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gbouras13 / pharokka

fast phage annotation program
MIT License
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mmseqs minor version #356

Open Mewgia opened 3 months ago

Mewgia commented 3 months ago

Description

Dear George, i have an issue with mmseqs: pharokka.py \ -i /home/yana/download/Escherichia_phage_Pu.fasta \ -o /home/yana/download/annotation/Pu --force \ -d /home/yana/download/pharokka/ \ -g prodigal \ -t 8 (with --fast or without, result is the same) 2024-08-20 10:23:50.474 | INFO | input_commands:instantiate_dirs:183 - Removing output directory /home/yana/download/annotation/Pu as -f or --force was specified. 2024-08-20 10:23:50.491 | INFO | main:main:95 - Starting Pharokka v1.7.3 2024-08-20 10:23:50.492 | INFO | main:main:96 - Command executed: Namespace(infile='/home/yana/download/Escherichia_phage_Pu.fasta', outdir='/home/yana/download/annotation/Pu', database='/home/yana/download/pharokka/', threads='8', force=True, prefix='Default', locustag='Default', gene_predictor='prodigal', meta=False, split=False, coding_table='11', evalue='1E-05', fast=True, 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, citation=False) 2024-08-20 10:23:50.492 | INFO | main:main:97 - Repository homepage is https://github.com/gbouras13/pharokka 2024-08-20 10:23:50.493 | INFO | main:main:98 - Written by George Bouras: george.bouras@adelaide.edu.au 2024-08-20 10:23:50.494 | INFO | main:main:100 - Checking database installation in /home/yana/download/pharokka/. 2024-08-20 10:23:50.495 | INFO | main:main:103 - All databases have been successfully checked. 2024-08-20 10:23:50.495 | INFO | main:main:119 - Checking dependencies. 2024-08-20 10:23:50.850 | INFO | input_commands:check_dependencies:383 - Phanotate version found is v1.6.5 2024-08-20 10:23:50.851 | INFO | input_commands:check_dependencies:392 - Phanotate version is ok. Traceback (most recent call last): File "/home/yana/.pyenv/versions/3.9.16/bin/pharokka.py", line 4, in import('pkg_resources').run_script('Pharokka==1.7.3', 'pharokka.py') File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/Pharokka-1.7.3-py3.9.egg/EGG-INFO/scripts/pharokka.py", line 489, in main() File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/Pharokka-1.7.3-py3.9.egg/EGG-INFO/scripts/pharokka.py", line 128, in main ) = check_dependencies(args.skip_mash) File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/Pharokka-1.7.3-py3.9.egg/EGG-INFO/scripts/input_commands.py", line 412, in check_dependencies mmseqs_minor_version = int(mmseqs_version.split(".")[1]) ValueError: invalid literal for int() with base 10: '6f452'

hope for your help, i'm new in phage annotation. Thanks a lot in advance.

gbouras13 commented 3 months ago

Hi @Mewgia

I think you have mmseqs v 15.6f452 installed. Pharokka needs mmseqs2==13.45111 installed.

It looks like you aren't using conda/mamba, so please try installing that version however you have installed mmseqs.

George

Mewgia commented 3 months ago

Yes, it works perfectly. Thanks for such a useful tool.

Mewgia commented 3 months ago

Dear George, one more question. I have three phage sequences and yesterday successfully annotated all of them using -g prodigal. Today I'm trying to annotate them using -g phanotate. Two phages were successfully annotated, but the third meets an error. 2024-08-21 15:28:45.737 | INFO | main:main:348 - Running PyHMMER on PHROGs. Traceback (most recent call last): File "/home/yana/.pyenv/versions/3.9.16/bin/pharokka.py", line 4, in import('pkg_resources').run_script('Pharokka==1.7.3', 'pharokka.py') File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/Pharokka-1.7.3-py3.9.egg/EGG-INFO/scripts/pharokka.py", line 489, in main() File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/Pharokka-1.7.3-py3.9.egg/EGG-INFO/scripts/pharokka.py", line 349, in main best_results_pyhmmer = run_pyhmmer( File "/home/yana/.pyenv/versions/3.9.16/lib/python3.9/site-packages/Pharokka-1.7.3-py3.9.egg/EGG-INFO/scripts/hmm.py", line 34, in run_pyhmmer with pyhmmer.easel.SequenceFile( File "pyhmmer/easel.pyx", line 6289, in pyhmmer.easel.SequenceFile.init File "pyhmmer/easel.pyx", line 6283, in pyhmmer.easel.SequenceFile.init ValueError: Could not determine alphabet of file: '/home/download/annotation/phan_Pu/phanotate_aas_tmp.fasta'

Hope for your help. Thank you.

gbouras13 commented 2 months ago

Hi @Mewgia,

I think it is because a gene is too small (or full or Ns) - so that pyhmmer can't figure out if it is nucleotide or protein.

I'd check 'phanotate_aas_tmp.fasta' - it likely has a gene that is NNNNN or something. It suggests phanotate is probably not a great model for this phage, so I'd use the prodigal gene calls.

George