Mikhail Kolmogorov
Mikhail Kolmogorov
Very likely you are running out of memory. Can you share more details about the system and send `flye.log`? If it is a memory error, my only suggestion would be...
I see, I think it's a memory issue. The log says there are 128Gb in total, but only 56Gb was available at the time of run. I'd try to run...
@JamesHowie14 the minimap2 error long say that the process was killed by the system. This is typically happens when you are running out of resources for a process. This is...
@JamesHowie14 normally minimap2 rarely takes more than 64Gb RAM even for a human-sized genome. I think the problem is that your genome just happened to be very repetitive, and this...
@JamesHowie14 thanks for the update. I think it could be both a lot of repeats and high heterozygosity. Both a very complicated to assemble. I don't think error-corrected reads will...
Hi Steffen, Yes, I am planning to submit a pull request in the near future. Will keep you posted. Thanks, Mikhail
Opened a pull request: https://github.com/lh3/minimap2/pull/687
@tillea I'm waiting for a confirmation from minimap2 developers that they are interested in adopting the patch. Then I'll be happy to update the pull request. Thanks for checking.
Sorry for the late response! This is a strange error. It seems that Flye successfully generated some files, but the file copy operation failed. Maybe you got unlucky and ran...
Hi, I think the reason for that is that hapdup is actually using unphased reads to polish, in addition to either of the haplotypes. This is an old strategy we...