Mikhail Kolmogorov

Sorry for my late response! 1. How much RAM does the machine your are using to run minimap2 manually have? It is a bit strange that you can process it...

Thanks for letting me know - I will specify networkx version 2.2 as a requirement for now. Will need to transition to Python3 at some point..

No, Ragout is independent from Flye. Ragout is currently supports only Python 2.7.

Hi Zack, It looks like there may be some piece of sequence shared by chromosome on their ends. This is causing chromosomes to be merged on the graph. There are...

Hi, Ok, so seems that HAL API have changed at some point.. Could you share a link to the exact version that you have installed? Thanks, Mikhail

Ok, I'm glad that it worked this time. I'm following up with the HAL developers on how to better resolve this.

@bernard-kim are you using hal2maf version from after this fix: https://github.com/ComparativeGenomicsToolkit/hal/issues/117? If so, could you please post the full `hal2mafMP.py` command line and describe your issue in that thread (referenced...

@stsmall thanks for the feedback. Yes, I think both of your suggestions are valid, I can't think about other alternatives right now. In fact, it might make sense to switch...

Hi, Very likely related to the repetitive nature of these regions. Flye is using secondary alignment to error-correct repetitive regions, but in this case the reads from different repeat copy...

You need to get and compile the latest code from github, `flye` branch (which is default). This code is not a part of a release yet. Instructions are here: https://github.com/fenderglass/Flye/blob/flye/docs/INSTALL.md#local-building-without-installation