2008-09-29 09:52:30,213 - Set mitab file: global.mitab 2008-09-29 09:52:30,213 - Set PORC file: porc_gene.dat 2008-09-29 09:52:30,213 - ==================== Pre-process ==================== 2008-09-29 09:52:30,218 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M 2008-09-29 09:52:35,150 - 466 different taxids in the source interactions (mitab file) 2008-09-29 09:52:35,150 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used. 2008-09-29 09:52:35,150 - Among them, we only consider physical interactions between 2 different proteins from the same species. 2008-09-29 09:52:35,150 - 177085 source interactions 2008-09-29 09:52:35,150 - 4659 proteins do not have Uniprot id 2008-09-29 09:52:35,150 - 4410 interactions do not have both Uniprot ids 2008-09-29 09:52:35,150 - 1397 interactions are not physical type 2008-09-29 09:52:35,150 - 4497 interactions are self interactions 2008-09-29 09:52:35,150 - 6955 interactions are between 2 different species 2008-09-29 09:52:35,150 - > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab 2008-09-29 09:52:35,151 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/9606/proteome_report.txt 2008-09-29 09:52:35,157 - 809 proteome ids 2008-09-29 09:52:35,157 - 804 taxids 2008-09-29 09:52:35,157 - Parse PORC data (format = one gene by line)... 2008-09-29 09:52:43,736 - > 249846 clusters are described in the PORC data 2008-09-29 09:52:43,736 - Used Memory: 805 M - Free Memory: 415 M - Total Memory: 1220 M - Max Memory: 2666 M 2008-09-29 09:52:45,661 - > 1805565 proteins are found in the PORC data 2008-09-29 09:52:45,661 - The predictions will be made for taxid 9606 2008-09-29 09:52:45,661 - Interactions will be predicted for NCBI taxid 9606 2008-09-29 09:52:45,661 - This NCBI taxid corresponds to 25 proteome id in Integr8 data 2008-09-29 09:52:45,661 - Used Memory: 1012 M - Free Memory: 208 M - Total Memory: 1220 M - Max Memory: 2666 M 2008-09-29 09:52:45,661 - Extract interactions with at least one taxid in [9606] 2008-09-29 09:52:54,838 - > 33841 interactions are present in the source file and will be written. 2008-09-29 09:52:54,839 - Write 33841 interactions in the mitab file KnownInteractions.mitab 2008-09-29 09:52:55,457 - Used Memory: 1145 M - Free Memory: 699 M - Total Memory: 1844 M - Max Memory: 2666 M 2008-09-29 09:52:55,457 - ==================== Up-cast ==================== 2008-09-29 09:52:55,457 - Combine protein-protein interactions and clusters of orthologous proteins. 2008-09-29 09:53:06,417 - 177085 source interactions 2008-09-29 09:53:06,417 - 49709 interactions miss at least one protein in the porcs 2008-09-29 09:53:06,417 - 113786 have been abstracted 2008-09-29 09:53:06,417 - > 110753 distinct interactions between 2 clusters are constructed 2008-09-29 09:53:06,417 - Used Memory: 1865 M - Free Memory: 360 M - Total Memory: 2225 M - Max Memory: 2666 M 2008-09-29 09:53:06,417 - ==================== Down-cast ==================== 2008-09-29 09:53:06,418 - Create file downCast.history.txt 2008-09-29 09:53:06,418 - Create file srcInteractionsUsed.txt 2008-09-29 09:53:09,003 - > 17284 binary interactions predicted 2008-09-29 09:53:09,004 - 20609 binary interactions have not been predicted because they are source interactions 2008-09-29 09:53:09,004 - 0 binary interactions have not been predicted because uniprot id missed 2008-09-29 09:53:09,004 - Used Memory: 1956 M - Free Memory: 473 M - Total Memory: 2429 M - Max Memory: 2666 M 2008-09-29 09:53:09,004 - ==================== Post-process ==================== 2008-09-29 09:53:09,004 - Write 17284 interactions in the mitab file InteroPorc.predictedInteractions.mitab 2008-09-29 09:53:09,258 - Used Memory: 1729 M - Free Memory: 689 M - Total Memory: 2418 M - Max Memory: 2666 M 2008-09-29 09:53:09,508 - 17284 interactions read from mitab file 2008-09-29 09:53:10,569 - 33841 interactions read from mitab file 2008-09-29 09:53:10,569 - Write 51125 interactions in the mitab file AllInteractions.mitab 2008-09-29 09:53:11,282 - Used Memory: 2135 M - Free Memory: 280 M - Total Memory: 2415 M - Max Memory: 2666 M 2008-09-29 09:53:11,282 - time elapsed: 0.6844 min 2008-09-29 09:53:11,282 - ====================================================== 2008-09-29 09:53:11,282 - 2008-09-29 09:53:11,282 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/ 2008-09-29 09:53:11,282 -