Missing pre-defined models

[cpavloud]

Hello!

I am running fargene using contigs as an input.
It was running ok but when I tried to run all the hmm models, I got the following error messages

The HMM file erm_type_a could not be found.
The HMM file erm_type_f could not be found.
The HMM file mph could not be found.
The HMM file aminoglycoside_model_a could not be found.
The HMM file aminoglycoside_model_b could not be found.
The HMM file aminoglycoside_model_c could not be found.
The HMM file aminoglycoside_model_d could not be found.
The HMM file aminoglycoside_model_e could not be found.
The HMM file aminoglycoside_model_f could not be found.
The HMM file aminoglycoside_model_g could not be found.
The HMM file aminoglycoside_model_h could not be found.

Either provide a valid path to a HMM or choose one of the following pre-defined models:
b1
class_b_1_2
class_b_3
class_a
class_c
class_d_1
class_d_2
qnr
tet_efflux
tet_rpg
tet_enzyme

Everything seemed to run smoothly for all the other models.

[bioforkgithub]

This is problem that i encountered while using the conda package. In the anaconda files i checked and found that all the models are not present there. Install it using the git clone procedure described under the installation section. Keep in mind to install it under the conda environment having python version 2.7 or the environment where fargene has been working.

[bioforkgithub]

Hi, Pardon me for not mentioning other details. The cloned repository has a folder for all the hmm models. go-to that folder and check whether all the hmm model files are there. This will serve as the option for --hmm-model option in the fargene program. Mention the complete path here with the model name. Next, in same git cloned folder you will see the main program for fargene. Open the program fargene_analysis.py and find the lines from 207-229. You will find the models and scores, they are in the order name,path,long_score,meta_score. You can check this order in the program Hmm model.py.use this option of long_score and meta_score. Now run fargene will all these options manually. PS: read all the option under fargene --help and then select them Hope this helps you. Kind regards bioforkgithub Sent from Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: Mery Touceda-Suárez ***@***.***> Sent: Thursday, August 10, 2023 5:27:16 PM To: fannyhb/fargene ***@***.***> Cc: bioforkgithub ***@***.***>; Mention ***@***.***> Subject: Re: [fannyhb/fargene] Missing pre-defined models (Issue #16) I have installed it using the git clone procedure, and still get the same error as @cpavloud<https://github.com/cpavloud>. Did the fix proposed by @bioforkgithub<https://github.com/bioforkgithub> work for anyone else? — Reply to this email directly, view it on GitHub<#16 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3KYOFRZGJKZ4QUFSERGWADXUT4VJANCNFSM6AAAAAARNSE6YA>. You are receiving this because you were mentioned.Message ID: ***@***.***>