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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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Problems running phylorank outliers #22

Open wanxn518 opened 7 months ago

wanxn518 commented 7 months ago

Hi donovan-h-parks,

I installed the software and the test data provided ran successfully, but when I ran my own data for testing, I encountered some:

Running phylorank decorate was successful:

phylorank decorate gtdbtk.unrooted.tree tax.txt test.decorated.tree
[2024-01-16 23:22:36] INFO: PhyloRank v0.1.12
[2024-01-16 23:22:36] INFO: phylorank decorate gtdbtk.unrooted.tree tax.txt test.decorated.tree
[2024-01-16 23:22:36] INFO: Reading tree.
[2024-01-16 23:22:36] INFO: Removing any previous internal node labels.
[2024-01-16 23:22:36] INFO: Reading taxonomy.
[2024-01-16 23:22:36] INFO: Calculating F-measure statistic for each taxa.
[2024-01-16 23:22:36] INFO: Calculating taxa within each lineage.
[2024-01-16 23:22:36] INFO: Processing 1 taxa at Domain rank.
 - processed 1 of 1 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Processing 2 taxa at Phylum rank.
 - processed 2 of 2 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Processing 18 taxa at Class rank.
 - processed 18 of 18 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Processing 56 taxa at Order rank.
 - processed 56 of 56 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Processing 218 taxa at Family rank.
 - processed 218 of 218 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Processing 215 taxa at Genus rank.
 - processed 215 of 215 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Processing 213 taxa at Species rank.
 - processed 213 of 213 (100.00%) taxa.
 - elapsed time: 0.00 minutes
[2024-01-16 23:22:36] INFO: Placing labels with unambiguous position in tree.
[2024-01-16 23:22:36] INFO: Establishing median relative divergence for taxonomic ranks.
[2024-01-16 23:22:36] INFO: Identified 2 phyla.
[2024-01-16 23:22:36] INFO: Using 2 phyla as rootings for inferring distributions.
[2024-01-16 23:22:36] INFO: Calculating information with rooting on Actinomycetota.
[2024-01-16 23:22:36] INFO: Identifying 221 genomes in the outgroup.
[2024-01-16 23:22:36] INFO: Identified 221 outgroup taxa in the tree.
[2024-01-16 23:22:36] INFO: Outgroup is not monophyletic. Tree will be rerooted at the MRCA of the outgroup.
[2024-01-16 23:22:36] INFO: The outgroup consisted of 221 taxa, while the MRCA has 227 leaf nodes.
[2024-01-16 23:22:36] INFO: Rerooting tree.
[2024-01-16 23:22:36] INFO: Calculating information with rooting on Chloroflexota.
[2024-01-16 23:22:36] INFO: Identifying 6 genomes in the outgroup.
[2024-01-16 23:22:36] INFO: Identified 6 outgroup taxa in the tree.
[2024-01-16 23:22:36] INFO: Outgroup is monophyletic.
[2024-01-16 23:22:36] INFO: Rerooting tree.
[2024-01-16 23:22:36] INFO: Resolving ambiguous taxon label placements using median relative divergences.
[2024-01-16 23:22:36] INFO: Writing out statistics for taxa.
[2024-01-16 23:22:36] INFO: Writing out taxonomy for extant taxa.
[2024-01-16 23:22:36] INFO: Writing out decorated tree.
[2024-01-16 23:22:36] INFO: Finished decorating tree.

However phylorank outliers encountered a problem when it prompted the "ValueError: Sample larger than population or is negative" Can you give me some help? Sincere thanks in advance!! image

Best, XiaoNan