Error with Phanotate

[TKsh6]

• pharokka version: 1.7.3
• Python version: 3.10
• Operating System: Linux

Description

I ran the command as below
pharokka.py -i 5_redundant/${line} -o 6_pharokka/${sample} -t 1 -f -d /beegfs/home/syl/database_db/pharokka
but I got this error

2024-11-09 15:53:56.912 | INFO     | external_tools:run:50 - Started running phanotate.py -f fasta -o 6_pharokka/42/phano
2024-11-09 15:53:58.339 | ERROR    | external_tools:run_tool:94 - Error calling phanotate.py -f fasta -o 6_pharokka/42/ph
2024-11-09 15:53:58.340 | ERROR    | processes:run_phanotate:291 - Error with Phanotate

I have read about the problem list in #350 ,but the fasta I put in is the assembly genome of isolated phage with several contigs. I have 47 phage genomes, 43 of them goes well with the command, but the rest 4 meet this problem.
So how can I do to deal with it?

[gbouras13]

Hi @TKsh6 - can you provide some more detail about the 4 genomes? or provide the phanotate error logs (in the log directory?) George

[pmaen]

I encountered (what I presume to be) the same error when running
pharokka.py -i GPD_sequences.fa -o pharokka -t 7 -d /home/paul/anaconda3/envs/pharokkaENV/bin/../databases/

2024-11-27 17:46:48.232 | INFO     | __main__:main:280 - Running Phanotate.
2024-11-27 17:46:48.232 | INFO     | external_tools:run:50 - Started running phanotate.py -f fasta -o pharokka/phanotate_out_tmp.fasta GPD_sequences.fa ...
2024-11-28 02:17:10.495 | ERROR    | external_tools:run_tool:94 - Error calling phanotate.py -f fasta -o pharokka/phanotate_out_tmp.fasta GPD_sequences.fa (return code -9)
2024-11-28 02:17:10.730 | ERROR    | processes:run_phanotate:296 - Error with Phanotate

In contrast to #350 the return code is -9. The fasta file is a large multifasta of many phage genomes, but there are no bacterial genomes. Is there a cutoff for how large a phage genome can be so Pharokka can handle it?