2008-09-29 08:49:32,385 - Set mitab file: global.mitab
2008-09-29 08:49:32,385 - Set PORC file: porc_gene.dat
2008-09-29 08:49:32,385 - ==================== Pre-process  ====================
2008-09-29 08:49:32,390 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 08:49:37,294 - 466 different taxids in the source interactions (mitab file)
2008-09-29 08:49:37,294 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 08:49:37,294 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 08:49:37,294 - 177085 source interactions
2008-09-29 08:49:37,294 - 4659 proteins do not have Uniprot id
2008-09-29 08:49:37,294 - 4410 interactions do not have both Uniprot ids
2008-09-29 08:49:37,294 - 1397 interactions are not physical type
2008-09-29 08:49:37,294 - 4497 interactions are self interactions
2008-09-29 08:49:37,294 - 6955 interactions are between 2 different species
2008-09-29 08:49:37,294 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 08:49:37,295 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/4932/proteome_report.txt
2008-09-29 08:49:37,300 - 809 proteome ids
2008-09-29 08:49:37,300 - 804 taxids
2008-09-29 08:49:37,301 - Parse PORC data (format = one gene by line)...
2008-09-29 08:49:45,880 -    > 249846 clusters are described in the PORC data
2008-09-29 08:49:45,880 - Used Memory: 805 M - Free Memory: 416 M - Total Memory: 1221 M - Max Memory: 2666 M
2008-09-29 08:49:47,808 -    > 1805565 proteins are found in the PORC data
2008-09-29 08:49:47,809 - The predictions will be made for taxid 4932
2008-09-29 08:49:47,809 - Interactions will be predicted for NCBI taxid 4932
2008-09-29 08:49:47,809 - This NCBI taxid corresponds to 40 proteome id in Integr8 data
2008-09-29 08:49:47,809 - Used Memory: 1013 M - Free Memory: 208 M - Total Memory: 1221 M - Max Memory: 2666 M
2008-09-29 08:49:47,809 - Extract interactions with at least one taxid in [4932]
2008-09-29 08:50:01,859 -    > 54015 interactions are present in the source file and will be written.
2008-09-29 08:50:01,860 - Write 54015 interactions in the mitab file KnownInteractions.mitab
2008-09-29 08:50:02,563 - Used Memory: 1541 M - Free Memory: 904 M - Total Memory: 2445 M - Max Memory: 2666 M
2008-09-29 08:50:02,563 - ==================== Up-cast      ====================
2008-09-29 08:50:02,563 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 08:50:13,795 - 177085 source interactions
2008-09-29 08:50:13,795 - 49709 interactions miss at least one protein in the porcs
2008-09-29 08:50:13,796 - 113786 have been abstracted
2008-09-29 08:50:13,796 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 08:50:13,796 - Used Memory: 1817 M - Free Memory: 849 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:50:13,796 - ==================== Down-cast    ====================
2008-09-29 08:50:13,796 - Create file downCast.history.txt
2008-09-29 08:50:13,796 - Create file srcInteractionsUsed.txt
2008-09-29 08:50:16,301 -    > 1791 binary interactions predicted
2008-09-29 08:50:16,302 - 44103 binary interactions have not been predicted because they are source interactions
2008-09-29 08:50:16,302 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 08:50:16,302 - Used Memory: 1894 M - Free Memory: 772 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:50:16,302 - ==================== Post-process ====================
2008-09-29 08:50:16,302 - Write 1791 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 08:50:16,330 - Used Memory: 1907 M - Free Memory: 759 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:50:16,427 - 1791 interactions read from mitab file
2008-09-29 08:50:18,250 - 54015 interactions read from mitab file
2008-09-29 08:50:18,251 - Write 55806 interactions in the mitab file AllInteractions.mitab
2008-09-29 08:50:24,272 - Used Memory: 1837 M - Free Memory: 829 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:50:24,273 - time elapsed: 0.8647 min
2008-09-29 08:50:24,273 - ======================================================
2008-09-29 08:50:24,273 - 
2008-09-29 08:50:24,273 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 08:50:24,273 -