{"action":"closed","issue":{"url":"https://api.github.com/repos/SysBioChalmers/RAVEN/issues/132","repository_url":"https://api.github.com/repos/SysBioChalmers/RAVEN","labels_url":"https://api.github.com/repos/SysBioChalmers/RAVEN/issues/132/labels{/name}","comments_url":"https://api.github.com/repos/SysBioChalmers/RAVEN/issues/132/comments","events_url":"https://api.github.com/repos/SysBioChalmers/RAVEN/issues/132/events","html_url":"https://github.com/SysBioChalmers/RAVEN/issues/132","id":345168498,"node_id":"MDU6SXNzdWUzNDUxNjg0OTg=","number":132,"title":"cnaProduce and gapReport fail on combineMetaCycKEGGModels ","user":{"login":"phemmy2k2","id":9355525,"node_id":"MDQ6VXNlcjkzNTU1MjU=","avatar_url":"https://avatars2.githubusercontent.com/u/9355525?v=4","gravatar_id":"","url":"https://api.github.com/users/phemmy2k2","html_url":"https://github.com/phemmy2k2","followers_url":"https://api.github.com/users/phemmy2k2/followers","following_url":"https://api.github.com/users/phemmy2k2/following{/other_user}","gists_url":"https://api.github.com/users/phemmy2k2/gists{/gist_id}","starred_url":"https://api.github.com/users/phemmy2k2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/phemmy2k2/subscriptions","organizations_url":"https://api.github.com/users/phemmy2k2/orgs","repos_url":"https://api.github.com/users/phemmy2k2/repos","events_url":"https://api.github.com/users/phemmy2k2/events{/privacy}","received_events_url":"https://api.github.com/users/phemmy2k2/received_events","type":"User","site_admin":false},"labels":[{"id":352988751,"node_id":"MDU6TGFiZWwzNTI5ODg3NTE=","url":"https://api.github.com/repos/SysBioChalmers/RAVEN/labels/help%20wanted","name":"help wanted","color":"128A0C","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-07-27T10:07:29Z","updated_at":"2018-08-21T18:47:55Z","closed_at":"2018-08-21T18:47:55Z","author_association":"NONE","body":"I combined metacyc and kegg models, then I discovered I can not apply the canProduce and gapReport function on the combined model. The following is the output error.\r\n\r\n#### Reproducing this issue:\r\n```matlab\r\n>> CombinedDraftModel=combineMetaCycKEGGModels(model_MetaCyc, balancedModel);\r\n\r\n>> I=canProduce(CombinedDraftModel);\r\nMatrix index is out of range for deletion.\r\n\r\nError in removeReactions (line 68)\r\n            reducedModel.grRules(indexesToDelete,:)=[];\r\n\r\nError in simplifyModel (line 148)\r\n            reducedModel=removeReactions(reducedModel,rxnsToDelete);\r\n\r\nError in haveFlux (line 45)\r\nsmallModel=simplifyModel(model,false,false,true,true);\r\n\r\nError in canProduce (line 25)\r\nproduced=haveFlux(model,10^-5,rxns);\r\n \r\n>> [noFluxRxns, noFluxRxnsRelaxed, subGraphs, notProducedMets, minToConnect,...\r\n    neededForProductionMat]=gapReport(CombinedDraftModel);\r\nGap analysis for COMBINED - Combined model from MetaCyc and KEGG draft models\r\n\r\nMatrix index is out of range for deletion.\r\n\r\nError in removeReactions (line 68)\r\n            reducedModel.grRules(indexesToDelete,:)=[];\r\n\r\nError in simplifyModel (line 148)\r\n            reducedModel=removeReactions(reducedModel,rxnsToDelete);\r\n\r\nError in haveFlux (line 45)\r\nsmallModel=simplifyModel(model,false,false,true,true);\r\n\r\nError in gapReport (line 66)\r\nI=haveFlux(model);\r\n```\r\n#### System information\r\n* Please report:\r\n1. RAVEN version 2.0 \r\n2. Windows Operating system \r\n**I hereby confirm that I have:**\r\n- [X] Followed the [guidelines](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) to install RAVEN.\r\n- [X] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?utf8=%E2%9C%93&q=is%3Aissue)\r\n- [X] If suitable, needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/RAVEN) about the issue\r\n\r\n"}}
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