ARM64 installation issue - M3 chip MacBook Pro

Question

ARM64 installation issue - M3 chip MacBook Pro

nicolasginet opened this issue 9 months ago · 5 comments

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

Answer 1 · 2024-04-22T16:35:22.000Z

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

Answer 2 · 2024-04-22T17:16:41.000Z

I think something has gone wrong attaching the mentioned output.

Answer 3 · 2024-04-23T07:29:00.000Z

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 <module> exec(compile(f.read(), __file__, 'exec')) File "/Users/nico/Documents/myCore/Bioinformatics/pharokka/bin/pharokka.py", line 489, in <module> 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. — Reply to this email directly, view it on GitHub <#834 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHFIR6VGMACFJ32UVMTCOILY6VAY5AVCNFSM6AAAAABGS5SNF2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZQGMYDCOBZGE>. You are receiving this because you authored the thread.

Answer 4 · 2024-04-23T07:52:04.000Z

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

Answer 5 · 2024-04-23T07:55:33.000Z

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