update/ecHumanGEM/v1.12.0/2022 07 03 23 31 31 #99

automator-metatlas · 2022-07-04T04:32:33Z

update ecHumanGEM based on v1.12.0

MATLAB is selecting SOFTWARE OPENGL rendering.

***************************************************************
   GECKO: Adding enzyme constraints to a genome-scale model
***************************************************************

Getting genome-scale model ready...[�Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

  - grRule #MAR04137: ENSG00000091140 and ENSG00000110435 and (ENSG00000131828 or ENSG00000163114) and ENSG00000150768 and ENSG00000168291
  - grRule #MAR07161: (ENSG00000113356 or ENSG00000121851) and (ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823) and (ENSG00000083223 or ENSG00000134744
  or ENSG00000149016) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817 and
  ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and ENSG00000137054
  and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453 and
  ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184
  - grRule #MAR07162: (ENSG00000113356 or ENSG00000121851) and (ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823) and (ENSG00000083223 or ENSG00000134744
  or ENSG00000149016) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817 and
  ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and ENSG00000137054
  and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453 and
  ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184
  - grRule #MAR00080: ((ENSG00000105929 and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883) or (ENSG00000113732 and ENSG00000117410 and
  ENSG00000147614 and ENSG00000185344 and ENSG00000185883) or (ENSG00000105929 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and ENSG00000185883) or (ENSG00000033627
  and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883) or (ENSG00000033627 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and
  ENSG00000185883) or (ENSG00000110719 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and ENSG00000185883) or (ENSG00000113732 and ENSG00000117410 and ENSG00000159720
  and ENSG00000185344 and ENSG00000185883) or (ENSG00000110719 and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883)) and ((ENSG00000047249 and
  ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000136888 and ENSG00000147416 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554
  and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000136888 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and
  ENSG00000114573 and ENSG00000128524 and ENSG00000136888 and ENSG00000143882 and ENSG00000147416 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573
  and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000147416 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and
  ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524
  and ENSG00000147416 and ENSG00000155097 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and
  ENSG00000143882 and ENSG00000147416 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100
  and ENSG00000147416 and ENSG00000155097 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and
  ENSG00000131100 and ENSG00000151418 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000143882 and ENSG00000147416
  and ENSG00000151418 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and
  ENSG00000143882 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000143882 and ENSG00000213760
  and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000155097 and
  ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000147416 and ENSG00000151418 and ENSG00000155097 and ENSG00000250565)
  or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000147416 and ENSG00000151418 and ENSG00000155097) or
  (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000155097 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249
  and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000151418 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and
  ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000147416 and ENSG00000151418) or (ENSG00000047249 and ENSG00000100554
  and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000147416 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and
  ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000151418) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573
  and ENSG00000116039 and ENSG00000128524 and ENSG00000143882 and ENSG00000151418 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and
  ENSG00000116039 and ENSG00000128524 and ENSG00000136888 and ENSG00000143882 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039
  and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000143882) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and
  ENSG00000131100 and ENSG00000136888 and ENSG00000143882 and ENSG00000147416))

 This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

  - (G1 or G2) and (G3 or G4)

 For these cases modify the grRules manually, writing all the possible combinations e.g.

  - (G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

 For other cases modify the correspondent grRules avoiding:

  1) Overall container brackets, e.g.
        "(G1 and G2)" should be "G1 and G2"

  2) Single unit enzymes enclosed into brackets, e.g.
        "(G1)" should be "G1"

  3) The use of uppercases for logical operators, e.g.
        "G1 OR G2" should be "G1 or G2"

  4) Unbalanced brackets, e.g.
        "((G1 and G2) or G3" should be "(G1 and G2) or G3"
]� 
[�> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In preprocessModel (line 27)
In enhanceGEM (line 51)]� 
 Done!

