segmentation fault

[Mrbland]

Hello,

Thank you for making great new tools for hifi reads. I am running hifiasm on an r5a.12xlarge AWS instance (48cpu, 384GB RAM), trying to assemble ~450Mb genome. My hifi fasta is ~24GB, 3.2 million reads with average read length ~10Kb. Hifiasm keeps crashing after the 3 read correction steps during Writing reads to disk with Segmentation fault.

Do I need to use an instance with more RAM or is there something else happening?

Thanks!

[chhylp123]

Could you please share the log file? 384GB RAM should be enough for such small genome.

[Mrbland]

I had been using -l0 and -l1 which caused the failure. I repeated with default purging and the assembly was successful (and looks quite good). I can try and replicate the light/no purging and share the logs in case it helps with future releases/issues.

[chhylp123]

Thanks a lot. It would be very helpful to get the log file.

[chhylp123]

@Mrbland The new version of hifiasm (v0.14) fixed a small bugs of purge_dups. Hope it can fix the your problems when using -l0 and -l1.

[Mrbland]

Great, I am trying it out right now and will let you know how it runs. Sorry, I haven't revisited this issue since I first posted.

[Mrbland]

@chhylp123 v0.14 works! I only tried -l0 and there was no seg fault. Thanks!

[chhylp123]

Great! Thanks for having a try.