2008-09-29 10:16:35,716 - Set mitab file: global.mitab
2008-09-29 10:16:35,716 - Set PORC file: porc_gene.dat
2008-09-29 10:16:35,717 - ==================== Pre-process  ====================
2008-09-29 10:16:35,721 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 10:16:40,734 - 466 different taxids in the source interactions (mitab file)
2008-09-29 10:16:40,735 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 10:16:40,735 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 10:16:40,735 - 177085 source interactions
2008-09-29 10:16:40,735 - 4659 proteins do not have Uniprot id
2008-09-29 10:16:40,735 - 4410 interactions do not have both Uniprot ids
2008-09-29 10:16:40,735 - 1397 interactions are not physical type
2008-09-29 10:16:40,735 - 4497 interactions are self interactions
2008-09-29 10:16:40,735 - 6955 interactions are between 2 different species
2008-09-29 10:16:40,735 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 10:16:40,735 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/10116/proteome_report.txt
2008-09-29 10:16:40,741 - 809 proteome ids
2008-09-29 10:16:40,741 - 804 taxids
2008-09-29 10:16:40,742 - Parse PORC data (format = one gene by line)...
2008-09-29 10:16:49,509 -    > 249846 clusters are described in the PORC data
2008-09-29 10:16:49,509 - Used Memory: 908 M - Free Memory: 656 M - Total Memory: 1564 M - Max Memory: 2666 M
2008-09-29 10:16:51,458 -    > 1805565 proteins are found in the PORC data
2008-09-29 10:16:51,458 - The predictions will be made for taxid 10116
2008-09-29 10:16:51,458 - Interactions will be predicted for NCBI taxid 10116
2008-09-29 10:16:51,458 - This NCBI taxid corresponds to 122 proteome id in Integr8 data
2008-09-29 10:16:51,458 - Used Memory: 1113 M - Free Memory: 451 M - Total Memory: 1564 M - Max Memory: 2666 M
2008-09-29 10:16:51,458 - Extract interactions with at least one taxid in [10116]
2008-09-29 10:17:00,380 -    > 2397 interactions are present in the source file and will be written.
2008-09-29 10:17:00,380 - Write 2397 interactions in the mitab file KnownInteractions.mitab
2008-09-29 10:17:00,446 - Used Memory: 1439 M - Free Memory: 734 M - Total Memory: 2173 M - Max Memory: 2666 M
2008-09-29 10:17:00,446 - ==================== Up-cast      ====================
2008-09-29 10:17:00,447 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 10:17:11,845 - 177085 source interactions
2008-09-29 10:17:11,845 - 49709 interactions miss at least one protein in the porcs
2008-09-29 10:17:11,845 - 113786 have been abstracted
2008-09-29 10:17:11,845 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 10:17:11,846 - Used Memory: 1681 M - Free Memory: 985 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 10:17:11,846 - ==================== Down-cast    ====================
2008-09-29 10:17:11,846 - Create file downCast.history.txt
2008-09-29 10:17:11,846 - Create file srcInteractionsUsed.txt
2008-09-29 10:17:11,917 - A inter-species interaction has been used here as a source interactionBinaryInteractionImpl{interactorA=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='Q6IBW4'}], alternativeIdentifiers=[], aliases=[Alias{type='uniprotkb', name='CAPH2'}, Alias{type='uniprotkb', name='NCAPH2'}], organism=Organism{identifiers=[CrossReference{database='taxid', identifier='9606', text='Homo sapiens'}]}}, interactorB=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='P42695'}], alternativeIdentifiers=[], aliases=[], organism=Organism{identifiers=[]}}, detectionMethods=[CrossReference{database='MI', identifier='0006', text='anti bait coimmunoprecipitation'}], interactionTypes=[CrossReference{database='MI', identifier='0218', text='physical interaction'}], publications=[CrossReference{database='pubmed', identifier='17268547'}], confidenceValues=[], sourceDatabases=[CrossReference{database='MI', identifier='0471', text='mint'}], interactionAcs=[CrossReference{database='mint', identifier='MINT-4329904'}], authors=[]}
2008-09-29 10:17:14,275 -    > 15864 binary interactions predicted
2008-09-29 10:17:14,276 - 1244 binary interactions have not been predicted because they are source interactions
2008-09-29 10:17:14,276 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 10:17:14,276 - Used Memory: 1696 M - Free Memory: 970 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 10:17:14,276 - ==================== Post-process ====================
2008-09-29 10:17:14,276 - Write 15864 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 10:17:14,422 - Used Memory: 1803 M - Free Memory: 863 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 10:17:14,720 - 15864 interactions read from mitab file
2008-09-29 10:17:14,768 - 2397 interactions read from mitab file
2008-09-29 10:17:14,769 - Write 18261 interactions in the mitab file AllInteractions.mitab
2008-09-29 10:17:14,892 - Used Memory: 1878 M - Free Memory: 788 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 10:17:14,892 - time elapsed: 0.65285 min
2008-09-29 10:17:14,892 - ======================================================
2008-09-29 10:17:14,893 - 
2008-09-29 10:17:14,893 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 10:17:14,893 -