prokaryote.hal File not found

mauricebarrett commented 2 years ago

Hi,

I recently install your tool and I am constructing the necessary database.

I am however running into the below error.

Thank you for any help in advance.

2022-02-24 12:00:54,073 [INFO]: Finished 2022-02-24 12:00:54,073 [INFO]: Step 2 2022-02-24 12:00:54,073 [INFO]: Formatting KOfam profiles Traceback (most recent call last): File "/Users/maurice/opt/anaconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in main() File "/Users/maurice/opt/anaconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main single_step, aspera, keep_temp, bin_path) File "/Users/maurice/opt/anaconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 97, in database_duilder kofam.kofam_formatter(ko_profiles_path) File "/Users/maurice/opt/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/kofam_profile_parser.py", line 112, in kofam_formatter with open(ko_profiles_path_extr / 'prokaryote.hal', 'r') as infile: FileNotFoundError: [Errno 2] No such file or directory: '/Users/maurice/databases/MicrobeAnnotator_DB/kofam_data/profiles/prokaryote.hal'

Sam-J-1 commented 2 years ago

Hi, I'm currently having the same issue. Did you manage to solve it?

MAllen91 commented 1 month ago

I am also having the same issue an update or resolution?

SaitouAsuka commented 1 month ago

I am also having the same issue an update or resolution?

It seens like the urls in kofam_profile_parser.py (line 71 and line 81) have been removed. I suggest you download the kofam databases manually and extract them. Here is the link: https://www.genome.jp/ftp/db/kofam/

Sam-J-1 commented 1 month ago

Hi,

I resolved it my running the code in ubuntu as its written for linux.

Many thanks, Sam

From: SaitouAsuka @.> Sent: 21 October 2024 11:15 To: cruizperez/MicrobeAnnotator @.> Cc: Samuel Jones @.>; Comment @.> Subject: Re: [cruizperez/MicrobeAnnotator] prokaryote.hal File not found (Issue #46)

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I am also having the same issue an update or resolution?

It seens like the urls from kofam_profile_parser.py (line 71 and line 81) have been removed. I suggest you download the kofam databases manually and extract them. Here is the link: https://www.genome.jp/ftp/db/kofam/

— Reply to this email directly, view it on GitHubhttps://github.com/cruizperez/MicrobeAnnotator/issues/46#issuecomment-2426239926, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A35C3J5QOH7Z4VELWP4YBYTZ4TH27AVCNFSM6AAAAABQE5X4E6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRWGIZTSOJSGY. You are receiving this because you commented.Message ID: @.***>

Sam-J-1 commented 1 month ago

by*

From: Samuel Jones @.> Sent: 21 October 2024 15:10 To: cruizperez/MicrobeAnnotator @.> Subject: Re: [cruizperez/MicrobeAnnotator] prokaryote.hal File not found (Issue #46)

Hi,

I resolved it my running the code in ubuntu as its written for linux.

Many thanks, Sam

From: SaitouAsuka @.> Sent: 21 October 2024 11:15 To: cruizperez/MicrobeAnnotator @.> Cc: Samuel Jones @.>; Comment @.> Subject: Re: [cruizperez/MicrobeAnnotator] prokaryote.hal File not found (Issue #46)

You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.

I am also having the same issue an update or resolution?

It seens like the urls from kofam_profile_parser.py (line 71 and line 81) have been removed. I suggest you download the kofam databases manually and extract them. Here is the link: https://www.genome.jp/ftp/db/kofam/

— Reply to this email directly, view it on GitHubhttps://github.com/cruizperez/MicrobeAnnotator/issues/46#issuecomment-2426239926, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A35C3J5QOH7Z4VELWP4YBYTZ4TH27AVCNFSM6AAAAABQE5X4E6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRWGIZTSOJSGY. You are receiving this because you commented.Message ID: @.***>

cruizperez / MicrobeAnnotator

prokaryote.hal File not found #46