2008-09-29 09:29:46,007 - Set mitab file: global.mitab
2008-09-29 09:29:46,007 - Set PORC file: porc_gene.dat
2008-09-29 09:29:46,007 - ==================== Pre-process  ====================
2008-09-29 09:29:46,012 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 09:29:51,061 - 466 different taxids in the source interactions (mitab file)
2008-09-29 09:29:51,061 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 09:29:51,061 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 09:29:51,061 - 177085 source interactions
2008-09-29 09:29:51,061 - 4659 proteins do not have Uniprot id
2008-09-29 09:29:51,061 - 4410 interactions do not have both Uniprot ids
2008-09-29 09:29:51,061 - 1397 interactions are not physical type
2008-09-29 09:29:51,061 - 4497 interactions are self interactions
2008-09-29 09:29:51,061 - 6955 interactions are between 2 different species
2008-09-29 09:29:51,061 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 09:29:51,061 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/7227/proteome_report.txt
2008-09-29 09:29:51,067 - 809 proteome ids
2008-09-29 09:29:51,067 - 804 taxids
2008-09-29 09:29:51,068 - Parse PORC data (format = one gene by line)...
2008-09-29 09:29:59,868 -    > 249846 clusters are described in the PORC data
2008-09-29 09:29:59,868 - Used Memory: 908 M - Free Memory: 657 M - Total Memory: 1565 M - Max Memory: 2666 M
2008-09-29 09:30:01,819 -    > 1805565 proteins are found in the PORC data
2008-09-29 09:30:01,819 - The predictions will be made for taxid 7227
2008-09-29 09:30:01,820 - Interactions will be predicted for NCBI taxid 7227
2008-09-29 09:30:01,820 - This NCBI taxid corresponds to 17 proteome id in Integr8 data
2008-09-29 09:30:01,820 - Used Memory: 1113 M - Free Memory: 452 M - Total Memory: 1565 M - Max Memory: 2666 M
2008-09-29 09:30:01,820 - Extract interactions with at least one taxid in [7227]
2008-09-29 09:30:11,001 -    > 28112 interactions are present in the source file and will be written.
2008-09-29 09:30:11,001 - Write 28112 interactions in the mitab file KnownInteractions.mitab
2008-09-29 09:30:11,555 - Used Memory: 1327 M - Free Memory: 842 M - Total Memory: 2169 M - Max Memory: 2666 M
2008-09-29 09:30:11,555 - ==================== Up-cast      ====================
2008-09-29 09:30:11,555 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 09:30:23,005 - 177085 source interactions
2008-09-29 09:30:23,006 - 49709 interactions miss at least one protein in the porcs
2008-09-29 09:30:23,006 - 113786 have been abstracted
2008-09-29 09:30:23,006 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 09:30:23,006 - Used Memory: 1710 M - Free Memory: 882 M - Total Memory: 2592 M - Max Memory: 2666 M
2008-09-29 09:30:23,006 - ==================== Down-cast    ====================
2008-09-29 09:30:23,006 - Create file downCast.history.txt
2008-09-29 09:30:23,006 - Create file srcInteractionsUsed.txt
2008-09-29 09:30:25,401 -    > 13255 binary interactions predicted
2008-09-29 09:30:25,402 - 9152 binary interactions have not been predicted because they are source interactions
2008-09-29 09:30:25,402 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 09:30:25,402 - Used Memory: 1702 M - Free Memory: 896 M - Total Memory: 2598 M - Max Memory: 2666 M
2008-09-29 09:30:25,402 - ==================== Post-process ====================
2008-09-29 09:30:25,402 - Write 13255 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 09:30:25,520 - Used Memory: 1795 M - Free Memory: 803 M - Total Memory: 2598 M - Max Memory: 2666 M
2008-09-29 09:30:25,824 - 13255 interactions read from mitab file
2008-09-29 09:30:26,589 - 28112 interactions read from mitab file
2008-09-29 09:30:26,589 - Write 41367 interactions in the mitab file AllInteractions.mitab
2008-09-29 09:30:27,173 - Used Memory: 2048 M - Free Memory: 545 M - Total Memory: 2593 M - Max Memory: 2666 M
2008-09-29 09:30:27,173 - time elapsed: 0.6860167 min
2008-09-29 09:30:27,173 - ======================================================
2008-09-29 09:30:27,173 - 
2008-09-29 09:30:27,173 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 09:30:27,173 -