Jeff Maughan

Has there been any update on this issue? I'm using minimap2 for purge_dups which requires a self-self alignment - but I also get a core dump (see below) similar to...

I should have noted in my question above that I am running this on 2Tb node and I have tried it with differing number of threads from 2 -128. They...

Thanks for you the very fast response! I realize that I can simply restart using -o set to the exact same prefix as the previous run - will this overwrite...

Thanks again for the quick replies. Much appreciated.

I apologize for reopening this thread. I have rerun the assembly with different -s values. None, however, produce completely unzipped haplotypes: The discrepancy in size decreases between the two haplotype...

The bin files are quite large: I could upload them to a ftp server to give you access to them (or if you have a place you would prefer that...

Yes, I will upload the files to our ftp server and then give you credentials for you to down load. Can you share your email with me to give you...

@caiobrunharo. I don't have a definitive answer to our problem, yet. But I think I know what happened - it wasn't that we had the wrong Hi-C reads, only that...

I apologize for reopening this thread, but I was able to get the correct Hi-C and have since run it. I'm attaching the hifiasm output here: [slurm-46199993.out.txt](https://github.com/chhylp123/hifiasm/files/7953408/slurm-46199993.out.txt). The assembly was...

These are the coverage thresholds (as pulled from the slurm): [M::purge_dups] homozygous read coverage threshold: 57 [M::purge_dups] purge duplication coverage threshold: 72 [M::stat] # heterozygous bases: 4945418176; # homozygous bases:...