Prodigal not working Pharokka v1.4.1

[raw-lab]

• pharokka version: 1.4.1
• Python version: 3.10
• Operating System: Linux

Description

2023-12-20 15:18:04.879 | INFO | input_commands:check_dependencies:529 - Pyrodigal version is v3.0.1 2023-12-20 15:18:04.879 | INFO | input_commands:check_dependencies:530 - Pyrodigal version is ok. 2023-12-20 15:18:04.883 | INFO | input_commands:validate_fasta:205 - Checking Input FASTA. 2023-12-20 15:18:04.886 | INFO | input_commands:validate_fasta:207 - FASTA checked. 2023-12-20 15:18:04.886 | INFO | input_commands:validate_gene_predictor:216 - Prodigal will be used for gene prediction. 2023-12-20 15:18:04.888 | INFO | main:main:277 - Implementing Prodigal using Pyrodigal. Traceback (most recent call last): File "/home/docwhite/miniconda3/envs/pharokka/bin/pharokka.py", line 447, in main() File "/home/docwhite/miniconda3/envs/pharokka/bin/pharokka.py", line 278, in main run_pyrodigal(input_fasta, out_dir, args.meta, args.coding_table) File "/home/docwhite/miniconda3/envs/pharokka/bin/processes.py", line 276, in run_pyrodigal orf_finder = pyrodigal.OrfFinder(meta=prodigal_metamode) AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'

What I Did

pharokka.py -i LP_CU-CL_31_18.fna -o test -d ~/miniconda3/envs/pharokka/databases/ -t 8 -g prodigal
pharokka.py -i LP_CU-CL_31_18.fna -o test -d ~/miniconda3/envs/pharokka/databases/ -t 8 -g prodigal --fast

It can't find pyrodigal.

[gbouras13]

Hi @raw-lab ,

This is because pyrodigal v3 is being used with the old Pharokka v1.4.1 version. The most recent version is 1.5.1.

Pyrodigal updated its API in v3 to GeneFinder not OrfFinder, breaking this.

Pharokka v1.5 implements a fix for this.

Therefore, I'd recommend updating pharokka to v1.5.1.

If you really want to use v1.4.1, please downgrade pyrodigal to v2.

George

[gbouras13]

Closing this issue as fix is to upgrade Pharokka