Error in post_processing

[pmaen]

• pharokka version: 1.7.4
• Python version: 3.10.14
• Operating System: Ubuntu 24.04 LTS

Description

When running Pharokka on a single phage genome I get the following error:

What I Did

pharokka.py -i jg004.fasta -o pharokka_jg004 -t 7 -d /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/
2024-11-28 13:34:39.366 | INFO     | __main__:main:95 - Starting Pharokka v1.7.4
2024-11-28 13:34:39.367 | INFO     | __main__:main:96 - Command executed: Namespace(infile='jg004.fasta', outdir='pharokka_jg004', database='/home/paul/anaconda3/envs/pharokkaENV/bin/../databases/', threads='7', force=False, prefix='Default', locustag='Default', gene_predictor='default', meta=False, split=False, coding_table='11', evalue='1E-05', fast=False, mmseqs2_only=False, meta_hmm=False, dnaapler=False, custom_hmm='', genbank=False, terminase=False, terminase_strand='nothing', terminase_start='nothing', skip_extra_annotations=False, skip_mash=False, minced_args='', mash_distance=0.2, trna_scan_model='general', citation=False)
2024-11-28 13:34:39.367 | INFO     | __main__:main:97 - Repository homepage is https://github.com/gbouras13/pharokka
2024-11-28 13:34:39.367 | INFO     | __main__:main:98 - Written by George Bouras: george.bouras@adelaide.edu.au
2024-11-28 13:34:39.367 | INFO     | __main__:main:100 - Checking database installation in /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/.
2024-11-28 13:34:39.367 | INFO     | __main__:main:103 - All databases have been successfully checked.
2024-11-28 13:34:39.368 | INFO     | __main__:main:119 - Checking dependencies.
2024-11-28 13:34:39.513 | INFO     | input_commands:check_dependencies:390 - Phanotate version found is v1.5.1
2024-11-28 13:34:39.513 | INFO     | input_commands:check_dependencies:399 - Phanotate version is ok.
2024-11-28 13:34:39.516 | INFO     | input_commands:check_dependencies:426 - MMseqs2 version found is v13.45111
2024-11-28 13:34:39.516 | INFO     | input_commands:check_dependencies:435 - MMseqs2 version is ok.
2024-11-28 13:34:39.589 | INFO     | input_commands:check_dependencies:459 - tRNAscan-SE version found is v2.0.12
2024-11-28 13:34:39.589 | INFO     | input_commands:check_dependencies:470 - tRNAscan-SE version is ok.
2024-11-28 13:34:39.634 | INFO     | input_commands:check_dependencies:494 - MinCED version found is v0.4.2
2024-11-28 13:34:39.635 | INFO     | input_commands:check_dependencies:505 - MinCED version is ok.
2024-11-28 13:34:39.636 | INFO     | input_commands:check_dependencies:531 - ARAGORN version found is v1.2.41
2024-11-28 13:34:39.636 | INFO     | input_commands:check_dependencies:542 - ARAGORN version is ok.
2024-11-28 13:34:39.641 | INFO     | input_commands:check_dependencies:559 - mash version found is v2.3
2024-11-28 13:34:39.641 | INFO     | input_commands:check_dependencies:566 - mash version is ok.
2024-11-28 13:34:40.369 | INFO     | input_commands:check_dependencies:585 - Dnaapler version found is v1.0.1
2024-11-28 13:34:40.369 | INFO     | input_commands:check_dependencies:592 - Dnaapler version is ok.
2024-11-28 13:34:40.369 | INFO     | input_commands:check_dependencies:604 - Pyrodigal version is v3.6.3
2024-11-28 13:34:40.370 | INFO     | input_commands:check_dependencies:605 - Pyrodigal version is ok.
2024-11-28 13:34:40.370 | INFO     | input_commands:check_dependencies:617 - Pyrodigal_gv version is v0.3.2
2024-11-28 13:34:40.370 | INFO     | input_commands:check_dependencies:618 - Pyrodigal_gv version is ok.
2024-11-28 13:34:40.375 | INFO     | input_commands:validate_fasta:237 - Checking input jg004.fasta.
2024-11-28 13:34:40.375 | INFO     | input_commands:validate_fasta:239 - Input jg004.fasta is in FASTA format.
2024-11-28 13:34:40.375 | INFO     | input_commands:validate_fasta:244 - Checking input jg004.fasta for duplicate FASTA headers.
2024-11-28 13:34:40.376 | INFO     | input_commands:validate_fasta:246 - All headers in jg004.fasta are unique.
2024-11-28 13:34:40.376 | INFO     | input_commands:validate_gene_predictor:275 - Phanotate will be used for gene prediction.
2024-11-28 13:34:40.376 | INFO     | __main__:main:280 - Running Phanotate.
