Bryce Kille

Hi @Dentalium, thanks for asking! Since MashMap is an "approximate" mapping method, it does not actually align any bases. When segments are not merged, the 10th column tracks how many...

Hi @Arthurdyu, Do you run into the same issue if you omit the `-c` flag? My guess is that one (or more) of the input assemblies is throwing off the...

Thanks for opening #163 (and sorry for forgetting about this one). Feel free to close this issue if the only remaining issue is the recombination filter.

Hi @doy-pin! Hmmm, you may have some bad input files. Each partitioned run is covering an average of 1.3Mbp, but there are no aligned regions common to all partitions. This...

Hi @evagunawan and @AbigailShockey, You are correct that (1) those lengths may be incorrect and that (2) it may affect the cluster coverage calculation. TLDR, the more contigs you have...

Hi @evagunawan, My apologies for the delay. I'm cutting a new release today with this issue fixed (you can see the referenced commit above for details). It should be on...

Hi @hdesale2408, Sorry for the delay in responding. Yes, there should not be SNPs between the same sequence in an alignment. There have been some [noted](https://github.com/marbl/parsnp/issues/112) (but rare) issues w/...

Hi @hdesale2408, This bug has been fixed in Parsnp 2.0. Please let me know if you continue to experience it!

Hi @naifahim, Could you please run your command with --verbose flag and then share both the command and the output? Thank you!

Hi @naifahim 40gb of storage should be enough for parsnp. May I ask how much RAM you have on your machine? Also, you are requesting 8 threads, which according to...