==================
Generating ecModel:
==================
Retrieving EC numbers...WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	MAR04137
	MAR07161
	MAR07162
	MAR00080

................................................................................................................................... Done!
Matching kcats...................................................................................................................................... Done!
Adding enzymes to reactions...WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	arm_MAR04137

WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	MAR04137

....WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	arm_MAR07161

WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	MAR07161

WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	arm_MAR07162

WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	MAR07162

.............................................................................WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	arm_MAR00080

WARNING: Potentially problematic ") AND (" in the grRules for reaction(s): 
	MAR00080

................................................................................................................ Done!
Improving model with curated data...[�Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

  - grRule #arm_MAR04137: ENSG00000091140 and ENSG00000110435 and (ENSG00000131828 or ENSG00000163114) and ENSG00000150768 and ENSG00000168291
  - grRule #arm_MAR07161: (ENSG00000113356 or ENSG00000121851) and (ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823) and (ENSG00000083223 or
  ENSG00000134744 or ENSG00000149016) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817
  and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and
  ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453
  and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184
  - grRule #arm_MAR07162: (ENSG00000113356 or ENSG00000121851) and (ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823) and (ENSG00000083223 or
  ENSG00000134744 or ENSG00000149016) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817
  and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and
  ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453
  and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184
  - grRule #arm_MAR00080: ((ENSG00000105929 and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883) or (ENSG00000113732 and ENSG00000117410 and
  ENSG00000147614 and ENSG00000185344 and ENSG00000185883) or (ENSG00000105929 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and ENSG00000185883) or (ENSG00000033627
  and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883) or (ENSG00000033627 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and
  ENSG00000185883) or (ENSG00000110719 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and ENSG00000185883) or (ENSG00000113732 and ENSG00000117410 and ENSG00000159720
  and ENSG00000185344 and ENSG00000185883) or (ENSG00000110719 and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883)) and ((ENSG00000047249 and
  ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000136888 and ENSG00000147416 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554
  and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000136888 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and
  ENSG00000114573 and ENSG00000128524 and ENSG00000136888 and ENSG00000143882 and ENSG00000147416 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573
  and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000147416 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and
  ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524
  and ENSG00000147416 and ENSG00000155097 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and
  ENSG00000143882 and ENSG00000147416 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100
  and ENSG00000147416 and ENSG00000155097 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and
  ENSG00000131100 and ENSG00000151418 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000143882 and ENSG00000147416
  and ENSG00000151418 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and
  ENSG00000143882 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000143882 and ENSG00000213760
  and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000155097 and
  ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000147416 and ENSG00000151418 and ENSG00000155097 and ENSG00000250565)
  or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000147416 and ENSG00000151418 and ENSG00000155097) or
  (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000155097 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249
  and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000151418 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and
  ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000147416 and ENSG00000151418) or (ENSG00000047249 and ENSG00000100554
  and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000147416 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and
  ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000151418) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573
  and ENSG00000116039 and ENSG00000128524 and ENSG00000143882 and ENSG00000151418 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and
  ENSG00000116039 and ENSG00000128524 and ENSG00000136888 and ENSG00000143882 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039
  and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000143882) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and
  ENSG00000131100 and ENSG00000136888 and ENSG00000143882 and ENSG00000147416))

 This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

  - (G1 or G2) and (G3 or G4)

 For these cases modify the grRules manually, writing all the possible combinations e.g.

  - (G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

 For other cases modify the correspondent grRules avoiding:

  1) Overall container brackets, e.g.
        "(G1 and G2)" should be "G1 and G2"

  2) Single unit enzymes enclosed into brackets, e.g.
        "(G1)" should be "G1"

  3) The use of uppercases for logical operators, e.g.
        "G1 OR G2" should be "G1 or G2"

  4) Unbalanced brackets, e.g.
        "((G1 and G2) or G3" should be "(G1 and G2) or G3"
]� 
[�> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In manualModifications (line 4)
In enhanceGEM (line 65)]� 
 Done!
Removing repeated rxn: MAR02404 & MAR10410_REV
Removing repeated rxn: MAR10410 & MAR02404_REV
[�Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

