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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
128 stars 33 forks source link

Problem running phylophlan #83

Open itiago opened 2 years ago

itiago commented 2 years ago

Hi I installed from conda, read the last issue and followed your comment on cloning the last version from github, which I did with conda phylophlan environment on, at the end had this message: Using /home/deepbio/miniconda2/envs/phylophlan/lib/python3.10/site-packages Finished processing dependencies for PhyloPhlAn==3.0.2 but still have the PhyloPhlAn version 3.0.60 (27 November 2020) Installed don't know why.

And when I try to run it I get this message: (phylophlan) deepbio@deepbio-virtual-machine:~/Documents/phylophlan3_DATABASES/phylophlan/phylophlan$ phylophlan -i /home/deepbio/Documents/Metagenomes/Spain/All/BIN_REFINEMENT/metawrap_50_10_bins -d /home/deepbio/Documents/phylophlan3_DATABASES --diversity medium -f phylophlan_write_default_configs.sh --nproc 4 [e] "/home/deepbio/miniconda2/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan_configs/" folder does not exists Traceback (most recent call last): File "/home/deepbio/miniconda2/envs/phylophlan/bin/phylophlan", line 33, in sys.exit(load_entry_point('PhyloPhlAn==3.0.2', 'console_scripts', 'phylophlan')()) File "/home/deepbio/miniconda2/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan.py", line 3194, in phylophlan_main project_name = check_args(args, sys.argv, verbose=args.verbose) File "/home/deepbio/miniconda2/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan.py", line 493, in check_args elif os.path.isfile(os.path.join(args.configs_folder, args.config_file)): File "/home/deepbio/miniconda2/envs/phylophlan/lib/python3.10/posixpath.py", line 76, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

Thanks for any help

fasnicar commented 2 years ago

Hi, it seems maybe you're not running the very last version you pulled from the repo, is that the case? My best guess would be that your phylophlan command is the old package installed through conda, while if you want to run the latest version pulled from Github you should execute the phylophlan.py script from the local folder.