2008-01-28 14:48:01,573 - Set mitab file: global.mitab
2008-01-28 14:48:01,573 - Set PORC file: porc_gene.dat
2008-01-28 14:48:01,573 - ==================== Pre-process  ====================
2008-01-28 14:48:01,578 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 1777 M
2008-01-28 14:48:04,945 - several Uniprot ac: P50591 and P50591.1
2008-01-28 14:48:05,768 - several Uniprot ac: P31658 and P31658.3
2008-01-28 14:48:05,769 - several Uniprot ac: P31658 and P31658.3
2008-01-28 14:48:06,377 - 478 different taxids in the source interactions (mitab file)
2008-01-28 14:48:06,377 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-01-28 14:48:06,378 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-01-28 14:48:06,378 - 185024 source interactions
2008-01-28 14:48:06,378 - 5860 proteins do not have Uniprot id
2008-01-28 14:48:06,378 - 5460 interactions do not have both Uniprot ids
2008-01-28 14:48:06,378 - 1648 interactions are not physical type
2008-01-28 14:48:06,378 - 4481 interactions are self interactions
2008-01-28 14:48:06,378 - 6352 interactions are between 2 different species
2008-01-28 14:48:06,378 -    > 167380 interactions can be used among the 185024 of the mitab file ../../DB/global.mitab
2008-01-28 14:48:06,378 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/562/proteome_report.txt
2008-01-28 14:48:06,383 - 666 proteome ids
2008-01-28 14:48:06,383 - 663 taxids
2008-01-28 14:48:06,384 - Parse PORC data (format = one gene by line)...
2008-01-28 14:48:14,006 -    > 215733 clusters are described in the PORC data
2008-01-28 14:48:14,006 - Used Memory: 672 M - Free Memory: 603 M - Total Memory: 1275 M - Max Memory: 1777 M
2008-01-28 14:48:16,320 -    > 1524313 proteins are found in the PORC data
2008-01-28 14:48:16,320 - 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
2008-01-28 14:48:16,320 - 0 species given by the user are added to the list for the predictions
2008-01-28 14:48:16,321 - 8 proteome id of a specific strain is added in the list of species
2008-01-28 14:48:16,321 - We have a list of 8 NCBI taxids (corresponding to 8 proteome ids) for which we will predict interactions
2008-01-28 14:48:16,321 - Used Memory: 1044 M - Free Memory: 209 M - Total Memory: 1253 M - Max Memory: 1777 M
2008-01-28 14:48:16,321 - Extract interactions with at least one taxid in [155864, 362663, 217992, 331112, 83333, 405955, 331111, 364106]
2008-01-28 14:48:23,195 -    > 298 interactions are present in the source file and will be written in KnownInteractions.mitab file
2008-01-28 14:48:23,195 - Write 298 interactions in the mitab file KnownInteractions.mitab
2008-01-28 14:48:23,211 - Used Memory: 1050 M - Free Memory: 755 M - Total Memory: 1805 M - Max Memory: 1805 M
2008-01-28 14:48:23,211 - ==================== Up-cast      ====================
2008-01-28 14:48:23,211 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-01-28 14:48:27,580 - several Uniprot ac: P50591 and P50591.1
2008-01-28 14:48:55,326 - 185024 source interactions
2008-01-28 14:48:55,326 - 78864 interactions miss at least one protein in the porcs
2008-01-28 14:48:55,326 - 93693 have been abstracted
2008-01-28 14:48:55,326 -    > 91886 distinct interactions between 2 clusters are constructed
2008-01-28 14:48:55,326 - Used Memory: 1539 M - Free Memory: 238 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:48:55,326 - ==================== Down-cast    ====================
2008-01-28 14:48:55,327 - Create file downCast.history.txt
2008-01-28 14:48:55,327 - Create file srcInteractionsUsed.txt
2008-01-28 14:49:00,937 -    > 58141 binary interactions predicted
2008-01-28 14:49:00,937 - 12779 binary interactions have not been predicted because they are source interactions
2008-01-28 14:49:00,937 - 0 binary interactions have not been predicted because uniprot id missed
2008-01-28 14:49:00,937 - Used Memory: 1033 M - Free Memory: 744 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:49:00,937 - ==================== Post-process ====================
2008-01-28 14:49:00,938 - Create file InteroPorc.predictedInteractions.mitab
2008-01-28 14:49:00,938 - Write 58141 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-01-28 14:49:01,354 - Used Memory: 1223 M - Free Memory: 552 M - Total Memory: 1775 M - Max Memory: 1777 M
2008-01-28 14:49:01,354 - time elapsed: 0.99626666 min
2008-01-28 14:49:01,354 - ======================================================
2008-01-28 14:49:01,354 - 
2008-01-28 14:49:01,355 - Thanks for using the interoPORC tool. All informations are available on http://biodev.extra.cea.fr/interoporc/
2008-01-28 14:49:01,355 -