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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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UnboundLocalError: cannot access local variable 'uniprotkb2uniref90' where it is not associated with a value #111

Open chennyhui opened 1 year ago

chennyhui commented 1 year ago

Hello,

I am following the S. aureus tutorial and got the following error while setting up the database. Also noted a high number of core proteins that failed to load. 

Re-trying to download 1436 core proteins that just failed, please wait as it might take some time
[e] unable convert UniProtKB ID to UniRef90 ID
Traceback (most recent call last):
  File "/Users/yihui/mambaforge/envs/phylophlEnv/bin/phylophlan_setup_database", line 33, in <module>
    sys.exit(load_entry_point('PhyloPhlAn==3.0.3', 'console_scripts', 'phylophlan_setup_database')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yihui/mambaforge/envs/phylophlEnv/lib/python3.11/site-packages/phylophlan/phylophlan_setup_database.py", line 407, in phylophlan_setup_database
    get_core_proteins(taxa2core_file_latest, args.get_core_proteins, args.output, args.output_extension, verbose=args.verbose)
  File "/Users/yihui/mambaforge/envs/phylophlEnv/lib/python3.11/site-packages/phylophlan/phylophlan_setup_database.py", line 333, in get_core_proteins
    for uniref90_id in (x[1].split('_')[-1] for x in uniprotkb2uniref90[1:]):
                                                     ^^^^^^^^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'uniprotkb2uniref90' where it is not associated with a value

Log file attached: saureus_phylophlan_setup_database.log

If it matters, this is on an M2 Mac with phylophlan 3.0.67 (24 August 2022).

Any help is greatly appreciated!