Mikhail Kolmogorov

@ptrebert Seems strange. My only guess would be that PacBio reads might not be properly split into subreads (we had a couple cases like that before). Try to process the...

@ptrebert pbclip finds PacBio reads that were not properly split into subreads. Depending on the DNA library, polymerase might make multiple passes over the fragment (which is used to produce...

@ptrebert I see - this could be tricky sometimes. Did you have any luck with other assemblers? Wtdbg2 might be a fast way to check.

@ptrebert good to know, thanks for the update! At this early stage of assembly, not much could be inferred from the logs, I think.. I guess it the log shows...

@jotes35 your expected genome size is 50kb (0.05 Mb). It needs to be "5m", not "0.05m" (assuming you are aiming for 5 Mb genome).

@jotes35 Please check the FAQ - it provides some answers to your question. Let me know if anything us unclear.

@eyayd could you post the log of the run with `--meta` option?

@eyayd Somethig might not be right with your sample. Your expected genome size is 100m, and the coverage should be roughly 50x. But based on overlaps, the coverage is 600x...

@zhangwenda0518 my only suggestion would be to try less threads for the consensus step (your log indicates you used 64 threads, I'd try 20 or 10). If that helps and...

@mxd1288 please submit the full `flye.log` file. Also, are you saying that manually running the minimap2 command line worked for you? It seemed to run out of memory originally, so...