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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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Bootstrap values are not showing up in the tree #103

Closed naomiohta closed 2 years ago

naomiohta commented 2 years ago

Hello, I am using Parsnp 1.5.3 on MacBook Pro and successfully finished the command as below, but I can't find the bootstrap values.

parsnp -g /Users/myname/reference_ref.gbk -d /Users/myname/serotype_fasta_contigs/*.fasta -c -p 4 -x -o /Users/myname/parsnpout/012422_x

When I try to visualize the tree file using iTOL and Figtree, they aren't displaying bootstrap values. Am I missing something? Thank you!

bkille commented 2 years ago

Hi @naomiohta, thanks for opening an issue! Can you see the bootstrap values in the .tree file?

valery-shap commented 2 years ago

Hello,

I have the same question. and I used the same command. This is head of .tree file: (one.fasta:0.00000100000050002909,((second.fasta:0.00000100000050002909,third.fasta:0.00000100000050002909):0.00032947413443052423,(((((((((((forth.fasta:0.00165147864484025526,fifth.fasta:0.00115577065595259191):0.00041196000646219347

Assume that these are only branch lengths. the same question as #50 Valery

naomiohta commented 2 years ago

Thank you @bkille for your prompt response. As @valery-shap showed, I can see similar values in my .tree file. I was thinking those are the bootstrap values, but are they branch lengths?

eddykay310 commented 2 years ago

Same issue here. I have been trying to understand why it is so if fasttree is used for constructing the tree and if there was a command line option that can be used but I guess there is none.

Thanks in advance for the help

bkille commented 2 years ago

@valery-shap, @naomiohta and @eddykay310, thanks for waiting and sorry for the delay. RAxML's default search algorithm no longer uses bootstrapping. If you would like to run RAxML yourself, I've pushed an updated that keeps the parsnp.snps.mblocks file, which contains the core SNPs that are to be input to RAxML or FastTree. You can run Parsnp with the --skip-phylogeny argument and then run RAxML on the parsnp.snps.mblocks file in your output directory using your desired arguments.

Unfortunately, there is currently an issue in bioconda preventing updates to bioconda tools. I'll reply to this thread once that issue is fixed and Parsnp v1.6.2 is available through conda.

valery-shap commented 2 years ago

Hello, Thank you for your reply! One more question: Harvest tool has the option of input ggr file and output -S output for multi-fasta SNPs . Isn’t it the same file parsnp.snps.mblocks?

bkille commented 2 years ago

Yes, that's correct, thanks! In the meantime you can definitely use harvesttools to obtain the multifasta SNP file.

naomiohta commented 2 years ago

Thanks so much for the update @bkille. I will run without the tree option. I am looking forward to the newer version!

Just to clarify, does Parsnp use RAxML and not FastTree2?

bkille commented 2 years ago

Yes, it runs RAxML by default, however you can use FastTree instead by passing the --use-fasttree flag.

bkille commented 2 years ago

Parsnp v1.6.2 is now available through conda. You can now skip the phylogeny step and then run your own analysis on the parsnp.snps.mblocks file.