2008-09-29 09:45:19,768 - Set mitab file: global.mitab
2008-09-29 09:45:19,768 - Set PORC file: porc_gene.dat
2008-09-29 09:45:19,768 - ==================== Pre-process  ====================
2008-09-29 09:45:19,773 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 09:45:24,716 - 466 different taxids in the source interactions (mitab file)
2008-09-29 09:45:24,716 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 09:45:24,716 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 09:45:24,716 - 177085 source interactions
2008-09-29 09:45:24,716 - 4659 proteins do not have Uniprot id
2008-09-29 09:45:24,716 - 4410 interactions do not have both Uniprot ids
2008-09-29 09:45:24,716 - 1397 interactions are not physical type
2008-09-29 09:45:24,716 - 4497 interactions are self interactions
2008-09-29 09:45:24,716 - 6955 interactions are between 2 different species
2008-09-29 09:45:24,716 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 09:45:24,717 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/10090/proteome_report.txt
2008-09-29 09:45:24,722 - 809 proteome ids
2008-09-29 09:45:24,723 - 804 taxids
2008-09-29 09:45:24,723 - Parse PORC data (format = one gene by line)...
2008-09-29 09:45:33,352 -    > 249846 clusters are described in the PORC data
2008-09-29 09:45:33,352 - Used Memory: 805 M - Free Memory: 416 M - Total Memory: 1221 M - Max Memory: 2666 M
2008-09-29 09:45:35,274 -    > 1805565 proteins are found in the PORC data
2008-09-29 09:45:35,275 - The predictions will be made for taxid 10090
2008-09-29 09:45:35,275 - Interactions will be predicted for NCBI taxid 10090
2008-09-29 09:45:35,275 - This NCBI taxid corresponds to 59 proteome id in Integr8 data
2008-09-29 09:45:35,275 - Used Memory: 1013 M - Free Memory: 208 M - Total Memory: 1221 M - Max Memory: 2666 M
2008-09-29 09:45:35,275 - Extract interactions with at least one taxid in [10090]
2008-09-29 09:45:44,222 -    > 5852 interactions are present in the source file and will be written.
2008-09-29 09:45:44,222 - Write 5852 interactions in the mitab file KnownInteractions.mitab
2008-09-29 09:45:44,348 - Used Memory: 1207 M - Free Memory: 610 M - Total Memory: 1817 M - Max Memory: 2666 M
2008-09-29 09:45:44,348 - ==================== Up-cast      ====================
2008-09-29 09:45:44,348 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 09:45:56,403 - 177085 source interactions
2008-09-29 09:45:56,403 - 49709 interactions miss at least one protein in the porcs
2008-09-29 09:45:56,403 - 113786 have been abstracted
2008-09-29 09:45:56,403 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 09:45:56,403 - Used Memory: 1811 M - Free Memory: 639 M - Total Memory: 2450 M - Max Memory: 2666 M
2008-09-29 09:45:56,403 - ==================== Down-cast    ====================
2008-09-29 09:45:56,404 - Create file downCast.history.txt
2008-09-29 09:45:56,404 - Create file srcInteractionsUsed.txt
2008-09-29 09:45:56,479 - 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 09:45:58,797 - A inter-species interaction has been used here as a source interactionBinaryInteractionImpl{interactorA=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='P68431'}], alternativeIdentifiers=[], aliases=[Alias{type='uniprotkb', name='HIST1H3A'}, Alias{type='uniprotkb', name='H3FA'}, Alias{type='uniprotkb', name='HIST1H3B'}, Alias{type='uniprotkb', name='H3FL'}, Alias{type='uniprotkb', name='HIST1H3C'}, Alias{type='uniprotkb', name='H3FC'}, Alias{type='uniprotkb', name='HIST1H3E'}, Alias{type='uniprotkb', name='H3FD'}, Alias{type='uniprotkb', name='HIST1H3F'}, Alias{type='uniprotkb', name='H3FI'}, Alias{type='uniprotkb', name='HIST1H3G'}, Alias{type='uniprotkb', name='H3FH'}, Alias{type='uniprotkb', name='HIST1H3H'}, Alias{type='uniprotkb', name='H3FK'}, Alias{type='uniprotkb', name='HIST1H3I'}, Alias{type='uniprotkb', name='H3FF'}, Alias{type='uniprotkb', name='HIST1H3J'}, Alias{type='uniprotkb', name='H3FJ'}, Alias{type='uniprotkb', name='HIST1H3D'}, Alias{type='uniprotkb', name='H3FB'}], organism=Organism{identifiers=[CrossReference{database='taxid', identifier='9606', text='Homo sapiens'}]}}, interactorB=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='Q9BVI0'}], alternativeIdentifiers=[], aliases=[], organism=Organism{identifiers=[]}}, detectionMethods=[CrossReference{database='MI', identifier='0107', text='surface plasmon resonance'}], interactionTypes=[CrossReference{database='MI', identifier='0407', text='direct interaction'}], publications=[CrossReference{database='pubmed', identifier='16415788'}], confidenceValues=[], sourceDatabases=[CrossReference{database='MI', identifier='0471', text='mint'}], interactionAcs=[CrossReference{database='mint', identifier='MINT-2829329'}], authors=[]}
2008-09-29 09:45:59,281 -    > 32161 binary interactions predicted
2008-09-29 09:45:59,282 - 2268 binary interactions have not been predicted because they are source interactions
2008-09-29 09:45:59,282 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 09:45:59,282 - Used Memory: 1925 M - Free Memory: 525 M - Total Memory: 2450 M - Max Memory: 2666 M
2008-09-29 09:45:59,282 - ==================== Post-process ====================
2008-09-29 09:45:59,282 - Write 32161 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 09:45:59,632 - Used Memory: 1840 M - Free Memory: 610 M - Total Memory: 2450 M - Max Memory: 2666 M
2008-09-29 09:46:04,764 - 32161 interactions read from mitab file
2008-09-29 09:46:04,980 - 5852 interactions read from mitab file
2008-09-29 09:46:04,980 - Write 38013 interactions in the mitab file AllInteractions.mitab
2008-09-29 09:46:05,229 - Used Memory: 1939 M - Free Memory: 727 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 09:46:05,229 - time elapsed: 0.7576 min
2008-09-29 09:46:05,229 - ======================================================
2008-09-29 09:46:05,229 - 
2008-09-29 09:46:05,229 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 09:46:05,229 -