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donovan-h-parks / PhyloRank

Assign taxonomic ranks based on evolutionary divergence.
GNU General Public License v3.0
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Identified 0 phyla #24

Open MarcelaHer opened 2 days ago

MarcelaHer commented 2 days ago

Hi,

We are having problems running your program. We get the message that we have 0 taxa, but we actually have three different phyla in our RED file.

The program run with the example data you have (using ar122_taxonomy_r95.tsv and ar122_r95.tree), but not with our data.

We would be grateful if you can help us. Thank you.

[2024-11-28 14:08:00] INFO: PhyloRank v0.1.12 [2024-11-28 14:08:00] INFO: phylorank outliers seqcode_bacteria_ktedono_nocardia_bacillus_type_align.raxml.bestTree.tre RED_bacteria_bacillus_copy.tsv Try_3EvolDist [2024-11-28 14:08:00] INFO: Reading tree. [2024-11-28 14:08:00] INFO: Reading taxonomy. [2024-11-28 14:08:00] INFO: Reading taxonomy from tree. [2024-11-28 14:08:00] INFO: Identified 0 taxa for use in inferring RED distribution.

Rank Taxa to Plot Taxa for Inference

[2024-11-28 14:08:00] INFO: Identified 0 phyla. [2024-11-28 14:08:00] INFO: Using 0 phyla as rootings for inferring distributions. [2024-11-28 14:08:00] ERROR: Rescaling requires at least 2 valid phyla.

donovan-h-parks commented 2 days ago

Hi. A phylum needs at least 2 classes for it to be considered by PhyloRank.

MarcelaHer commented 2 days ago

Hi Donovan,

Many thanks for your help but it also doesn’t work for us.

Please would you mind checking our files?

Many thanks, Marcela

From: Donovan H. Parks @.> Date: Thursday, 28 November 2024 at 14:22 To: donovan-h-parks/PhyloRank @.> Cc: Marcela Hernandez Garcia (BIO - Staff) @.>, Author @.> Subject: Re: [donovan-h-parks/PhyloRank] Identified 0 phyla (Issue #24)

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Hi. A phylum needs at least 2 classes for it to be considered by PhyloRank.

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donovan-h-parks commented 2 days ago

Hi Marcela. You can email you tree and I can take a quick look. Also note that if your tree has a plausible rooting, you can run PhyloRank with a fixed root using the --fixed_root flag. This is generally recommended over calculating the median RED over all phyla rootings.

MarcelaHer commented 1 day ago

Please could you send us your email? Thanks