x55deb319d102]
wtdbg2(+0xd42b)[0x55deb319d42b]
wtdbg2(+0x19b55)[0x55deb31a9b55]
wtdbg2(+0x7cf70)[0x55deb320cf70]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fd5cb75cd90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fd5cb75ce40]
wtdbg2(+0x5619)[0x55deb3195619]
Aborted (core dumped)

[barslmn]

Maybe Ram can help you with this.

[Ram]

They need the other RAM lol

Answer 1

[colindaven]

Sounds like you need more RAM - try to repeat on a bigger machine with perhaps 256 -512 GB RAM or more. The genome size should be smaller, certainly not 60 GB.

[bagdevi.mishra]

The chicken genome has 39 chromosomes containing 1.1 Gb with 20,000-23,000 protein-coding genes.

[Maliha]

Thanks for the comment. I will try to run it on a computer with 512gb RAM. However, Please correct me if I am wrong but I found it here that the genome size is 60g - gallus gallus

[colindaven]

No, 60gb of bases were sequenced (think coverage). This is not the genome size.