PheArrMe/test/error.log at main · SysSynBio/PheArrMe · GitHub

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Command failed for medium tartr__M_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium tartr__M_medium
Command failed for medium 2hb_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium 2hb_medium
Command failed for medium amdglc_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium amdglc_medium
Command failed for medium methsucc_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium methsucc_medium
Command failed for medium 2mop_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium 2mop_medium
Command failed for medium glypro_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium glypro_medium
Command failed for medium tym_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium tym_medium
Command failed for medium gal14lac_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium gal14lac_medium
Command failed for medium cs_c_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium cs_c_medium
Command failed for medium glycogen_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium glycogen_medium
Command failed for medium mannan_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium mannan_medium
Command failed for medium pectin_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium pectin_medium
Command failed for medium acgala_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium acgala_medium
Command failed for medium abt_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium abt_medium
Command failed for medium rbl__B_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium rbl__B_medium
Command failed for medium stys_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium stys_medium
Command failed for medium xylt_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium xylt_medium
Command failed for medium decacid_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium decacid_medium
Command failed for medium caproic_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium caproic_medium
Command failed for medium citac_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium citac_medium
Command failed for medium citm_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium citm_medium
Command failed for medium ghb_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium ghb_medium
Command failed for medium malon_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium malon_medium
Command failed for medium sebacid_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium sebacid_medium
Command failed for medium 5oxopro_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium 5oxopro_medium
Command failed for medium 23btdl_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium 23btdl_medium
Command failed for medium R_actn_medium:
Traceback (most recent call last):
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/johncasey/miniconda3/envs/BiologMe_new/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium R_actn_medium
Command failed for medium tartr__M_medium:
Traceback (most recent call last):
  File "/Users/casey26/anaconda3/envs/BiologMe/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium tartr__M_medium
Command failed for medium amdglc_medium:
Traceback (most recent call last):
  File "/Users/casey26/anaconda3/envs/BiologMe/bin/carve", line 8, in <module>
    sys.exit(main())
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/cli/carve.py", line 357, in main
    maincall(
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/cli/carve.py", line 240, in maincall
    multiGapFill(model, universe_model, media, media_db, scores=scores, max_uptake=max_uptake, inplace=True)
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 139, in multiGapFill
    gapFill(model, universe, constraints=constraints, min_growth=min_growth,
  File "/Users/casey26/anaconda3/envs/BiologMe/lib/python3.8/site-packages/carveme/reconstruction/gapfilling.py", line 74, in gapFill
    raise RuntimeError('Failed to gapfill model for medium {}'.format(tag))
RuntimeError: Failed to gapfill model for medium amdglc_medium