2008-09-29 09:44:08,019 - Set mitab file: global.mitab
2008-09-29 09:44:08,019 - Set PORC file: porc_gene.dat
2008-09-29 09:44:08,019 - ==================== Pre-process  ====================
2008-09-29 09:44:08,024 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 09:44:12,958 - 466 different taxids in the source interactions (mitab file)
2008-09-29 09:44:12,958 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 09:44:12,958 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 09:44:12,958 - 177085 source interactions
2008-09-29 09:44:12,958 - 4659 proteins do not have Uniprot id
2008-09-29 09:44:12,958 - 4410 interactions do not have both Uniprot ids
2008-09-29 09:44:12,958 - 1397 interactions are not physical type
2008-09-29 09:44:12,958 - 4497 interactions are self interactions
2008-09-29 09:44:12,958 - 6955 interactions are between 2 different species
2008-09-29 09:44:12,959 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 09:44:12,959 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/3702/proteome_report.txt
2008-09-29 09:44:12,965 - 809 proteome ids
2008-09-29 09:44:12,965 - 804 taxids
2008-09-29 09:44:12,966 - Parse PORC data (format = one gene by line)...
2008-09-29 09:44:21,606 -    > 249846 clusters are described in the PORC data
2008-09-29 09:44:21,606 - Used Memory: 805 M - Free Memory: 416 M - Total Memory: 1221 M - Max Memory: 2666 M
2008-09-29 09:44:23,528 -    > 1805565 proteins are found in the PORC data
2008-09-29 09:44:23,529 - The predictions will be made for taxid 3702
2008-09-29 09:44:23,529 - Interactions will be predicted for NCBI taxid 3702
2008-09-29 09:44:23,529 - This NCBI taxid corresponds to 3 proteome id in Integr8 data
2008-09-29 09:44:23,529 - Used Memory: 1012 M - Free Memory: 209 M - Total Memory: 1221 M - Max Memory: 2666 M
2008-09-29 09:44:23,529 - Extract interactions with at least one taxid in [3702]
2008-09-29 09:44:32,592 -    > 3610 interactions are present in the source file and will be written.
2008-09-29 09:44:32,593 - Write 3610 interactions in the mitab file KnownInteractions.mitab
2008-09-29 09:44:32,686 - Used Memory: 1083 M - Free Memory: 734 M - Total Memory: 1817 M - Max Memory: 2666 M
2008-09-29 09:44:32,686 - ==================== Up-cast      ====================
2008-09-29 09:44:32,686 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 09:44:44,846 - 177085 source interactions
2008-09-29 09:44:44,846 - 49709 interactions miss at least one protein in the porcs
2008-09-29 09:44:44,846 - 113786 have been abstracted
2008-09-29 09:44:44,846 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 09:44:44,847 - Used Memory: 1619 M - Free Memory: 825 M - Total Memory: 2444 M - Max Memory: 2666 M
2008-09-29 09:44:44,847 - ==================== Down-cast    ====================
2008-09-29 09:44:44,847 - Create file downCast.history.txt
2008-09-29 09:44:44,847 - Create file srcInteractionsUsed.txt
2008-09-29 09:44:47,131 -    > 14722 binary interactions predicted
2008-09-29 09:44:47,132 - 612 binary interactions have not been predicted because they are source interactions
2008-09-29 09:44:47,132 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 09:44:47,132 - Used Memory: 1896 M - Free Memory: 548 M - Total Memory: 2444 M - Max Memory: 2666 M
2008-09-29 09:44:47,132 - ==================== Post-process ====================
2008-09-29 09:44:47,132 - Write 14722 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 09:44:47,388 - Used Memory: 1681 M - Free Memory: 763 M - Total Memory: 2444 M - Max Memory: 2666 M
2008-09-29 09:44:47,611 - 14722 interactions read from mitab file
2008-09-29 09:44:47,690 - 3610 interactions read from mitab file
2008-09-29 09:44:47,690 - Write 18332 interactions in the mitab file AllInteractions.mitab
2008-09-29 09:44:47,915 - Used Memory: 1808 M - Free Memory: 636 M - Total Memory: 2444 M - Max Memory: 2666 M
2008-09-29 09:44:47,915 - time elapsed: 0.66485 min
2008-09-29 09:44:47,915 - ======================================================
2008-09-29 09:44:47,915 - 
2008-09-29 09:44:47,915 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 09:44:47,915 -