"Segmentation fault" when writing reads to disk

[flixitt]

Good morning,

I am trying to run Hifiasm on long reads sequenced by Nanopore (R10), but my run crashes every time the program attempts to write the reads.​

I submitted the run through SLURM (64 CPUs, 300 GB of memory).​

Here is the end of the log:

Thank you very much for any help you can provide !

[chhylp123]

Hifiasm won't crashed at this stage in most cases. It would be better that you can check there is other issues like out of memory.

[flixitt]

Thanks for the quick response!

I ran some tests with 500–600 GB of memory, but the results are the same. Additionally, I have over 200 GB of free space on the server, so the issue doesn't stem from there.

I'll attempt to create a new environment; perhaps the libraries are corrupted.

Thanks again!

[faulk-lab]

I am having the same issue. Any fix?

[danpal96]

I encountered the same error, in my case, it was because I hadn’t created the output directory. It might be helpful if hifiasm could check whether the output file is writable beforehand, to prevent the segmentation fault.