2008-09-29 08:25:44,549 - Set mitab file: global.mitab
2008-09-29 08:25:44,549 - Set PORC file: porc_gene.dat
2008-09-29 08:25:44,549 - ==================== Pre-process  ====================
2008-09-29 08:25:44,554 - Used Memory: 3 M - Free Memory: 476 M - Total Memory: 479 M - Max Memory: 2666 M
2008-09-29 08:25:49,565 - 466 different taxids in the source interactions (mitab file)
2008-09-29 08:25:51,159 - We use UniprotKB ids for proteins. Only interactions with both Uniprot ids can be used.
2008-09-29 08:25:51,160 - Among them, we only consider physical interactions between 2 different proteins from the same species.
2008-09-29 08:25:51,160 - 177085 source interactions
2008-09-29 08:25:51,160 - 4659 proteins do not have Uniprot id
2008-09-29 08:25:51,160 - 4410 interactions do not have both Uniprot ids
2008-09-29 08:25:51,160 - 1397 interactions are not physical type
2008-09-29 08:25:51,160 - 4497 interactions are self interactions
2008-09-29 08:25:51,160 - 6955 interactions are between 2 different species
2008-09-29 08:25:51,160 -    > 160274 interactions can be used among the 177085 of the mitab file ../../DB/global.mitab
2008-09-29 08:25:51,160 - Compute the mapping from proteomeIds to NCBI taxids from file /opt/appli/interoporc/results/1148/proteome_report.txt
2008-09-29 08:25:51,166 - 809 proteome ids
2008-09-29 08:25:51,166 - 804 taxids
2008-09-29 08:25:51,167 - Parse PORC data (format = one gene by line)...
2008-09-29 08:25:59,986 -    > 249846 clusters are described in the PORC data
2008-09-29 08:25:59,986 - Used Memory: 954 M - Free Memory: 709 M - Total Memory: 1663 M - Max Memory: 2666 M
2008-09-29 08:26:01,941 -    > 1805565 proteins are found in the PORC data
2008-09-29 08:26:01,941 - The predictions will be made for taxid 1148
2008-09-29 08:26:01,941 - Interactions will be predicted for NCBI taxid 1148
2008-09-29 08:26:01,941 - This NCBI taxid corresponds to 41 proteome id in Integr8 data
2008-09-29 08:26:01,941 - Used Memory: 1164 M - Free Memory: 499 M - Total Memory: 1663 M - Max Memory: 2666 M
2008-09-29 08:26:01,942 - Extract interactions with at least one taxid in [1148]
2008-09-29 08:26:09,908 -    > 222 interactions are present in the source file and will be written.
2008-09-29 08:26:09,908 - Write 222 interactions in the mitab file KnownInteractions.mitab
2008-09-29 08:26:09,926 - Used Memory: 1059 M - Free Memory: 1118 M - Total Memory: 2177 M - Max Memory: 2666 M
2008-09-29 08:26:09,926 - ==================== Up-cast      ====================
2008-09-29 08:26:09,926 - Combine protein-protein interactions and clusters of orthologous proteins.
2008-09-29 08:26:22,336 - 177085 source interactions
2008-09-29 08:26:22,337 - 49709 interactions miss at least one protein in the porcs
2008-09-29 08:26:22,337 - 113786 have been abstracted
2008-09-29 08:26:22,337 -    > 110753 distinct interactions between 2 clusters are constructed
2008-09-29 08:26:22,337 - Used Memory: 1675 M - Free Memory: 991 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:26:22,337 - ==================== Down-cast    ====================
2008-09-29 08:26:22,337 - Create file downCast.history.txt
2008-09-29 08:26:22,337 - Create file srcInteractionsUsed.txt
2008-09-29 08:26:24,388 -    > 2037 binary interactions predicted
2008-09-29 08:26:24,388 - 1630 binary interactions have not been predicted because they are source interactions
2008-09-29 08:26:24,388 - 0 binary interactions have not been predicted because uniprot id missed
2008-09-29 08:26:24,388 - Used Memory: 1864 M - Free Memory: 802 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:26:24,388 - ==================== Post-process ====================
2008-09-29 08:26:24,388 - Write 2037 interactions in the mitab file InteroPorc.predictedInteractions.mitab
2008-09-29 08:26:24,425 - Used Memory: 1877 M - Free Memory: 789 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:26:24,467 - 2037 interactions read from mitab file
2008-09-29 08:26:24,473 - 222 interactions read from mitab file
2008-09-29 08:26:24,473 - Write 2259 interactions in the mitab file AllInteractions.mitab
2008-09-29 08:26:24,507 - Used Memory: 1920 M - Free Memory: 746 M - Total Memory: 2666 M - Max Memory: 2666 M
2008-09-29 08:26:24,507 - time elapsed: 0.66588336 min
2008-09-29 08:26:24,507 - ======================================================
2008-09-29 08:26:24,507 - 
2008-09-29 08:26:24,507 - Thanks for using the interoPORC tool. All information is available on http://biodev.extra.cea.fr/interoporc/
2008-09-29 08:26:24,507 -