2024-11-28 13:34:40.377 | INFO     | external_tools:run:50 - Started running phanotate.py -f fasta -o pharokka_jg004/phanotate_out_tmp.fasta jg004.fasta ...
2024-11-28 13:35:03.459 | INFO     | external_tools:run:52 - Done running phanotate.py -f fasta -o pharokka_jg004/phanotate_out_tmp.fasta jg004.fasta
2024-11-28 13:35:03.459 | INFO     | external_tools:run:50 - Started running phanotate.py -f tabular -o pharokka_jg004/phanotate_out.txt jg004.fasta ...
2024-11-28 13:35:25.007 | INFO     | external_tools:run:52 - Done running phanotate.py -f tabular -o pharokka_jg004/phanotate_out.txt jg004.fasta
2024-11-28 13:35:25.061 | INFO     | __main__:main:309 - Starting tRNA-scanSE.
2024-11-28 13:35:25.062 | INFO     | external_tools:run:50 - Started running tRNAscan-SE --thread 7 -G -Q -j pharokka_jg004/trnascan_out.gff jg004.fasta ...
2024-11-28 13:35:27.101 | INFO     | external_tools:run:52 - Done running tRNAscan-SE --thread 7 -G -Q -j pharokka_jg004/trnascan_out.gff jg004.fasta
2024-11-28 13:35:27.102 | INFO     | processes:run_minced:832 - Running MinCED.
2024-11-28 13:35:27.102 | INFO     | external_tools:run:50 - Started running minced jg004.fasta pharokka_jg004/pharokka_minced_spacers.txt pharokka_jg004/pharokka_minced.gff ...
2024-11-28 13:35:27.207 | INFO     | external_tools:run:52 - Done running minced jg004.fasta pharokka_jg004/pharokka_minced_spacers.txt pharokka_jg004/pharokka_minced.gff
2024-11-28 13:35:27.208 | INFO     | processes:run_aragorn:864 - Running Aragorn.
2024-11-28 13:35:27.208 | INFO     | external_tools:run:50 - Started running aragorn -l -gcbact -w -m -o pharokka_jg004/pharokka_aragorn.txt jg004.fasta ...
2024-11-28 13:35:27.231 | INFO     | external_tools:run:52 - Done running aragorn -l -gcbact -w -m -o pharokka_jg004/pharokka_aragorn.txt jg004.fasta
2024-11-28 13:35:27.232 | INFO     | __main__:main:317 - Starting MMseqs2.
2024-11-28 13:35:27.232 | INFO     | processes:run_mmseqs:685 - Running MMseqs2 on PHROG Database.
2024-11-28 13:35:27.232 | INFO     | external_tools:run:50 - Started running mmseqs createdb pharokka_jg004/phanotate_aas_tmp.fasta pharokka_jg004/target_dir/target_seqs ...
2024-11-28 13:35:27.957 | INFO     | external_tools:run:52 - Done running mmseqs createdb pharokka_jg004/phanotate_aas_tmp.fasta pharokka_jg004/target_dir/target_seqs
2024-11-28 13:35:27.957 | INFO     | external_tools:run:50 - Started running mmseqs search -e 1E-05 /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/phrogs_profile_db pharokka_jg004/target_dir/target_seqs pharokka_jg004/mmseqs/results_mmseqs pharokka_jg004/tmp_dir/ -s 8.5 --threads 7 ...
2024-11-28 13:41:13.938 | INFO     | external_tools:run:52 - Done running mmseqs search -e 1E-05 /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/phrogs_profile_db pharokka_jg004/target_dir/target_seqs pharokka_jg004/mmseqs/results_mmseqs pharokka_jg004/tmp_dir/ -s 8.5 --threads 7
2024-11-28 13:41:13.938 | INFO     | external_tools:run:50 - Started running mmseqs createtsv /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/phrogs_profile_db pharokka_jg004/target_dir/target_seqs pharokka_jg004/mmseqs/results_mmseqs pharokka_jg004/mmseqs_results.tsv --full-header --threads 7 ...
2024-11-28 13:41:13.986 | INFO     | external_tools:run:52 - Done running mmseqs createtsv /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/phrogs_profile_db pharokka_jg004/target_dir/target_seqs pharokka_jg004/mmseqs/results_mmseqs pharokka_jg004/mmseqs_results.tsv --full-header --threads 7
2024-11-28 13:41:13.986 | INFO     | processes:run_mmseqs:685 - Running MMseqs2 on CARD Database.
2024-11-28 13:41:13.987 | INFO     | external_tools:run:50 - Started running mmseqs createdb pharokka_jg004/phanotate_aas_tmp.fasta pharokka_jg004/CARD_target_dir/target_seqs ...
2024-11-28 13:41:13.998 | INFO     | external_tools:run:52 - Done running mmseqs createdb pharokka_jg004/phanotate_aas_tmp.fasta pharokka_jg004/CARD_target_dir/target_seqs
2024-11-28 13:41:13.998 | INFO     | external_tools:run:50 - Started running mmseqs search --min-seq-id 0.8 -c 0.4 /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/CARD pharokka_jg004/CARD_target_dir/target_seqs pharokka_jg004/CARD/results_mmseqs pharokka_jg004/CARD_dir/ -s 8.5 --threads 7 ...
