2008-09-29 09:27:56,584 - Set mitab file: global.mitab
2008-09-29 09:27:56,584 - Set PORC file: porc_gene.dat
2008-09-29 09:27:56,584 - ==================== Pre-process  ====================
2008-09-29 09:27:56,589 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 09:28:01,529 - 466 different taxids in the source interactions (mitab file)
2008-09-29 09:28:01,529 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 09:28:01,529 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 09:28:01,529 - 177085 source interactions
2008-09-29 09:28:01,529 - 4659 proteins do not have Uniprot id
2008-09-29 09:28:01,529 - 4410 interactions do not have both Uniprot ids
2008-09-29 09:28:01,529 - 1397 interactions are not physical type
2008-09-29 09:28:01,529 - 4497 interactions are self interactions
2008-09-29 09:28:01,529 - 6955 interactions are between 2 different species
2008-09-29 09:28:01,529 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 09:28:01,529 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/6239/proteome_report.txt
2008-09-29 09:28:01,535 - 809 proteome ids
2008-09-29 09:28:01,535 - 804 taxids
2008-09-29 09:28:01,536 - Parse PORC data (format = one gene by line)...
2008-09-29 09:28:10,140 -    > 249846 clusters are described in the PORC data
2008-09-29 09:28:10,140 - Used Memory: 800 M - Free Memory: 422 M - Total Memory: 1222 M - Max Memory: 2666 M
2008-09-29 09:28:12,068 -    > 1805565 proteins are found in the PORC data
2008-09-29 09:28:12,068 - The predictions will be made for taxid 6239
2008-09-29 09:28:12,069 - Interactions will be predicted for NCBI taxid 6239
2008-09-29 09:28:12,069 - This NCBI taxid corresponds to 9 proteome id in Integr8 data
2008-09-29 09:28:12,069 - Used Memory: 1008 M - Free Memory: 214 M - Total Memory: 1222 M - Max Memory: 2666 M
2008-09-29 09:28:12,069 - Extract interactions with at least one taxid in [6239]
2008-09-29 09:28:21,138 -    > 5224 interactions are present in the source file and will be written.
2008-09-29 09:28:21,138 - Write 5224 interactions in the mitab file KnownInteractions.mitab
2008-09-29 09:28:21,255 - Used Memory: 1159 M - Free Memory: 652 M - Total Memory: 1811 M - Max Memory: 2666 M
2008-09-29 09:28:21,255 - ==================== Up-cast      ====================
2008-09-29 09:28:21,255 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 09:28:33,511 - 177085 source interactions
2008-09-29 09:28:33,511 - 49709 interactions miss at least one protein in the porcs
2008-09-29 09:28:33,511 - 113786 have been abstracted
2008-09-29 09:28:33,512 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 09:28:33,512 - Used Memory: 1740 M - Free Memory: 696 M - Total Memory: 2436 M - Max Memory: 2666 M
2008-09-29 09:28:33,512 - ==================== Down-cast    ====================
2008-09-29 09:28:33,512 - Create file downCast.history.txt
2008-09-29 09:28:33,512 - Create file srcInteractionsUsed.txt
2008-09-29 09:28:36,106 -    > 11205 binary interactions predicted
2008-09-29 09:28:36,107 - 2958 binary interactions have not been predicted because they are source interactions
2008-09-29 09:28:36,107 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 09:28:36,107 - Used Memory: 1702 M - Free Memory: 734 M - Total Memory: 2436 M - Max Memory: 2666 M
2008-09-29 09:28:36,107 - ==================== Post-process ====================
2008-09-29 09:28:36,107 - Write 11205 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 09:28:36,222 - Used Memory: 1779 M - Free Memory: 657 M - Total Memory: 2436 M - Max Memory: 2666 M
2008-09-29 09:28:36,396 - 11205 interactions read from mitab file
2008-09-29 09:28:41,200 - 5224 interactions read from mitab file
2008-09-29 09:28:41,200 - Write 16429 interactions in the mitab file AllInteractions.mitab
2008-09-29 09:28:41,326 - Used Memory: 1723 M - Free Memory: 943 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 09:28:41,326 - time elapsed: 0.7456167 min
2008-09-29 09:28:41,326 - ======================================================
2008-09-29 09:28:41,326 - 
2008-09-29 09:28:41,326 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 09:28:41,326 -