2008-01-28 14:49:01,591 - Set mitab file: global.mitab
2008-01-28 14:49:01,591 - Set PORC file: porc_gene.dat
2008-01-28 14:49:01,591 - ==================== Pre-process  ====================
2008-01-28 14:49:01,596 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 1777 M
2008-01-28 14:49:04,937 - several Uniprot ac: P50591 and P50591.1
2008-01-28 14:49:05,754 - several Uniprot ac: P31658 and P31658.3
2008-01-28 14:49:05,754 - several Uniprot ac: P31658 and P31658.3
2008-01-28 14:49:06,357 - 478 different taxids in the source interactions (mitab file)
2008-01-28 14:49:06,357 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-01-28 14:49:06,357 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-01-28 14:49:06,358 - 185024 source interactions
2008-01-28 14:49:06,358 - 5860 proteins do not have Uniprot id
2008-01-28 14:49:06,358 - 5460 interactions do not have both Uniprot ids
2008-01-28 14:49:06,358 - 1648 interactions are not physical type
2008-01-28 14:49:06,358 - 4481 interactions are self interactions
2008-01-28 14:49:06,358 - 6352 interactions are between 2 different species
2008-01-28 14:49:06,358 -    > 167380 interactions can be used among the 185024 of the mitab file ../../DB/global.mitab
2008-01-28 14:49:06,358 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/210/proteome_report.txt
2008-01-28 14:49:06,363 - 666 proteome ids
2008-01-28 14:49:06,363 - 663 taxids
2008-01-28 14:49:06,364 - Parse PORC data (format = one gene by line)...
2008-01-28 14:49:13,886 -    > 215733 clusters are described in the PORC data
2008-01-28 14:49:13,887 - Used Memory: 690 M - Free Memory: 578 M - Total Memory: 1268 M - Max Memory: 1777 M
2008-01-28 14:49:19,029 -    > 1524313 proteins are found in the PORC data
2008-01-28 14:49:19,030 - 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
2008-01-28 14:49:19,030 - 0 species given by the user are added to the list for the predictions
2008-01-28 14:49:19,030 - 3 proteome id of a specific strain is added in the list of species
2008-01-28 14:49:19,030 - We have a list of 3 NCBI taxids (corresponding to 3 proteome ids) for which we will predict interactions
2008-01-28 14:49:19,030 - Used Memory: 919 M - Free Memory: 820 M - Total Memory: 1739 M - Max Memory: 1777 M
2008-01-28 14:49:19,030 - Extract interactions with at least one taxid in [357544, 85962, 85963]
2008-01-28 14:49:23,001 -    > 1439 interactions are present in the source file and will be written in KnownInteractions.mitab file
2008-01-28 14:49:23,002 - Write 1439 interactions in the mitab file KnownInteractions.mitab
2008-01-28 14:49:23,044 - Used Memory: 1137 M - Free Memory: 658 M - Total Memory: 1795 M - Max Memory: 1795 M
2008-01-28 14:49:23,044 - ==================== Up-cast      ====================
2008-01-28 14:49:23,044 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-01-28 14:49:30,840 - several Uniprot ac: P50591 and P50591.1
2008-01-28 14:49:57,993 - 185024 source interactions
2008-01-28 14:49:57,993 - 78864 interactions miss at least one protein in the porcs
2008-01-28 14:49:57,993 - 93693 have been abstracted
2008-01-28 14:49:57,994 -    > 91886 distinct interactions between 2 clusters are constructed
2008-01-28 14:49:57,994 - Used Memory: 1436 M - Free Memory: 341 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:49:57,994 - ==================== Down-cast    ====================
2008-01-28 14:49:57,994 - Create file downCast.history.txt
2008-01-28 14:49:57,994 - Create file srcInteractionsUsed.txt
2008-01-28 14:50:02,795 -    > 5562 binary interactions predicted
2008-01-28 14:50:02,796 - 1211 binary interactions have not been predicted because they are source interactions
2008-01-28 14:50:02,796 - 0 binary interactions have not been predicted because uniprot id missed
2008-01-28 14:50:02,797 - Used Memory: 1103 M - Free Memory: 674 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:50:02,797 - ==================== Post-process ====================
2008-01-28 14:50:02,797 - Create file InteroPorc.predictedInteractions.mitab
2008-01-28 14:50:02,797 - Write 5562 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-01-28 14:50:02,878 - Used Memory: 1143 M - Free Memory: 634 M - Total Memory: 1777 M - Max Memory: 1777 M
2008-01-28 14:50:02,878 - time elapsed: 1.0213667 min
2008-01-28 14:50:02,878 - ======================================================
2008-01-28 14:50:02,878 - 
2008-01-28 14:50:02,878 - Thanks for using the interoPORC tool. All informations are available on http://biodev.extra.cea.fr/interoporc/
2008-01-28 14:50:02,878 -