2024-11-28 13:42:01.258 | INFO     | external_tools:run:52 - Done running mmseqs search --min-seq-id 0.8 -c 0.4 /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/CARD pharokka_jg004/CARD_target_dir/target_seqs pharokka_jg004/CARD/results_mmseqs pharokka_jg004/CARD_dir/ -s 8.5 --threads 7
2024-11-28 13:42:01.259 | INFO     | external_tools:run:50 - Started running mmseqs createtsv /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/CARD pharokka_jg004/CARD_target_dir/target_seqs pharokka_jg004/CARD/results_mmseqs pharokka_jg004/CARD_results.tsv --full-header --threads 7 ...
2024-11-28 13:42:01.273 | INFO     | external_tools:run:52 - Done running mmseqs createtsv /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/CARD pharokka_jg004/CARD_target_dir/target_seqs pharokka_jg004/CARD/results_mmseqs pharokka_jg004/CARD_results.tsv --full-header --threads 7
2024-11-28 13:42:01.274 | INFO     | processes:run_mmseqs:685 - Running MMseqs2 on VFDB Database.
2024-11-28 13:42:01.274 | INFO     | external_tools:run:50 - Started running mmseqs createdb pharokka_jg004/phanotate_aas_tmp.fasta pharokka_jg004/VFDB_target_dir/target_seqs ...
2024-11-28 13:42:01.286 | INFO     | external_tools:run:52 - Done running mmseqs createdb pharokka_jg004/phanotate_aas_tmp.fasta pharokka_jg004/VFDB_target_dir/target_seqs
2024-11-28 13:42:01.287 | INFO     | external_tools:run:50 - Started running mmseqs search --min-seq-id 0.8 -c 0.4 /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/vfdb pharokka_jg004/VFDB_target_dir/target_seqs pharokka_jg004/VFDB/results_mmseqs pharokka_jg004/VFDB_dir/ -s 8.5 --threads 7 ...
2024-11-28 13:43:21.887 | INFO     | external_tools:run:52 - Done running mmseqs search --min-seq-id 0.8 -c 0.4 /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/vfdb pharokka_jg004/VFDB_target_dir/target_seqs pharokka_jg004/VFDB/results_mmseqs pharokka_jg004/VFDB_dir/ -s 8.5 --threads 7
2024-11-28 13:43:21.888 | INFO     | external_tools:run:50 - Started running mmseqs createtsv /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/vfdb pharokka_jg004/VFDB_target_dir/target_seqs pharokka_jg004/VFDB/results_mmseqs pharokka_jg004/vfdb_results.tsv --full-header --threads 7 ...
2024-11-28 13:43:21.916 | INFO     | external_tools:run:52 - Done running mmseqs createtsv /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/vfdb pharokka_jg004/VFDB_target_dir/target_seqs pharokka_jg004/VFDB/results_mmseqs pharokka_jg004/vfdb_results.tsv --full-header --threads 7
2024-11-28 13:43:21.917 | INFO     | __main__:main:348 - Running PyHMMER on PHROGs.
2024-11-28 13:43:36.228 | INFO     | __main__:main:364 - Post Processing Output.
2024-11-28 13:43:36.252 | INFO     | post_processing:create_mmseqs_tophits:2146 - Processing MMseqs2 outputs.
2024-11-28 13:43:36.252 | INFO     | post_processing:create_mmseqs_tophits:2147 - Processing PHROGs output.
2024-11-28 13:43:36.570 | INFO     | post_processing:process_vfdb_results:2351 - Processing VFDB output.
2024-11-28 13:43:36.578 | INFO     | post_processing:process_vfdb_results:2437 - 0 VFDB virulence factors identified.
2024-11-28 13:43:36.579 | INFO     | post_processing:process_card_results:2455 - Processing CARD output.
2024-11-28 13:43:36.587 | INFO     | post_processing:process_card_results:2578 - 0 CARD AMR genes identified.
2024-11-28 13:43:36.664 | INFO     | __main__:main:435 - Converting gff to genbank.
Traceback (most recent call last):
  File "/home/paul/anaconda3/envs/pharokkaENV/bin/pharokka.py", line 489, in <module>
    main()
  File "/home/paul/anaconda3/envs/pharokkaENV/bin/pharokka.py", line 437, in main
    convert_gff_to_gbk(input_fasta, out_dir, out_dir, prefix, pharok.prot_seq_df)
  File "/home/paul/anaconda3/envs/pharokkaENV/bin/processes.py", line 809, in convert_gff_to_gbk
    if feature.strand == 1:
AttributeError: 'SeqFeature' object has no attribute 'strand'

From what I see it has to do with the version of biopython. According to the conda install pharokka should be compatible with the newest biopython, however in version 1.8.2 there is no strand attribute anymore.

[pmaen]

#372 fixes this and removes some redundant/non-functional code