Specified taxanomy name not in NCBI taxanomy database.

[lijunyuan]

Dears, I installed the [MitoFlex] following your instruction with all needed modules in the conda built environment, and updated the NCBI taxanomy database using ./ncbi.py, finally the .etetoolkit directory was created at my home. I tried the ./MitoFlex.py load-modules, and the result showed that all the modules were OK: [18:30:05 INFO ] (MitoFlex -> pre@411) : MitoFlex 0.2.9, run 1 [18:30:05 INFO ] (MitoFlex -> pre@414) : Arguments after parsed : [18:30:05 INFO ] (MitoFlex -> pre@415) : ['__calling=load-modules'] [18:30:05 INFO ] (MitoFlex -> load_modules@382) : Loading filter module. [18:30:05 INFO ] (MitoFlex -> load_modules@384) : Loading assemble module. [18:30:06 INFO ] (MitoFlex -> load_modules@386) : Loading findmitoscaf module. [18:30:35 INFO ] (MitoFlex -> load_modules@388) : Loading annotation module. [18:30:35 INFO ] (MitoFlex -> load_modules@390) : Loading visualize module. [18:30:35 INFO ] (MitoFlex -> load_modules@395) : All modules are loaded correctly. [18:30:35 INFO ] (MitoFlex -> post@477) : All done! Time elapsed : 30.42s.

However, when I tried ../MitoFlex.py --config test_config.py, an error occurred showing that: Specified taxanomy name not in NCBI taxanomy database. Error occured, exiting.

Would you please help to see what is the problem, thanks !

Lijunyuan

[Prunoideae]

Looks like your taxonomy database is still not correctly set up. This error occurs when a name not existed in taxonomy database was given to MitoFlex as taxonomy filter. In the test case it should be Arthropoda, which should exist in the taxonomy database if it's setup correctly.

Can you try to execute these lines in the python environment you will run MitoFlex in:

from ete3 import NCBITaxa
ncbi = NCBITaxa()
result = ncbi.get_name_translator(["Arthropoda"])
print(result)

If your setup is correct, it should output:

>>> from ete3 import NCBITaxa
>>> ncbi = NCBITaxa()
>>> result = ncbi.get_name_translator(["Arthropoda"])
>>> print(result)
{'Arthropoda': [6656]}
>>>

[lijunyuan]

Thanks for your promptly reply, and I have tried as you suggested, but it returned empty like this: (MitoFlex) which python3 ~/anaconda3/envs/MitoFlex/bin/python3 (MitoFlex) python3 Python 3.6.10 |Anaconda, Inc.| (default, May 8 2020, 02:54:21) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

from ete3 import NCBITaxa ncbi = NCBITaxa() result = ncbi.get_name_translator(["Arthropoda"]) print(result) {}

[Prunoideae]

This is weird, so the NCBI taxonomy database is not set up yet, what's the output of the ncbi.py when you execute it?

[lijunyuan]

For unknown reasons I can run the program this time after I run the ncbi.py again, thanks for your help! By the way, is there any method for me to check whether the assemblied sequence is a circular or incompletely linear?

[Prunoideae]

You can check the Circos.png in output folder, if the sequence is circular, it will be shown as a complete ring, otherwise a gap will be drawn between the end and the start, or multiple sequences with gaps will be drawn.