Mikhail Kolmogorov

Flye does not keep the information about read assignment, unfortunately. I think filtering reads might be a solution - I would start from keeping only (i) primary alignments, (ii) MAPQ...

Confirming this for MacOs + Python 3.9.7

Hi, Thank you for the feedback! Could you send me "abruijn.log" file at [email protected], so I can take a look on it? Mikhail

Hi, Looks like some kind of a corner case resulted into an error during polishing. Do you think you can send me the file with bubbles (`40-polishing/bubbles_1.fasta'`) so I can...

Thank you! Strangely, I was able to process this file without any issues on my machine. I suspect that it might be an issue with the threads - some servers...

Closing due to inactivity - feel free to reopen if the issue remains.

Hi, There are two possible reasons for this error: either (i) a config file "/opt/Flye/flye/config/bin_cfg/nano_r94_homopolymers.mat" is corrupted or (ii) polisher code is hitting some kind of edge case. I think...

Hmm, this file looks ok, with the exception that there are Windows-style line breaks (e.g. "\r\n" instead of "\n"). Did you modify this file on a Windows machine? Otherwise, this...

Just as a sanity quick check, you can try to run polisher in a standalone mode using `--polish-target`. Try it on an any other dataset (for which you have a...

Good to know, thanks! Closing the issue then - don't have access to any ppc machines.