2008-09-29 08:26:31,759 - Set mitab file: global.mitab
2008-09-29 08:26:31,760 - Set PORC file: porc_gene.dat
2008-09-29 08:26:31,760 - ==================== Pre-process  ====================
2008-09-29 08:26:31,764 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 08:26:36,742 - 466 different taxids in the source interactions (mitab file)
2008-09-29 08:26:36,742 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 08:26:36,742 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 08:26:36,742 - 177085 source interactions
2008-09-29 08:26:36,742 - 4659 proteins do not have Uniprot id
2008-09-29 08:26:36,742 - 4410 interactions do not have both Uniprot ids
2008-09-29 08:26:36,742 - 1397 interactions are not physical type
2008-09-29 08:26:36,742 - 4497 interactions are self interactions
2008-09-29 08:26:36,742 - 6955 interactions are between 2 different species
2008-09-29 08:26:36,742 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 08:26:36,742 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/562/proteome_report.txt
2008-09-29 08:26:36,748 - 809 proteome ids
2008-09-29 08:26:36,748 - 804 taxids
2008-09-29 08:26:36,749 - Parse PORC data (format = one gene by line)...
2008-09-29 08:26:45,505 -    > 249846 clusters are described in the PORC data
2008-09-29 08:26:45,505 - Used Memory: 926 M - Free Memory: 618 M - Total Memory: 1544 M - Max Memory: 2666 M
2008-09-29 08:26:47,451 -    > 1805565 proteins are found in the PORC data
2008-09-29 08:26:47,451 - The taxid 562 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 08:26:47,451 - 0 species given by the user are added to the list for the predictions
2008-09-29 08:26:47,451 - 8 proteome id of a specific strain is added in the list of species
2008-09-29 08:26:47,451 - We have a list of 8 NCBI taxids (corresponding to 8 proteome ids) for which we will predict interactions
2008-09-29 08:26:47,451 - Used Memory: 1137 M - Free Memory: 407 M - Total Memory: 1544 M - Max Memory: 2666 M
2008-09-29 08:26:47,451 - Extract interactions with at least one taxid in [155864, 511145, 362663, 217992, 331112, 405955, 331111, 364106]
2008-09-29 08:26:55,992 -    > 300 interactions are present in the source file and will be written.
2008-09-29 08:26:55,992 - Write 300 interactions in the mitab file KnownInteractions.mitab
2008-09-29 08:26:56,012 - Used Memory: 1096 M - Free Memory: 1094 M - Total Memory: 2190 M - Max Memory: 2666 M
2008-09-29 08:26:56,013 - ==================== Up-cast      ====================
2008-09-29 08:26:56,013 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 08:27:08,090 - 177085 source interactions
2008-09-29 08:27:08,091 - 49709 interactions miss at least one protein in the porcs
2008-09-29 08:27:08,091 - 113786 have been abstracted
2008-09-29 08:27:08,091 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 08:27:08,091 - Used Memory: 1803 M - Free Memory: 863 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:27:08,091 - ==================== Down-cast    ====================
2008-09-29 08:27:08,091 - Create file downCast.history.txt
2008-09-29 08:27:08,092 - Create file srcInteractionsUsed.txt
2008-09-29 08:27:11,834 -    > 88864 binary interactions predicted
2008-09-29 08:27:11,835 - 13457 binary interactions have not been predicted because they are source interactions
2008-09-29 08:27:11,835 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 08:27:11,835 - Used Memory: 1729 M - Free Memory: 937 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:27:11,835 - ==================== Post-process ====================
2008-09-29 08:27:11,835 - Write 88864 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 08:27:12,566 - Used Memory: 1721 M - Free Memory: 945 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:27:20,096 - 88864 interactions read from mitab file
2008-09-29 08:27:20,101 - 300 interactions read from mitab file
2008-09-29 08:27:20,101 - Write 89164 interactions in the mitab file AllInteractions.mitab
2008-09-29 08:27:25,627 - Used Memory: 2211 M - Free Memory: 414 M - Total Memory: 2625 M - Max Memory: 2666 M
2008-09-29 08:27:25,627 - time elapsed: 0.89771664 min
2008-09-29 08:27:25,627 - ======================================================
2008-09-29 08:27:25,627 - 
2008-09-29 08:27:25,627 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 08:27:25,627 -