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gbouras13 / pharokka

fast phage annotation program
MIT License
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Error with Phanotate (return code 1) #350

Closed Norina28 closed 2 months ago

Norina28 commented 3 months ago

Description

I am trying to run pharokka (w/ & w/o fast option) on SA genomes but I always get this same error: .... 2024-06-27 15:15:05.043 | INFO | main:main:280 - Running Phanotate. 2024-06-27 15:15:05.046 | INFO | external_tools:run:50 - Started running phanotate.py -f fasta -o /home/ecella/ATB/SAMD00009489_pharrokka2/phanotate_out_tmp.fasta ./SAMD00009489.fa ... 2024-06-27 15:22:58.067 | ERROR | external_tools:run_tool:94 - Error calling phanotate.py -f fasta -o /home/SAMD00009489_pharrokka2/phanotate_out_tmp.fasta ./SAMD00009489.fa (return code 1) 2024-06-27 15:22:58.069 | ERROR | processes:run_phanotate:291 - Error with Phanotate

What I Did

pharokka.py -i ./SAMD00009489.fa -d ~/pharokka_v1.4.0_databases -o ~/ATB/SAMD00009489_pharrokka2 -t 16 --fast

Thank you so much

kakadaisy commented 2 months ago

I have encountered the same problem. Have you resolved it，please？

gbouras13 commented 2 months ago

Hi @kakadaisy @Norina28 ,

Are you running Pharokka on entire SA (Staph aureus?) bacterial genomes? Phanotate is not designed for large bacterial sized chromosomes.

If you are indeed running Pharokka on phage genome isolates, then this is certainly a big problem :) If so, would you be able to upload an example input FASTA so I can reproduce the errors?

George

Norina28 commented 2 months ago

Hi @gbouras13 thank you for your reply. Yes, I was running Pharokka on the complete Staph aureus genomes. Okay, then this explains a lot. ◡̈ I'll find a tool to extract the phage genomes and then I'll run it. Thank you!

Ele

gbouras13 commented 2 months ago

No problem - I'd use something like PhiSpy or Genomad :).

Closing this issue now.

George

kakadaisy commented 2 months ago

Hello, @gbouras13 thank you for your reply. I ran it after removing the genome of the host bacteria. This is the genome I used, and I uploaded my phage genome. Could you please help me check what the problem is? Thank you [Uploading P-20N5.zip…]()