Dario Copetti

Hello, The job eventually completed the megareads step, and now it is looking like it is running the Celera Assembler. The stdout shows this: ``` ERROR: failed to merge alignments...

Good point: it looks more like a all-vs-all rather than a read-to-reference type of exercise. Heng Li advised me to map ONT reads to unitigs, which is another strategy as...

another way to look at the (impressive!) quality of these assemblies and where I would like to act:  This is the distribution of the coverage upon realignment of the...

Thanks for the feedback! Unfortunately we don't have Hi-C data (probably we will get it though), and this attempt is for a different way of scaffolding in a phased manner....

OK, but then how do I solve the memory issue? I don't think it is normal that a 800 Mb genome should need more than 1 TB memory

What do you mean for data quality issues? This is how the HiFi data looks like, the median QV is 32  what else could I do about it?

yep, I agree that the low frequency k-mers are the issue. But if we add coverage and move some of those k-mers to the right, then there will be more...

same here, I get the Segmentation fault error when the process uses about half of the total memory (in my case ~65 GB out of 126). My version is 0.3-r179...

Hi, Can it be that your genome is heterozygous? In that case, highly divergent allelic regions will be assembled on separate contigs, increasing the total size of the assembly to...

Thanks, I will delete it. But according to the error, will I have other 816 folders to delete? `LateTaskFailureError: 'Counted a total of 817 failure(s) and 4921 success(es).'` I never...