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soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
GNU General Public License v3.0
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ARM64 installation issue - M3 chip MacBook Pro #834

Open nicolasginet opened 2 months ago

nicolasginet commented 2 months ago

Context

I am using PHARROKA (available on Github) to annotate bacteriophage genomes. MMseq2 is a required dependency. It was working perfectly on my MacBook Pro purchased in 2011. I recently switched to a new one (MacBook M3-pro) and it is not working anymore (see the above PHARROKA output involving MMseqs). I am very far from being a developer and I am only a self-taught bioinformatician. I am thus seeking help !

I used Brew to install MMseqs, my OS is Mac OS X Sonoma 14.4.1.

Thanks !

Nico

milot-mirdita commented 2 months ago

Is there an error message or anything else? MMseqs2 works fine on my Apple Silicon MacBook

milot-mirdita commented 2 months ago

I think something has gone wrong attaching the mentioned output.

nicolasginet commented 2 months ago

Hello !

Thank you for your reply. I just ran PHARROKA and got the following message. Hope it will help !

Nico

/Users/Nico/miniforge3/envs/HieVi/bin/pharokka.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import('pkg_resources').require('Pharokka==1.7.1') 2024-04-23 09:26:28.672 | INFO | input_commands:instantiate_dirs:183 - Removing output directory Output/ROSA-like as -f or --force was specified. 2024-04-23 09:26:28.676 | INFO | main:main:95 - Starting Pharokka v1.7.1 2024-04-23 09:26:28.676 | INFO | main:main:96 - Command executed: Namespace(infile='Input/ROSA-like/rosa-like.fasta', outdir='Output/ROSA-like', database='Databases', threads='1', force=True, prefix='Default', locustag='ROSA-like', 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=True, terminase_strand='pos', terminase_start='1', skip_extra_annotations=False, skip_mash=False, minced_args='', mash_distance=0.2, citation=False) 2024-04-23 09:26:28.676 | INFO | main:main:97 - Repository homepage is https://github.com/gbouras13/pharokka 2024-04-23 09:26:28.676 | INFO | main:main:98 - Written by George Bouras: @.*** 2024-04-23 09:26:28.676 | INFO | main:main:100 - Checking database installation in Databases. 2024-04-23 09:26:28.677 | INFO | main:main:103 - All databases have been successfully checked. 2024-04-23 09:26:28.677 | INFO | main:main:119 - Checking dependencies. 2024-04-23 09:26:28.777 | INFO | input_commands:check_dependencies:379 - Phanotate version found is v1.6.5 2024-04-23 09:26:28.778 | INFO | input_commands:check_dependencies:388 - Phanotate version is ok. Traceback (most recent call last): File "/Users/Nico/miniforge3/envs/HieVi/bin/pharokka.py", line 7, in exec(compile(f.read(), file, 'exec')) File "/Users/nico/Documents/myCore/Bioinformatics/pharokka/bin/pharokka.py", line 489, in main() File "/Users/nico/Documents/myCore/Bioinformatics/pharokka/bin/pharokka.py", line 128, in main ) = check_dependencies(args.skip_mash) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/nico/Documents/myCore/Bioinformatics/pharokka/bin/input_commands.py", line 407, in check_dependencies mmseqs_major_version = int(mmseqs_version.split(".")[0]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: invalid literal for int() with base 10: '15-6f452'

Le 22 avr. 2024 à 19:17, Milot Mirdita @.***> a écrit :

I think something has gone wrong attaching the mentioned output.

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milot-mirdita commented 2 months ago

I let @gbouras13 know, our version string is a bit inconsistent between platforms. Should be fixed soon in pharokka.

gbouras13 commented 2 months ago

Hi @nicolasginet,

I'm the Pharokka developer - thanks for spotting this. I'll put in a fix soon.

In the meantime @nicolasginet if you just comment out the MMSeqs2 related lines by putting a '#' at the front in /Users/nico/Documents/myCore/Bioinformatics/pharokka/bin/input_commands.py (lines 393-419)

starting

https://github.com/gbouras13/pharokka/blob/947c45685169af20a1aba9f78f682516f33c0611/bin/input_commands.py#L393

then Pharokka should hopefully work for you.

Also feel free to make an issue in Pharokka if the issue persists or you run into a different bug.

George