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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Out of memory while assembling a polyploid phased assembly #592

Open pashapu43 opened 10 months ago

pashapu43 commented 10 months ago

Hi,

I am trying to assemble a phased genome of a hexaploid species (expected genome size ~ 4Gb) with 356 GB HiFi reads and 85 GB omni C data. However, the assembly process gets killed due to memory issues (oom_kill event) even with 1.3 TB of allocated memory. Here is the full command i used: hifiasm -o Tgenome.asm -t 50 --h1 DTG-OmniC-72_R1_001.fastq.gz,DTG-OmniC-90_R1_001.fastq.gz --h2 DTG-OmniC-72_R2_001.fastq.gz,DTG-OmniC-90_R2_001.fastq.gz T*.hifi_reads.bam.fastq.gz

How much memory should I allocate? Is there a way to reduce the memory usage? Here I am attaching the log file.

Thank you hifiasm.log

chhylp123 commented 10 months ago

Sorry for the late reply. Well it may need more memory like 1.5TB since hifiasm got killed at the HiFi error correction step. If you would like to reduce the memory requirement, you may have a try to use less number of CPU threads specified by -t.