FileNotFoundError

[chengzhongyi8]

Hi, Thanks for developing this tool. I use it to predict viral classification. However, I meet some problems: my command: genomad annotate ../checkv_contigs.fa genomad /public/zycheng/database/virus.db/genomad_db_v1.3 And the log:

  Executing geNomad annotate (v1.5.2). This will perform gene calling in the input sequences and annotate the predicted proteins with geNomad's  markers. 
[09:58:03] Executing genomad annotate.                                                                                                                    
[09:58:03] Creating the genomad/checkv_contigs_annotate directory.                                                                                        
Traceback (most recent call last):
  File "/public/home/zycheng/anaconda3/envs/genomad/bin/genomad", line 10, in <module>
    sys.exit(cli())
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/rich_click/rich_group.py", line 21, in main
    rv = super().main(*args, standalone_mode=False, **kwargs)
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/cli.py", line 425, in annotate
    genomad.annotate.main(
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/modules/annotate.py", line 167, in main
    database_obj = database.Database(database_path)
  File "/public/home/zycheng/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/database.py", line 10, in __init__
    with open(database_directory / "version.txt") as fin:
FileNotFoundError: [Errno 2] No such file or directory: '/public/zycheng/database/virus.db/genomad_db/version.txt'

I downloaded the database from Zenodo and extract it manually, and there are only four files, without version.txt.

Best, Zhongyi

[apcamargo]

The Zenodo release should have the version.txt file. Which version of the database did you download? I'll check that

[chengzhongyi8]

I download dbv1.3 (https://zenodo.org/record/7793532).

[apcamargo]

I just downloaded it and version.txt is there. Not really sure what happened on your end, but you can just create the version.txt file within the genomad_db_v1.3 directory. Just run this command:

echo "1.3" > genomad_db_v1.3/version.txt

[chengzhongyi8]

Thanks a lot!

[apcamargo]

No problem!