[7:32:09 | INFO | main]: utilities.Configuration
Reading configuration from file. 

[7:32:09 | INFO | main]: utilities.Configuration
Using the following parameters: 
Experiment.name : "S2ii"
Experiment.description : "Stream2"
Experiment.projectPath : /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/
Experiment.primer5 : GGAAGAGGAAAGAAGTGCAGA
Experiment.primer3 : TCTTGTGCTCGCGAGGCAATCA
SelectionCycle.name : [S2R4, S2iiR6, S2iiR6Negative, S2iiR8AH, S2iiR8Negative]
SelectionCycle.round : [4, 6, 6, 8, 8]
SelectionCycle.isControlSelection : [False, False, False, False, False]
SelectionCycle.isCounterSelection : [False, False, True, False, True]
AptaplexParser.isPerFile : True
AptaplexParser.forwardFiles : [/media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/S2ii/NG-13097_36_lib195126_5449_8_1.fastq, /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/S2ii/NG-13097_39_lib195129_5449_8_1.fastq, /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/S2ii/NG-13097_40_lib195130_5449_8_1.fastq, /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/S2ii/NG-13097_S2iiR7AH_lib199556_5451_8_1.fastq, /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/S2ii/NG-13097_Trop2H_lib199554_5451_8_1.fastq]
AptaplexParser.reader : FastqReader
Aptacluster.RandomizedRegionSize : 42
Aptacluster.LSHDimension : 30
Aptacluster.LSHIterations : 5
Aptacluster.KmerSize : 3
Aptasim.HmmDegree : 2
Aptasim.RandomizedRegionSize : 40
Aptasim.NumberOfSequences : 500000
Aptasim.NumberOfSeeds : 100
Aptasim.MinSeedAffinity : 80
Aptasim.MaxSequenceCount : 10
Aptasim.MaxSequenceAffinity : 25
Aptasim.NucleotideDistribution : [0.25, 0.25, 0.25, 0.25]
Aptasim.SelectionPercentage : 0.20
Aptasim.BaseMutationRates : [0.25, 0.25, 0.25, 0.25]
Aptasim.MutationProbability : 0.05
Aptasim.AmplificationEfficiency : 0.995
Aptatrace.KmerLength : 6
Aptatrace.FilterClusters : True
Aptatrace.OutputClusters : True
Aptatrace.Alpha : 5
Export.Cycles : [S2R4, S2iiR6, S2iiR6Negative, S2iiR8AH, S2iiR8Negative]
Performance.maxNumberOfCores : 4
AptamerPool.backend : MapDBAptamerPool
MapDBSelectionCycle.bloomFilterCollisionProbability : 0.001
Export.IncludePrimerRegions : true
Export.PoolCardinalityFormat : frequencies
AptaplexParser.BlockingQueueSize : 500
ClusterContainer.backend : MapDBClusterContainer
MapDBAptamerPool.bloomFilterCollisionProbability : 0.001
SelectionCycle.backend : MapDBSelectionCycle
MapDBStructurePool.bloomFilterCollisionProbability : 0.001
StructurePool.backend : MapDBStructurePool
Aptacluster.EditDistance : 5
Export.compress : true
Parser.backend : AptaplexParser
AptaplexParser.BarcodeTolerance : 1
MapDBAptamerPool.bloomFilterCapacity : 500000000
Export.MinimalClusterSize : 1
MapDBAptamerPool.maxTreeMapCapacity : 1000000
AptaplexParser.PrimerTolerance : 3
AptaplexParser.PairedEndMaxMutations : 5
Export.SequenceFormat : fastq
Aptacluster.KmerCutoffIterations : 10000
MapDBStructurePool.maxTreeMapCapacity : 500000
AptaplexParser.PairedEndMaxScoreValue : 55
AptaplexParser.PairedEndMinOverlap : 15
 

[7:32:09 | INFO | main]: aptasuite.CLI
If you use this software in your research, please cite AptaTRACE as Dao, P., Hoinka, J., Takahashi, M., Zhou, J., Ho, M., Wang, Y., Costa, F., Rossi, J. J., Backofen, R., Burnett, J., Przytycka, T. M. (2016). AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments. Cell Systems, 3(1), 62–70. http://doi.org/10.1016/j.cels.2016.07.003 

[7:32:09 | INFO | main]: aptasuite.CLI
Starting AptaTRACE 

[7:32:09 | INFO | main]: aptasuite.CLI
Loading data from disk 

[7:32:09 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Instantiating MapDBAptamerPool 

[7:32:09 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Searching for existing datasets in /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata 

[7:32:09 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0000.mapdb 

[7:32:20 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0000.mapdb 

[7:32:24 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0000.mapdb 

[7:32:24 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 1000000
Processed in 15.108 seconds. 

[7:32:24 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0001.mapdb 

[7:32:34 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0001.mapdb 

[7:32:39 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0001.mapdb 

[7:32:39 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 2000000
Processed in 14.507 seconds. 

[7:32:39 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0002.mapdb 

[7:32:49 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0002.mapdb 

[7:32:53 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0002.mapdb 

[7:32:53 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 3000000
Processed in 14.607 seconds. 

