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Matteopaluh / KEMET

KEGG Module Evaluation Tool
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"ktest" file error - due to file naming convention #9

Closed ggezwp123 closed 2 years ago

ggezwp123 commented 2 years ago

I met an error. $./kemet.py genomes/x23.fna -a eggnog --skip_hmm

Traceback (most recent call last): File "/root/KEMET/./kemet.py", line 2440, in if ktest in sorted(os.listdir()): NameError: name 'ktest' is not defined

What is the problem?

Matteopaluh commented 2 years ago

Hi,

I believe the error could be due to not adding a properly named eggnog annotation file in the KEGG_ANNOTATION folder.

In the above case, it should be called x23.emapper.annotations (i.e. the eggnog output extension, with the name of your genome/MAG of choice before it).

Let me know if maybe renaming files solves it!

ggezwp123 commented 2 years ago

$./kemet.py genomes/x23.fna -a eggnog --skip_hmm

Traceback (most recent call last): File "/root/KEMET/./kemet.py", line 11, in from reframed import load_cbmodel, save_cbmodel ModuleNotFoundError: No module named 'reframed'

I added a eggnog annotation file named x23.emapper.annotations in the KEGG_ANNOTATION folder. But I still met a new error

Matteopaluh commented 2 years ago

Great, so I believe the first one should be considered as solved.

from reframed import load_cbmodel, save_cbmodel
ModuleNotFoundError: No module named 'reframed'

^ this states that you're not using a conda environment with Reframed installed, as stated in the installation info: You could solve this by properly following the indications, i.e. running pip install reframed on your terminal, with the kemet conda environment active.

ggezwp123 commented 2 years ago

I forgot that I have reboot my virture machine. HAHAHA! My problems have solved. THANK YOU! I believe this program is a powerful and convenient tool!

Matteopaluh commented 2 years ago

Good! Glad all was sorted out easily.

And thanks a lot for the kind words, hope more people will find it useful as well!