  - grRule #arm_MAR04137: ENSG00000091140 and ENSG00000110435 and (ENSG00000131828 or ENSG00000163114) and ENSG00000150768 and ENSG00000168291
  - grRule #arm_MAR07161: (ENSG00000113356 or ENSG00000121851) and (ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823) and (ENSG00000083223 or
  ENSG00000134744 or ENSG00000149016) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817
  and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and
  ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453
  and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184
  - grRule #arm_MAR07162: (ENSG00000113356 or ENSG00000121851) and (ENSG00000090060 or ENSG00000115421 or ENSG00000164329 or ENSG00000218823) and (ENSG00000083223 or
  ENSG00000134744 or ENSG00000149016) and ENSG00000005075 and ENSG00000013503 and ENSG00000047315 and ENSG00000058600 and ENSG00000066379 and ENSG00000068654 and ENSG00000099817
  and ENSG00000099821 and ENSG00000100142 and ENSG00000100413 and ENSG00000102978 and ENSG00000105258 and ENSG00000107951 and ENSG00000125630 and ENSG00000132664 and
  ENSG00000137054 and ENSG00000144231 and ENSG00000147669 and ENSG00000148606 and ENSG00000161980 and ENSG00000163882 and ENSG00000168002 and ENSG00000168495 and ENSG00000171453
  and ENSG00000177700 and ENSG00000181222 and ENSG00000186141 and ENSG00000186184
  - grRule #arm_MAR00080: ((ENSG00000105929 and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883) or (ENSG00000113732 and ENSG00000117410 and
  ENSG00000147614 and ENSG00000185344 and ENSG00000185883) or (ENSG00000105929 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and ENSG00000185883) or (ENSG00000033627
  and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883) or (ENSG00000033627 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and
  ENSG00000185883) or (ENSG00000110719 and ENSG00000113732 and ENSG00000117410 and ENSG00000159720 and ENSG00000185883) or (ENSG00000113732 and ENSG00000117410 and ENSG00000159720
  and ENSG00000185344 and ENSG00000185883) or (ENSG00000110719 and ENSG00000113732 and ENSG00000117410 and ENSG00000147614 and ENSG00000185883)) and ((ENSG00000047249 and
  ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000136888 and ENSG00000147416 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554
  and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000136888 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and
  ENSG00000114573 and ENSG00000128524 and ENSG00000136888 and ENSG00000143882 and ENSG00000147416 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573
  and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000147416 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and
  ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524
  and ENSG00000147416 and ENSG00000155097 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and
  ENSG00000143882 and ENSG00000147416 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100
  and ENSG00000147416 and ENSG00000155097 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and
  ENSG00000131100 and ENSG00000151418 and ENSG00000155097) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000143882 and ENSG00000147416
  and ENSG00000151418 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and
  ENSG00000143882 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000143882 and ENSG00000213760
  and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000155097 and
  ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000147416 and ENSG00000151418 and ENSG00000155097 and ENSG00000250565)
  or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000147416 and ENSG00000151418 and ENSG00000155097) or
  (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000155097 and ENSG00000213760 and ENSG00000250565) or (ENSG00000047249
  and ENSG00000100554 and ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000151418 and ENSG00000155097 and ENSG00000250565) or (ENSG00000047249 and
  ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000147416 and ENSG00000151418) or (ENSG00000047249 and ENSG00000100554
  and ENSG00000114573 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000147416 and ENSG00000213760) or (ENSG00000047249 and ENSG00000100554 and
  ENSG00000114573 and ENSG00000116039 and ENSG00000128524 and ENSG00000131100 and ENSG00000143882 and ENSG00000151418) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573
  and ENSG00000116039 and ENSG00000128524 and ENSG00000143882 and ENSG00000151418 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and
  ENSG00000116039 and ENSG00000128524 and ENSG00000136888 and ENSG00000143882 and ENSG00000250565) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000116039
  and ENSG00000128524 and ENSG00000131100 and ENSG00000136888 and ENSG00000143882) or (ENSG00000047249 and ENSG00000100554 and ENSG00000114573 and ENSG00000128524 and
  ENSG00000131100 and ENSG00000136888 and ENSG00000143882 and ENSG00000147416))

 This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

  - (G1 or G2) and (G3 or G4)

 For these cases modify the grRules manually, writing all the possible combinations e.g.

