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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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Order of genomes in ini file matters? #46

Closed sconlan closed 6 years ago

sconlan commented 6 years ago

It seems like the order in which genomes are added to the parsnp ini file is:

  1. not consistent platform to platform. I get different orders from the OS X and Linus compiled versions
  2. seems to matter. For otherwise identical ini files, the output trees and %core differ based on order of the genomes in the ini file
  3. doesn't seem to be controllable be by the user.

Is there a way to control the order that the genomes are added? Alternatively, is there a way to feed an ini file directly to parsnp so I can experiment with this?

sconlan commented 6 years ago

I have tested this with the compiled Linux version (Parsnp-Linux64-v1.2) by shuffling* the order of the input files. The order DOESN'T seem to matter. Closing this issue but adding a note to issue #45 since I still can't resolve the difference in outputs from parsnp compiled for operating systems.