GFF generating failure when supplying own proteomes

[wwood]

Supply Prokka-annotated faa files gave this error:

$ enrichm annotate --protein_directory proteomes/ --ko_hmm --output ko_hmm_test
[2019-07-02 11:12:26 AM] INFO: Command: /srv/sw/miniconda3/envs/enrichm_0.5.0rc1/bin/enrichm annotate --protein_directory proteomes/ --ko_hmm --output ko_hmm_test                                                
[2019-07-02 11:12:26 AM] INFO: Running the annotate pipeline
[2019-07-02 11:12:26 AM] INFO: Running pipeline: annotate
[2019-07-02 11:12:26 AM] INFO: Setting up for genome annotation
[2019-07-02 11:12:26 AM] INFO: Using provided proteins
[2019-07-02 11:12:26 AM] INFO: Preparing genomes for annotation
[2019-07-02 11:12:28 AM] INFO: Starting annotation:
[2019-07-02 11:12:28 AM] INFO:     - Annotating genomes with ko ids using HMMs
[2019-07-02 11:49:59 AM] INFO:     - Generating ko frequency table
[2019-07-02 11:49:59 AM] INFO:     - Writing results to file: ko_hmm_test/ko_hmm_frequency_table.tsv
[2019-07-02 11:50:00 AM] INFO: Generating .gff files:
...
[2019-07-02 11:50:00 AM] INFO:     - Generating .gff file for wierdbin1.prokka_archaea
Traceback (most recent call last):
  File "/srv/sw/miniconda3/envs/enrichm_0.5.0rc1/bin/enrichm", line 374, in <module>
    r.run_enrichm(args, sys.argv)
  File "/srv/sw/miniconda3/envs/enrichm_0.5.0rc1/lib/python3.6/site-packages/enrichm/run.py", line 359, in run_enrichm                                                                                            
    args.protein_files)
  File "/srv/sw/miniconda3/envs/enrichm_0.5.0rc1/lib/python3.6/site-packages/enrichm/annotate.py", line 893, in annotate_pipeline                                                                                 
    self.generate_gff_files(genomes_list)
  File "/srv/sw/miniconda3/envs/enrichm_0.5.0rc1/lib/python3.6/site-packages/enrichm/annotate.py", line 634, in generate_gff_files                                                                                
    Writer.write_gff(genome, gff_output)
  File "/srv/sw/miniconda3/envs/enrichm_0.5.0rc1/lib/python3.6/site-packages/enrichm/writer.py", line 69, in write_gff                                                                                            
    'prodigal_id=%s' % sequence.prod_id,
AttributeError: 'Sequence' object has no attribute 'prod_id'

I guess it is expecting a prodigal style header maybe?

[geronimp]

Hey,

I can't replicate this error using the master branch. Which is ahead of the conda/pip releases so I think this issue is resolved. I'll release master as 0.5.1, and let me know if that works for you.

Cheers,
J

[geronimp]

Hey @wwood am I okay to close this issue?

[wwood]

Yep, ok

…

________________________________ From: Joel Boyd <notifications@github.com> Sent: Saturday, November 16, 2019 7:10:59 PM To: geronimp/enrichM <enrichM@noreply.github.com> Cc: Ben J Woodcroft <donttrustben@gmail.com>; Mention <mention@noreply.github.com> Subject: Re: [geronimp/enrichM] GFF generating failure when supplying own proteomes (#84) Hey @wwood<https://github.com/wwood> am I okay to close this issue? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#84?email_source=notifications&email_token=AAADX5AUOCHDTKMZMUFB6MDQT62KHA5CNFSM4H6XEFG2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEHNEQA#issuecomment-554619456>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5GN5XVIAESLIIY3D33QT62KHANCNFSM4H6XEFGQ>.