  - (G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

 For other cases modify the correspondent grRules avoiding:

  1) Overall container brackets, e.g.
        "(G1 and G2)" should be "G1 and G2"

  2) Single unit enzymes enclosed into brackets, e.g.
        "(G1)" should be "G1"

  3) The use of uppercases for logical operators, e.g.
        "G1 OR G2" should be "G1 or G2"

  4) Unbalanced brackets, e.g.
        "((G1 and G2) or G3" should be "(G1 and G2) or G3"
]� 
[�> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In manualModifications (line 61)
In enhanceGEM (line 65)]� 

==============================================================
Generating ecModel with shared pool assumption (ecModel_batch):
==============================================================
prot_abundance file is empty or not available. A default value of f=0.5 is set instead
Constrained ecModel is feasible
WARNING: Reaction HMR_9034_REV is not present in the reaction list

Matching data to enzymes in model... Done!
Total protein amount measured = 0 g/gDW
Total enzymes measured = 0 enzymes
Enzymes in model with 0 g/gDW = 0 enzymes
Total protein amount not measured = 0.50572 g/gDW
Total enzymes not measured = 2665 enzymes
Total protein in model = 0.50572 g/gDW
The ECmodel is not overconstrained.
***************************************************************
Fitting sigma factor....................... Done!
[�Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information, click <a href="matlab:opengl('problems')">here</a>.]� 
Saving simulation results files...
File successfully saved.
Sigma factor (fitted for growth on glucose): 0.17

=============
Saving models:
=============
Saving ecHumanGEM1.12.0:
Converting RAVEN structure to COBRA..
Each model.subSystems{x} is a character array, and this format is retained.
Document written
Each model.subSystems{x} is a character array, and this format is retained.
Saving ecHumanGEM_batch1.12.0:
Converting RAVEN structure to COBRA..
Each model.subSystems{x} is a character array, and this format is retained.
Document written
Each model.subSystems{x} is a character array, and this format is retained.

based on SysBioChalmers/Human-GEM#341

mihai-sysbio and others added 16 commits June 5, 2022 10:00

chore: rename branch master to main

b85d1de

chore: update gurobi path

6b76de5

fix: correctly check out gecko branch

2f9f525

chore: update model paths

28e20ff

feat: use model branch

2c94dfe

feat: download models without main branch

778140e

chore: load sbml instead of mat

98b9d1a

fix: revert to using .mat format

fcb7d6a

fix: update reference to Human-GEM compartment

9df2141

based on SysBioChalmers/Human-GEM#341

refactor: use hub instead of git for cloning

ca7ba0b

refactor: reuse variable for default branch

4d58ff2

Merge branch 'main' into chore/rename-master-to-main

b059617

fix: revert accidental removal of Gurobi version from config

5e0655e

refactor: switch from hub to gh cli

7dbe783

fix: use commit message as PR title

1b1867c

chore: update ecHumanGEM based on v1.12.0

b436c3b

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update/ecHumanGEM/v1.12.0/2022 07 03 23 31 31 #99

update/ecHumanGEM/v1.12.0/2022 07 03 23 31 31 #99

automator-metatlas commented Jul 4, 2022

update/ecHumanGEM/v1.12.0/2022 07 03 23 31 31 #99

Are you sure you want to change the base?

update/ecHumanGEM/v1.12.0/2022 07 03 23 31 31 #99

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automator-metatlas commented Jul 4, 2022