Segmentation Fault

[mellamosummer]

Good morning,

I am running HiFiASM with HiFi & HiC reads and am encountering a segmentation fault after the HiC reads have been indexed. I am running HiFiASM version 0.24.0 with 800Gb and 32 threads. The expected genome size is ~3Gb. Could you help troubleshoot this issue? I've attached the log file here:

HiFiASM.35702257.txt

[chhylp123]

Can you just rerun it using the current bin files? Looks like out of memory.

[mellamosummer]

Thanks for your quick response! I tried to rerun it with the current bin files and still encountered the same segmentation fault. Our cluster log indicates that it used less than half of the allocated mem.

[chhylp123]

Do you have the log file for the second round of running?

[mellamosummer]

Yes! Here it is:

HiFiASM.35713762.txt

[Alexdami17]

I encountered a similar segmentation fault with my OmniC data. I had thought it was memory-related but the problem persisted even with 1 TB RAM for a genome of ~750 MB. I got around it by first converting the bzip2 (.bz2) format to gzip (.gz). Then, I ran QC on the reads and removed low-quality reads using cutadapt. With the trimmed reads, hifiasm completed the run producing primary assembly, hap1, and hap2 files. Also in a previous run, Hifiasm worked fine producing primary assembly without the OmniC data. @chhylp123 Does Hifiasm report an error immediately if the HiC file format is invalid or returns a segfault later on?