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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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FastTree output tree is missing #147

Closed gregorysprenger closed 4 months ago

gregorysprenger commented 4 months ago

parsnp.tree is not created when using --use-fasttree with Parsnp. I looked through the parsnp python file and only the output of RAxML is renamed to parsnp.tree (via shutil.move). Though, the FastTree phylogeny is placed in <outputDirectory>/log/fasttree.out. It is not a terminating error.

I was able to replicate this not only with my test data, but also with the example mers_virus data within this repository.

Installation:

# Bioconda is added to my conda environment and this installs without error
conda create -n parsnp parsnp -y
conda activate parsnp

Commands:

# Using FastTree
## ERROR - parsnp.tree:         newick format tree is missing!
parsnp -v -d genomes/ -r ref/England1.fna -o Parsnp2.0.3-fasttree -p 2 -c --use-fasttree
# Using RAxML
## Completes successfully 
parsnp -v -d genomes/ -r ref/England1.fna -o Parsnp2.0.3-fasttree -p 2 -c
bkille commented 4 months ago

Thank you for the detailed report! I won't be able to address this until next week unfortunately, but it should be an easy fix.