[6:30:31 | CONFIG | main]: aptasuite.Aptasuite
System Information:
Java Version: 1.8.0_151
JavaFX Version: null
OS Name: Windows 10
OS Version: 10.0
OS Architecture: amd64
CPU cores: 8
System Memory: 514850816 Mb
 

[6:30:31 | INFO | main]: utilities.Configuration
Reading configuration from file. 

[6:30:31 | INFO | main]: utilities.Configuration
Using the following parameters: 
Experiment.name : "structures prediction 280618"
Experiment.description : "structure prediction for analyzed MDM2 data"
Experiment.primer5 : GTATACCTGCAGCTGAGG
Experiment.primer3 : GATGACACTACGTGACCA
Aptatrace.KmerLength : 6
Aptatrace.FilterClusters : True
Aptatrace.OutputClusters : True
Aptatrace.Alpha : 10
Performance.maxNumberOfCores : 30
MapDBAptamerPool.bloomFilterCapacity : 500000000
MapDBAptamerPool.bloomFilterCollisionProbability : 0.001
MapDBAptamerPool.maxTreeMapCapacity : 1000000
MapDBSelectionCycle.bloomFilterCollisionProbability : 0.001
MapDBStructurePool.bloomFilterCollisionProbability : 0.001
MapDBStructurePool.maxTreeMapCapacity : 500000
Experiment.projectPath : D:\bioIT\DATA\mdm2\2150618
AptamerPool.backend : MapDBAptamerPool
Aptasim.AmplificationEfficiency : 0.995
AptaplexParser.isPerFile : true
Export.IncludePrimerRegions : true
AptaplexParser.reader : FastqReader
AptaplexParser.BlockingQueueSize : 5000
Aptacluster.KmerSize : 3
StructurePool.backend : MapDBStructurePool
Aptasim.NucleotideDistribution : [0.25, 0.25, 0.25, 0.25]
Aptasim.MinSeedAffinity : 80
Export.compress : true
Aptasim.BaseMutationRates : [0.25, 0.25, 0.25, 0.25]
Aptasim.HmmDegree : 2
Export.MinimalClusterSize : 1
Aptasim.MaxSequenceAffinity : 25
Aptasim.SelectionPercentage : 0.2
Aptasim.MutationProbability : 0.05
Export.SequenceFormat : fastq
AptaplexParser.PairedEndMaxScoreValue : 55
AptaplexParser.PairedEndMinOverlap : 15
Export.PoolCardinalityFormat : frequencies
AptaplexParser.StoreReverseComplement : false
ClusterContainer.backend : MapDBClusterContainer
Export.ClusterFilterCriteria : ClusterSize
SelectionCycle.backend : MapDBSelectionCycle
Aptasim.NumberOfSeeds : 100
MapDBStructurePool.maxTreeMapCapacityBppm : 150000
Aptacluster.EditDistance : 5
Aptasim.NumberOfSequences : 1000000
Parser.backend : AptaplexParser
AptaplexParser.BarcodeTolerance : 1
Aptasim.MaxSequenceCount : 10
AptaplexParser.PrimerTolerance : 3
AptaplexParser.PairedEndMaxMutations : 5
MapDBAllocateStartSize : 1073741824
Aptacluster.KmerCutoffIterations : 10000
MapDBAllocateIncrement : 104857600
Aptacluster.LSHIterations : 5
Aptasim.RandomizedRegionSize : 40
 

[6:30:31 | INFO | main]: aptasuite.CLI
Starting Structure Predition 

[6:30:31 | INFO | main]: aptasuite.CLI
Loading data from disk 

[6:30:32 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Instantiating MapDBAptamerPool 

[6:30:32 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Searching for existing datasets in D:\bioIT\DATA\mdm2\2150618\pooldata 

[6:30:32 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Found a total of 14 files on disk. 

[6:30:32 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0000.mapdb 

[6:30:32 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0000.mapdb 

[6:30:39 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0000.mapdb 

[6:30:39 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 1000000
Processed in 7.527 seconds. 

[6:30:39 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0001.mapdb 

[6:30:39 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0001.mapdb 

[6:30:46 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0001.mapdb 

[6:30:46 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 2000000
Processed in 6.934 seconds. 

[6:30:46 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0002.mapdb 

[6:30:46 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0002.mapdb 

[6:30:54 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0002.mapdb 

[6:30:54 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 3000000
Processed in 7.614 seconds. 

[6:30:54 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0003.mapdb 

[6:30:54 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0003.mapdb 

[6:31:01 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0003.mapdb 

[6:31:01 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 4000000
Processed in 7.393 seconds. 

[6:31:01 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0004.mapdb 

[6:31:01 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0004.mapdb 

[6:31:08 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0004.mapdb 

[6:31:08 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 5000000
Processed in 6.811 seconds. 

[6:31:08 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0005.mapdb 

[6:31:08 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0005.mapdb 

[6:31:15 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0005.mapdb 

[6:31:15 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 6000000
Processed in 6.845 seconds. 

[6:31:15 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0006.mapdb 

[6:31:15 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0006.mapdb 

[6:31:22 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0006.mapdb 

[6:31:22 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 7000000
Processed in 7.699 seconds. 

[6:31:22 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0007.mapdb 

[6:31:22 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0007.mapdb 

[6:31:30 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0007.mapdb 

[6:31:30 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 8000000
Processed in 7.611 seconds. 

[6:31:30 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0008.mapdb 

[6:31:30 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0008.mapdb 

[6:31:37 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0008.mapdb 

[6:31:37 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 9000000
Processed in 7.111 seconds. 

[6:31:37 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0009.mapdb 

[6:31:37 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0009.mapdb 

[6:31:44 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0009.mapdb 

[6:31:44 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 10000000
Processed in 6.656 seconds. 

[6:31:44 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0010.mapdb 

[6:31:44 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0010.mapdb 

[6:31:50 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0010.mapdb 

[6:31:50 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 11000000
Processed in 6.716 seconds. 

[6:31:50 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0011.mapdb 

[6:31:50 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0011.mapdb 

[6:31:58 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0011.mapdb 

[6:31:58 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 12000000
Processed in 7.647 seconds. 

[6:31:58 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0012.mapdb 

[6:31:58 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0012.mapdb 

[6:32:06 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0012.mapdb 

[6:32:06 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 13000000
Processed in 7.66 seconds. 

[6:32:06 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing D:\bioIT\DATA\mdm2\2150618\pooldata\data0013.mapdb 

[6:32:06 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from D:\bioIT\DATA\mdm2\2150618\pooldata\inverse_data0013.mapdb 

[6:32:07 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from D:\bioIT\DATA\mdm2\2150618\pooldata\bounds_data0013.mapdb 

[6:32:07 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 228858
Total number of aptamers: 13228858
Processed in 1.603 seconds. 

[6:32:07 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Found and loaded a total of 13228858 aptamers from disk. 

[6:32:07 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
AptamerPool instantiation took 95.858 seconds