Hifiasm is getting killed while trying to assemble a genome

Question

[pranavdatar01]

I am trying to assemble a genome (90x coverage, mean read quality: 30). The system on which I am working has 128 memory threads and 188 GB RAM. I am trying to assemble using the following command: hifiasm -o assembly -t 16 -f0 _______.sra.fastq, but it is getting killed. Even the log file is empty. I even tried to decrease the number of threads and even used -f0, but nothing is working out. How do I figure this out?

[Panos]

How large do you expect the genome to be? For some human genomes that I tried it (i.e. genome size ~3Gbp), peak memory usage was ~160GB RAM (HiFi data, 50x coverage).

In my case, I ran hifiasm like this:

hifiasm -o assembly.asm -t16 hifi_reads.bam.fastq.gz

[pranavdatar01]

I am expecting the genome to be around 1.5 Gb.

[GenoMax]

I even tried to decrease the number of threads and even used -f0, but nothing is working out.

What kind of dataset is this? How many reads are there and what is the total data size?

As already noted by @Panos, the process is likely running out of memory (are you the only user on this system, if not other processes could reduce the available memory). Reducing the number of threads (you were alredy using a reasonable number to begin with) can only do so much.

[pranavdatar01]

These are PacBio HiFi reads (total reads 5,237,005), and the total data size is 255 GB.

I am the only user on the system.