2008-01-28 14:54:15,295 - Set mitab file: global.mitab
2008-01-28 14:54:15,296 - Set PORC file: porc_gene.dat
2008-01-28 14:54:15,296 - ==================== Pre-process  ====================
2008-01-28 14:54:15,301 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 1777 M
2008-01-28 14:54:18,909 - several Uniprot ac: P50591 and P50591.1
2008-01-28 14:54:19,915 - several Uniprot ac: P31658 and P31658.3
2008-01-28 14:54:19,915 - several Uniprot ac: P31658 and P31658.3
2008-01-28 14:54:20,617 - 478 different taxids in the source interactions (mitab file)
2008-01-28 14:54:20,618 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-01-28 14:54:20,618 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-01-28 14:54:20,618 - 185024 source interactions
2008-01-28 14:54:20,618 - 5860 proteins do not have Uniprot id
2008-01-28 14:54:20,618 - 5460 interactions do not have both Uniprot ids
2008-01-28 14:54:20,618 - 1648 interactions are not physical type
2008-01-28 14:54:20,618 - 4481 interactions are self interactions
2008-01-28 14:54:20,618 - 6352 interactions are between 2 different species
2008-01-28 14:54:20,618 -    > 167380 interactions can be used among the 185024 of the mitab file ../../DB/global.mitab
2008-01-28 14:54:20,618 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/10090/proteome_report.txt
2008-01-28 14:54:20,624 - 666 proteome ids
2008-01-28 14:54:20,624 - 663 taxids
2008-01-28 14:54:20,625 - Parse PORC data (format = one gene by line)...
2008-01-28 14:54:27,116 -    > 215733 clusters are described in the PORC data
2008-01-28 14:54:27,116 - Used Memory: 935 M - Free Memory: 153 M - Total Memory: 1088 M - Max Memory: 1777 M
2008-01-28 14:54:30,968 -    > 1524313 proteins are found in the PORC data
2008-01-28 14:54:30,968 - The predictions will be made for taxid 10090
2008-01-28 14:54:30,968 - Interactions will be predicted for NCBI taxid 10090
2008-01-28 14:54:30,968 - This NCBI taxid corresponds to 59 proteome id in Integr8 data
2008-01-28 14:54:30,968 - Used Memory: 1019 M - Free Memory: 325 M - Total Memory: 1344 M - Max Memory: 1777 M
2008-01-28 14:54:30,968 - Extract interactions with at least one taxid in [10090]
2008-01-28 14:54:37,358 -    > 5531 interactions are present in the source file and will be written in KnownInteractions.mitab file
2008-01-28 14:54:37,358 - Write 5531 interactions in the mitab file KnownInteractions.mitab
2008-01-28 14:54:37,465 - Used Memory: 1139 M - Free Memory: 625 M - Total Memory: 1764 M - Max Memory: 1777 M
2008-01-28 14:54:37,465 - ==================== Up-cast      ====================
2008-01-28 14:54:37,465 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-01-28 14:54:42,006 - several Uniprot ac: P50591 and P50591.1
2008-01-28 14:55:06,348 - 185024 source interactions
2008-01-28 14:55:06,348 - 78864 interactions miss at least one protein in the porcs
2008-01-28 14:55:06,348 - 93693 have been abstracted
2008-01-28 14:55:06,348 -    > 91886 distinct interactions between 2 clusters are constructed
2008-01-28 14:55:06,348 - Used Memory: 1540 M - Free Memory: 237 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:55:06,348 - ==================== Down-cast    ====================
2008-01-28 14:55:06,348 - Create file downCast.history.txt
2008-01-28 14:55:06,349 - Create file srcInteractionsUsed.txt
2008-01-28 14:55:06,441 - 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=[]}
2008-01-28 14:55:11,251 - A inter-species interaction has been used here as a source interactionBinaryInteractionImpl{interactorA=Interactor{identifiers=[CrossReference{database='uniprotkb', identifier='P62805'}], alternativeIdentifiers=[], aliases=[Alias{type='uniprotkb', name='HIST1H4A'}, Alias{type='uniprotkb', name='H4/A'}, Alias{type='uniprotkb', name='H4FA'}, Alias{type='uniprotkb', name='HIST1H4B'}, Alias{type='uniprotkb', name='H4/I'}, Alias{type='uniprotkb', name='H4FI'}, Alias{type='uniprotkb', name='HIST1H4C'}, Alias{type='uniprotkb', name='H4/G'}, Alias{type='uniprotkb', name='H4FG'}, Alias{type='uniprotkb', name='HIST1H4D'}, Alias{type='uniprotkb', name='H4/B'}, Alias{type='uniprotkb', name='H4FB'}, Alias{type='uniprotkb', name='HIST1H4E'}, Alias{type='uniprotkb', name='H4/J'}, Alias{type='uniprotkb', name='H4FJ'}, Alias{type='uniprotkb', name='HIST1H4F'}, Alias{type='uniprotkb', name='H4/C'}, Alias{type='uniprotkb', name='H4FC'}, Alias{type='uniprotkb', name='HIST1H4H'}, Alias{type='uniprotkb', name='H4/H'}, Alias{type='uniprotkb', name='H4FH'}, Alias{type='uniprotkb', name='HIST1H4I'}, Alias{type='uniprotkb', name='H4/M'}, Alias{type='uniprotkb', name='H4FM'}, Alias{type='uniprotkb', name='HIST1H4J'}, Alias{type='uniprotkb', name='H4/E'}, Alias{type='uniprotkb', name='H4FE'}, Alias{type='uniprotkb', name='HIST1H4K'}, Alias{type='uniprotkb', name='H4/D'}, Alias{type='uniprotkb', name='H4FD'}, Alias{type='uniprotkb', name='HIST1H4L'}, Alias{type='uniprotkb', name='H4/K'}, Alias{type='uniprotkb', name='H4FK'}, Alias{type='uniprotkb', name='H4/N'}, Alias{type='uniprotkb', name='H4F2'}, Alias{type='uniprotkb', name='H4FN'}, Alias{type='uniprotkb', name='HIST4H4'}, Alias{type='uniprotkb', name='HIST2H4A'}, Alias{type='uniprotkb', name='HIST2H4'}], 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-2829358'}], authors=[]}
2008-01-28 14:55:11,448 -    > 29678 binary interactions predicted
2008-01-28 14:55:11,448 - 1940 binary interactions have not been predicted because they are source interactions
2008-01-28 14:55:11,448 - 0 binary interactions have not been predicted because uniprot id missed
2008-01-28 14:55:11,448 - Used Memory: 1160 M - Free Memory: 617 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:55:11,448 - ==================== Post-process ====================
2008-01-28 14:55:11,448 - Create file InteroPorc.predictedInteractions.mitab
2008-01-28 14:55:11,448 - Write 29678 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-01-28 14:55:11,717 - Used Memory: 1157 M - Free Memory: 620 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:55:11,717 - time elapsed: 0.94026667 min
2008-01-28 14:55:11,717 - ======================================================
2008-01-28 14:55:11,717 - 
2008-01-28 14:55:11,717 - Thanks for using the interoPORC tool. All informations are available on http://biodev.extra.cea.fr/interoporc/
2008-01-28 14:55:11,717 -