cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Error in build_universe download of BiGG data #105

Closed Noonanav closed 3 years ago

Noonanav commented 3 years ago

I am attempting to build a Cyanobacterial universe. The build_universe --draft command produces the error below. build_universe --curated --cyanobacteria also produces an error.

(CarveMe) Averys-MacBook-Pro:testing_dir averynoonan$ build_universe --draft
Downloading universal data from BiGG...
100%

Downloading model-specific data from BiGG...
100%

Traceback (most recent call last):
  File "/Users/averynoonan/anaconda3/envs/CarveMe/bin/build_universe", line 8, in <module>
    sys.exit(main())
  File "/Users/averynoonan/anaconda3/envs/CarveMe/lib/python3.7/site-packages/carveme/cli/build_universe.py", line 207, in main
    outputfile=args.output)
  File "/Users/averynoonan/anaconda3/envs/CarveMe/lib/python3.7/site-packages/carveme/cli/build_universe.py", line 34, in maincall
    gprs = create_gpr_table(data, outputfile=bigg_gprs)
  File "/Users/averynoonan/anaconda3/envs/CarveMe/lib/python3.7/site-packages/carveme/universe/bigg_download.py", line 293, in create_gpr_table
    for protein in gpr.proteins:
AttributeError: 'NoneType' object has no attribute 'proteins'`
cdanielmachado commented 3 years ago

Hi, you don't need to build the universe yourself, it is already built. Just run carveme with carve -u cyanobacteria.