Internal node truncated taxonomic affiliation

[franco magurno]

Hi,
I hope is not a redundant topic, if yes please re-direct me to the existing thread.


In GAPPA have many sequences assigned to a basal node of a clade with ALL children:

Thermodesulfobacteriota;Syntrophobacteria;Syntrophobacterales;...

 In jplace would be:

 {"p": [
      [1940, -45708.6256088126, 0.3574714303, 0.0099697359, 0.1134640132],
      [1916, -45708.9134304243, 0.2680661644, 0.0685649208, 0.1138244082],
      [1939, -45708.9137102743, 0.2679911565, 0.1473485298, 0.1138213233],
      [1902, -45709.9534425545, 0.0947480915, 0.0404398995, 0.1053605157]
      ],
    "n": ["Otu009"]


With 1940 the common ancestor, and the other nodes belonging to the clade.

Even lowering the threshold to 0.8 I keep getting:

 Otu009 0 0 1 1 former_Deltaproteobacteria_supercluster
Otu009 1 1 1 1 former_Deltaproteobacteria_supercluster;Thermodesulfobacteriota



Probably I missed something, because I was expecting Syntrophobacterales as taxonomic affiliation. I already checked the taxonomy file and there are no mismatches.

Thank you, 
Franco

[Lucas Czech]

Hi Franco,

I assume you are talking about the "assign" command? Could you please post the exact command you are using here, and ideally a minimal example to replicate the behavior you are observing? From just that small snippet, I am not seeing what is going on there and where the issue might be.

Cheers

Lucas

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[franco magurno]

More details about the analysis:


gappa edit accumulate --jplace-path epa_result.jplace --threshold 0.9 

gappa examine assign --jplace-path accumulated.jplace --taxon-file taxonomy_final_affiliation_update_Caldisericota.txt --file-prefix SRB2_2 --per-query-results


In attachment the jplace files and taxonomy
Cheers,

Franco