2008-02-04 12:24:45,794 - Set mitab file: global.mitab
2008-02-04 12:24:45,794 - Set PORC file: porc_gene.dat
2008-02-04 12:24:45,794 - ==================== Pre-process  ====================
2008-02-04 12:24:45,799 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 1777 M
2008-02-04 12:24:49,119 - several Uniprot ac: P50591 and P50591.1
2008-02-04 12:24:49,930 - several Uniprot ac: P31658 and P31658.3
2008-02-04 12:24:49,930 - several Uniprot ac: P31658 and P31658.3
2008-02-04 12:24:50,531 - 478 different taxids in the source interactions (mitab file)
2008-02-04 12:24:50,531 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-02-04 12:24:50,531 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-02-04 12:24:50,531 - 185024 source interactions
2008-02-04 12:24:50,531 - 5860 proteins do not have Uniprot id
2008-02-04 12:24:50,531 - 5460 interactions do not have both Uniprot ids
2008-02-04 12:24:50,531 - 1648 interactions are not physical type
2008-02-04 12:24:50,531 - 4481 interactions are self interactions
2008-02-04 12:24:50,532 - 6352 interactions are between 2 different species
2008-02-04 12:24:50,532 -    > 167380 interactions can be used among the 185024 of the mitab file ../../DB/global.mitab
2008-02-04 12:24:50,532 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/10116/proteome_report.txt
2008-02-04 12:24:50,537 - 666 proteome ids
2008-02-04 12:24:50,537 - 663 taxids
2008-02-04 12:24:50,538 - Parse PORC data (format = one gene by line)...
2008-02-04 12:24:58,250 -    > 215733 clusters are described in the PORC data
2008-02-04 12:24:58,250 - Used Memory: 702 M - Free Memory: 535 M - Total Memory: 1237 M - Max Memory: 1777 M
2008-02-04 12:25:01,280 -    > 1524313 proteins are found in the PORC data
2008-02-04 12:25:01,280 - The predictions will be made for taxid 10116
2008-02-04 12:25:01,280 - Interactions will be predicted for NCBI taxid 10116
2008-02-04 12:25:01,280 - This NCBI taxid corresponds to 122 proteome id in Integr8 data
2008-02-04 12:25:01,280 - Used Memory: 942 M - Free Memory: 363 M - Total Memory: 1305 M - Max Memory: 1777 M
2008-02-04 12:25:01,280 - Extract interactions with at least one taxid in [10116]
2008-02-04 12:25:08,127 -    > 2178 interactions are present in the source file and will be written in KnownInteractions.mitab file
2008-02-04 12:25:08,127 - Write 2178 interactions in the mitab file KnownInteractions.mitab
2008-02-04 12:25:08,204 - Used Memory: 928 M - Free Memory: 910 M - Total Memory: 1838 M - Max Memory: 1838 M
2008-02-04 12:25:08,204 - ==================== Up-cast      ====================
2008-02-04 12:25:08,204 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-02-04 12:25:15,834 - several Uniprot ac: P50591 and P50591.1
2008-02-04 12:25:45,749 - 185024 source interactions
2008-02-04 12:25:45,750 - 78864 interactions miss at least one protein in the porcs
2008-02-04 12:25:45,750 - 93693 have been abstracted
2008-02-04 12:25:45,750 -    > 91886 distinct interactions between 2 clusters are constructed
2008-02-04 12:25:45,750 - Used Memory: 1440 M - Free Memory: 337 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-02-04 12:25:45,750 - ==================== Down-cast    ====================
2008-02-04 12:25:45,750 - Create file downCast.history.txt
2008-02-04 12:25:45,750 - Create file srcInteractionsUsed.txt
2008-02-04 12:25:46,221 - A inter-species interaction has been used here as a source interactionBinaryInteractionImpl{interactorA=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='Q13585'}], alternativeIdentifiers=[], aliases=[Alias{type='uniprotkb', name='GPR50'}], organism=Organism{identifiers=[CrossReference{database='taxid', identifier='9606', text='Homo sapiens'}]}}, interactorB=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='P63096'}], alternativeIdentifiers=[], aliases=[], organism=Organism{identifiers=[]}}, detectionMethods=[CrossReference{database='MI', identifier='0007', text='anti tag coimmunoprecipitation'}], interactionTypes=[CrossReference{database='MI', identifier='0218', text='physical interaction'}], publications=[CrossReference{database='pubmed', identifier='16778767'}], confidenceValues=[], sourceDatabases=[CrossReference{database='MI', identifier='0471', text='mint'}], interactionAcs=[CrossReference{database='mint', identifier='MINT-2836319'}], authors=[]}
2008-02-04 12:25:50,735 -    > 13469 binary interactions predicted
2008-02-04 12:25:50,737 - 1165 binary interactions have not been predicted because they are source interactions
2008-02-04 12:25:50,737 - 0 binary interactions have not been predicted because uniprot id missed
2008-02-04 12:25:50,737 - Used Memory: 1204 M - Free Memory: 573 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-02-04 12:25:50,737 - ==================== Post-process ====================
2008-02-04 12:25:50,737 - Create file InteroPorc.predictedInteractions.mitab
2008-02-04 12:25:50,737 - Write 13469 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-02-04 12:25:50,892 - Used Memory: 1084 M - Free Memory: 481 M - Total Memory: 1565 M - Max Memory: 1777 M
2008-02-04 12:25:50,892 - time elapsed: 1.0848833 min
2008-02-04 12:25:50,892 - ======================================================
2008-02-04 12:25:50,892 - 
2008-02-04 12:25:50,892 - Thanks for using the interoPORC tool. All informations are available on http://biodev.extra.cea.fr/interoporc/
2008-02-04 12:25:50,892 -