Closed lijunyuan closed 1 year ago
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]}
>>>
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) {}
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?
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?
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.
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