Hi everyone,
After several attempts, I managed to install MetaPhlAn4 on my Macbook M1 ARM64 running OSX 12.6. However, I encountered issues when trying to use Miniconda3 for arm64 following the steps outlined on the official Wiki page.
Here is the command I used to create an isolated conda environment and install MetaPhlAn:
conda create --name mpa -c conda-forge -c bioconda python=3.7 metaphlan
or
conda create --name mpa -c conda-forge -c bioconda python=3.10 metaphlan
Unfortunately, I received the following error:
Could not load conda plugin `conda-libmamba-solver`:
dlopen(/Users/david/miniforge3/lib/python3.10/site-packages/libmambapy/bindings.cpython-310-darwin.so, 0x0002): Library not loaded: '@rpath/libarchive.13.dylib'
Referenced from: '/Users/david/miniforge3/lib/libmamba.2.0.0.dylib'
Reason: tried: '/Users/david/miniforge3/lib/libarchive.13.dylib' (no such file), '/Users/david/miniforge3/lib/python3.10/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/david/miniforge3/lib/python3.10/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/david/miniforge3/bin/../lib/libarchive.13.dylib' (no such file), '/Users/david/miniforge3/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file)
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package python conflicts for:
metaphlan -> biopython -> python[version='>=2.7,<3|>=3.10,<3.11.0a0|>=3.10,<3.11.0a0|>=3.12,<3.13.0a0|>=3.12,<3.13.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.9,<3.10.0a0|>=3.11,<3.12.0a0|>=3.11,<3.12.0a0|>=3.12.0rc3,<3.13.0a0|>=3.12.0rc3,<3.13.0a0|>=3.7,<4.0|>=3.6,<4.0|>=3.6',build=*_cpython]
python=3.10
metaphlan -> python[version='2.7.*|>=3|>=3.7']The following specifications were found to be incompatible with your system:
- feature:/osx-arm64::__osx==12.6=0
- metaphlan -> matplotlib-base -> __osx[version='>=10.9']
- python=3.10 -> ncurses[version='>=6.4,<7.0a0'] -> __osx[version='>=10.9']
Your installed version is: 12.6
Frustrated with this, I successfully installed MetaPhlAn using the pip approach:
pip install metaphlan
However, when attempting to profile a metagenome using the command:
metaphlan SRR9641941_1.fastq,SRR9641941_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 9 --input_type fastq -o profiled_metagenome.txt
I encountered the error:
No MetaPhlAn BowTie2 database found (--index option)!
Even though the database was seemingly installed successfully:
metaphlan --install
The database is installed
I specified the database location:
metaphlan SRR9641941_1.fastq,SRR9641941_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 9 --input_type fastq -o profiled_metagenome.txt --bowtie2db /Users/david/miniforge3/lib/python3.10/site-packages/metaphlan/metaphlan_databases
But received the error:
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location bowtie2db
Upon checking the database directory, everything seems in order:
ls /Users/david/miniforge3/lib/python3.10/site-packages/metaphlan/metaphlan_databases
Output:
README.txt mpa_vOct22_CHOCOPhlAnSGB_202212.pkl mpa_vOct22_CHOCOPhlAnSGB_202212_VSG.fna
mpa_latest mpa_vOct22_CHOCOPhlAnSGB_202212_SGB.fna mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5
mpa_vOct22_CHOCOPhlAnSGB_202212.fna mpa_vOct22_CHOCOPhlAnSGB_202212_VINFO.csv mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar
I’m seeking assistance on resolving this issue. Any suggestions or guidance would be greatly appreciated.
Thanks in advance!