Bryce Kille

@naifahim For your issue, I see in the output the critical error: ``` CRITICAL - Set of filtered genomes are too divergent for parsnp, please use stricter ANI thresholds for...

@afsansarwer Similarly, your output shows that the partitions share no aligned regions in common: ``` 13:55:06 - INFO - Partition stats: Mean bp covered = 1807625.40 Mean LCB count =...

> Is 4gb RAM a problem? > > > Sometimes linux got shut down automatically. That is a very little amount of RAM, especially if you are running the partitions...

The RAM requirement varies depending on the number, quality, and divergence of genomes as well as the partition size and number of concurrent partitions (i.e. `-p`). For 800 M. tuberculosis,...

Hi @naifahim, I completely understand your constraints. Please try running ``` parsnp -r reference.fna -d a -a c -o result --verbose --use-mash -p 1 ``` Also, note that it will...

The command above should be fine. It uses Mash instead of FastANI. This should work better for your computer. If you have any more questions, please feel free to send...

Hi @naifahim, Yes, it sounds like your genomes are rather divergent. FastANI likely requires more RAM, so that may be the issue. If you'd like, feel free to send me...

Hi @DrMahsaRahnama76 , Yes, the fix will apply to the next release of Parsnp (2.1.2). However, this issue unfortunately may be with [HarvestTools](https://github.com/marbl/harvest-tools), which expects the xmfa file to be...

@fish2022Jul, Parsnp v2.1.2 is on conda now. Please let me know if you run into any issues. @Kadsae, to clarify, you are seeing off by one errors in v2.1.2 as...

Hi @Kadsae, This is very strange. Other than some error reporting improvements, the only [change between v2.1.1 and v2.1.2](https://github.com/marbl/parsnp/compare/v2.1.1...v2.1.2) is the use of the `##FormatVersion Mauve` header instead of `##FormatVersion...