2008-09-29 08:48:38,798 - Set mitab file: global.mitab
2008-09-29 08:48:38,799 - Set PORC file: porc_gene.dat
2008-09-29 08:48:38,799 - ==================== Pre-process  ====================
2008-09-29 08:48:38,803 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 08:48:43,817 - 466 different taxids in the source interactions (mitab file)
2008-09-29 08:48:43,818 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 08:48:43,818 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 08:48:43,818 - 177085 source interactions
2008-09-29 08:48:43,818 - 4659 proteins do not have Uniprot id
2008-09-29 08:48:43,818 - 4410 interactions do not have both Uniprot ids
2008-09-29 08:48:43,818 - 1397 interactions are not physical type
2008-09-29 08:48:43,818 - 4497 interactions are self interactions
2008-09-29 08:48:43,818 - 6955 interactions are between 2 different species
2008-09-29 08:48:43,818 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 08:48:43,818 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/210/proteome_report.txt
2008-09-29 08:48:43,824 - 809 proteome ids
2008-09-29 08:48:43,824 - 804 taxids
2008-09-29 08:48:43,825 - Parse PORC data (format = one gene by line)...
2008-09-29 08:48:52,620 -    > 249846 clusters are described in the PORC data
2008-09-29 08:48:52,620 - Used Memory: 908 M - Free Memory: 657 M - Total Memory: 1565 M - Max Memory: 2666 M
2008-09-29 08:48:54,569 -    > 1805565 proteins are found in the PORC data
2008-09-29 08:48:54,570 - The taxid 210 can not be mapped to Integr8 identifier. It is either incorrect or not in Integr8 species list. Check http://www.ebi.ac.uk/integr8/OrganismSearch.do?action=browseOrgs&currentclicked=BROWSE_SPECIES
2008-09-29 08:48:54,570 - 0 species given by the user are added to the list for the predictions
2008-09-29 08:48:54,570 - 3 proteome id of a specific strain is added in the list of species
2008-09-29 08:48:54,570 - We have a list of 3 NCBI taxids (corresponding to 3 proteome ids) for which we will predict interactions
2008-09-29 08:48:54,570 - Used Memory: 1113 M - Free Memory: 452 M - Total Memory: 1565 M - Max Memory: 2666 M
2008-09-29 08:48:54,570 - Extract interactions with at least one taxid in [357544, 85962, 85963]
2008-09-29 08:49:03,184 -    > 25 interactions are present in the source file and will be written.
2008-09-29 08:49:03,184 - Write 25 interactions in the mitab file KnownInteractions.mitab
2008-09-29 08:49:03,189 - Used Memory: 1404 M - Free Memory: 766 M - Total Memory: 2170 M - Max Memory: 2666 M
2008-09-29 08:49:03,189 - ==================== Up-cast      ====================
2008-09-29 08:49:03,190 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 08:49:15,111 - 177085 source interactions
2008-09-29 08:49:15,112 - 49709 interactions miss at least one protein in the porcs
2008-09-29 08:49:15,112 - 113786 have been abstracted
2008-09-29 08:49:15,112 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 08:49:15,112 - Used Memory: 1723 M - Free Memory: 943 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:49:15,112 - ==================== Down-cast    ====================
2008-09-29 08:49:15,112 - Create file downCast.history.txt
2008-09-29 08:49:15,113 - Create file srcInteractionsUsed.txt
2008-09-29 08:49:17,418 -    > 11375 binary interactions predicted
2008-09-29 08:49:17,418 - 1206 binary interactions have not been predicted because they are source interactions
2008-09-29 08:49:17,418 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 08:49:17,418 - Used Memory: 1679 M - Free Memory: 987 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:49:17,418 - ==================== Post-process ====================
2008-09-29 08:49:17,418 - Write 11375 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 08:49:17,553 - Used Memory: 1758 M - Free Memory: 908 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:49:17,732 - 11375 interactions read from mitab file
2008-09-29 08:49:17,733 - 25 interactions read from mitab file
2008-09-29 08:49:17,733 - Write 11400 interactions in the mitab file AllInteractions.mitab
2008-09-29 08:49:17,891 - Used Memory: 1678 M - Free Memory: 988 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:49:17,891 - time elapsed: 0.65146667 min
2008-09-29 08:49:17,891 - ======================================================
2008-09-29 08:49:17,891 - 
2008-09-29 08:49:17,891 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 08:49:17,891 -