Bryce Kille

@BioMinnie sorry for the delayed response. The command looks fine, so unfortunately no easy fix there. I'll look into this error by running parsnp on a comparably large dataset, but...

@wolfgangcz Just to clarify, does the command you're running include the angled brackets (``)? If so, you should remove them. In command line help messages, angled brackets are only there...

Yea the .gbk parsing has caused issues in the past. A future goal of mine is to offload the responsibility of manual file parsing to Biopython. I wouldn't be surprised...

@sunctx I used the Klebsiella genomes referenced in https://github.com/marbl/harvest/issues/22. There are roughly ~1300 of them. I also used the ANI recruitment strategy, since the default recruitment includes genomes that don't...

Hi @robfenton! Thank you for opening an issue and also for detailing the version, command, and OS. Just to clarify, the only difference I am seeing is that sequence `09578-19-1.fasta`...

Hmmm. Thanks for pointing this out. I'm not immediately aware of what could be causing this. I'm assuming both versions came from Conda?

Hmm that is strange. The link you posted earlier to the script you ran no longer seems to work. If you can pass that to me, I can run Parsnp...

@valery-shap to clarify, you were observing the ``` *** ERROR *** TreeFromSeqVect_UPGMA, CLUSTER_6 not supported ``` issue as well, but resolved it by lowering the number of threads used?

I've tested a couple directories multiple times and haven't been able to replicate the issue. Can someone please provide an example set?

@innovate-invent thanks for forwarding this to us! I was unable to replicate this issue with the following approach: * Ran Parsnp against two files, 1.fna and 11.fna (as well as...