[7:32:53 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0003.mapdb 

[7:33:04 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0003.mapdb 

[7:33:08 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0003.mapdb 

[7:33:08 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 4000000
Processed in 14.718 seconds. 

[7:33:08 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0004.mapdb 

[7:33:18 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0004.mapdb 

[7:33:22 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0004.mapdb 

[7:33:23 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 5000000
Processed in 14.45 seconds. 

[7:33:23 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0005.mapdb 

[7:33:33 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0005.mapdb 

[7:33:38 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0005.mapdb 

[7:33:38 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 6000000
Processed in 15.111 seconds. 

[7:33:38 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0006.mapdb 

[7:33:48 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0006.mapdb 

[7:33:52 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0006.mapdb 

[7:33:52 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 1000000
Total number of aptamers: 7000000
Processed in 14.601 seconds. 

[7:33:52 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Processing /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/data0007.mapdb 

[7:33:54 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading inverse view from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/inverse_data0007.mapdb 

[7:33:55 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Reading bounds data from /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/pooldata/bounds_data0007.mapdb 

[7:33:55 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
Total number of aptamers in file: 176707
Total number of aptamers: 7176707
Processed in 2.654 seconds. 

[7:33:55 | INFO | main]: lib.aptamer.datastructures.MapDBAptamerPool
Found and loaded a total of 7176707 aptamers from disk. 

[7:33:55 | CONFIG | main]: lib.aptamer.datastructures.MapDBAptamerPool
AptamerPool instantiation took 105.766 seconds 

[7:33:55 | INFO | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle S2R4 

[7:33:55 | CONFIG | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/cycledata/4_S2R4.mapdb' for selection cycle S2R4. 

[7:33:56 | INFO | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle S2iiR6 

[7:33:56 | CONFIG | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/cycledata/6_S2iiR6.mapdb' for selection cycle S2iiR6. 

[7:33:59 | INFO | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle S2iiR6Negative 

[7:33:59 | CONFIG | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/cycledata/6_S2iiR6Negative.mapdb' for selection cycle S2iiR6Negative. 

[7:34:02 | INFO | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle S2iiR8AH 

[7:34:02 | CONFIG | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/cycledata/8_S2iiR8AH.mapdb' for selection cycle S2iiR8AH. 

[7:34:03 | INFO | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Processing selection cycle S2iiR8Negative 

[7:34:03 | CONFIG | main]: lib.aptamer.datastructures.MapDBSelectionCycle
Reading from file '/media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/cycledata/8_S2iiR8Negative.mapdb' for selection cycle S2iiR8Negative. 

[7:34:06 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Instantiating MapDBStructurePool 

[7:34:06 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Searching for existing datasets in /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata 

[7:34:06 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0000.mapdb 

[7:35:19 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0000.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 500000 

[7:35:19 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0001.mapdb 

[7:36:30 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0001.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 1000000 

[7:36:30 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0002.mapdb 

[7:37:43 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0002.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 1500000 

[7:37:43 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0003.mapdb 

[7:38:49 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0003.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 2000000 

[7:38:49 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0004.mapdb 

[7:39:48 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0004.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 2500000 

[7:39:48 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0005.mapdb 

[7:41:00 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0005.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 3000000 

[7:41:00 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0006.mapdb 

[7:42:12 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0006.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 3500000 

[7:42:12 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0007.mapdb 

[7:43:25 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0007.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 4000000 

[7:43:25 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0008.mapdb 

[7:44:36 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0008.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 4500000 

[7:44:36 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0009.mapdb 

[7:45:48 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0009.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 5000000 

[7:45:48 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0010.mapdb 

[7:47:00 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0010.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 5500000 

[7:47:00 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0011.mapdb 

[7:48:13 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0011.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 6000000 

[7:48:13 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0012.mapdb 

[7:49:26 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0012.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 6500000 

[7:49:26 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0013.mapdb 

[7:50:39 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0013.mapdb
Total number of aptamers in file: 500000
Total number of aptamers: 7000000 

[7:50:39 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Processing file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0014.mapdb 

[7:50:48 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded file /media/alex/5CBA3604BA35DB6A/Users/AlexMartin/Documents/UbuntuSequencingFolder/Test/structuredata/data0014.mapdb
Total number of aptamers in file: 176707
Total number of aptamers: 7176707 

[7:50:48 | INFO | main]: lib.aptamer.datastructures.MapDBStructurePool
Found and loaded a total of 7176707 structures on disk. 

[7:50:48 | CONFIG | main]: lib.aptamer.datastructures.MapDBStructurePool
StructurePool instantiation took 1001.602 seconds 

[7:50:48 | INFO | main]: lib.aptatrace.AptaTraceMotif

Reading secondary structures of aptamers from database... 

[7:50:49 | CONFIG | main]: lib.aptatrace.AptaTraceMotif

Warning: aptamers have different lengths!
 

[8:13:11 | INFO | main]: lib.aptatrace.AptaTraceMotif

Clustering significant kmers... 

[8:13:11 | INFO | main]: lib.aptatrace.AptaTraceMotif
There are 87 seeds/clusters. 

[8:13:11 | INFO | main]: lib.aptatrace.AptaTraceMotif

Compute context trace and PWM of each cluster...