E:\AST\HE4>java -Xmx300G -jar aptasuite.jar -cluster -predict structure -trace -export pool,cycles,structures,clusters,clustertables -config E:\AST\HE4\configuration.aptasuite
Reading configuration from file.
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/E:/AST/HE4/lib/ch.qos.logback.logback-classic-1.1.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/E:/AST/HE4/lib/org.slf4j.slf4j-simple-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
20:06:04.402 [main] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false
20:06:04.402 [main] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean'
20:06:04.402 [main] DEBUG o.a.c.b.converters.BooleanConverter -     No conversion required, value is already a Boolean
20:06:04.402 [main] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0
20:06:04.402 [main] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte'
20:06:04.412 [main] DEBUG o.a.c.b.converters.ByteConverter -     Converted to Byte value '0'
20:06:04.412 [main] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
20:06:04.412 [main] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character'
20:06:04.412 [main] DEBUG o.a.c.b.c.CharacterConverter -     No conversion required, value is already a Character
20:06:04.412 [main] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double'
20:06:04.412 [main] DEBUG o.a.c.b.converters.DoubleConverter -     Converted to Double value '0.0'
20:06:04.412 [main] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float'
20:06:04.412 [main] DEBUG o.a.c.b.converters.FloatConverter -     Converted to Float value '0.0'
20:06:04.412 [main] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer'
20:06:04.412 [main] DEBUG o.a.c.b.converters.IntegerConverter -     No conversion required, value is already a Integer
20:06:04.412 [main] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long'
20:06:04.412 [main] DEBUG o.a.c.b.converters.LongConverter -     Converted to Long value '0'
20:06:04.412 [main] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short'
20:06:04.412 [main] DEBUG o.a.c.b.converters.ShortConverter -     Converted to Short value '0'
20:06:04.412 [main] DEBUG o.a.c.b.c.BigDecimalConverter - Setting default value: 0.0
20:06:04.412 [main] DEBUG o.a.c.b.c.BigDecimalConverter - Converting 'BigDecimal' value '0.0' to type 'BigDecimal'
20:06:04.412 [main] DEBUG o.a.c.b.c.BigDecimalConverter -     No conversion required, value is already a BigDecimal
20:06:04.412 [main] DEBUG o.a.c.b.c.BigIntegerConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.c.BigIntegerConverter - Converting 'BigInteger' value '0' to type 'BigInteger'
20:06:04.412 [main] DEBUG o.a.c.b.c.BigIntegerConverter -     No conversion required, value is already a BigInteger
20:06:04.412 [main] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false
20:06:04.412 [main] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean'
20:06:04.412 [main] DEBUG o.a.c.b.converters.BooleanConverter -     No conversion required, value is already a Boolean
20:06:04.412 [main] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte'
20:06:04.412 [main] DEBUG o.a.c.b.converters.ByteConverter -     Converted to Byte value '0'
20:06:04.412 [main] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
20:06:04.412 [main] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character'
20:06:04.412 [main] DEBUG o.a.c.b.c.CharacterConverter -     No conversion required, value is already a Character
20:06:04.412 [main] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double'
20:06:04.412 [main] DEBUG o.a.c.b.converters.DoubleConverter -     Converted to Double value '0.0'
20:06:04.412 [main] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float'
20:06:04.412 [main] DEBUG o.a.c.b.converters.FloatConverter -     Converted to Float value '0.0'
20:06:04.412 [main] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer'
20:06:04.412 [main] DEBUG o.a.c.b.converters.IntegerConverter -     No conversion required, value is already a Integer
20:06:04.412 [main] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long'
20:06:04.412 [main] DEBUG o.a.c.b.converters.LongConverter -     Converted to Long value '0'
20:06:04.412 [main] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0
20:06:04.412 [main] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short'
20:06:04.412 [main] DEBUG o.a.c.b.converters.ShortConverter -     Converted to Short value '0'
20:06:04.422 [main] DEBUG o.a.c.b.converters.StringConverter - Setting default value:
20:06:04.422 [main] DEBUG o.a.c.b.converters.StringConverter - Converting 'String' value '' to type 'String'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Z@56aac163
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'boolean[]' value '[Z@56aac163' to type 'boolean[]'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a boolean[]
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [B@5a1c0542
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'byte[]' value '[B@5a1c0542' to type 'byte[]'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a byte[]
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [C@394e1a0f
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'char[]' value '[C@394e1a0f' to type 'char[]'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a char[]
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [D@1d29cf23
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'double[]' value '[D@1d29cf23' to type 'double[]'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a double[]
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [F@167fdd33
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'float[]' value '[F@167fdd33' to type 'float[]'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a float[]
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [I@4d95d2a2
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'int[]' value '[I@4d95d2a2' to type 'int[]'
20:06:04.422 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a int[]
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [J@3b088d51
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'long[]' value '[J@3b088d51' to type 'long[]'
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a long[]
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [S@74650e52
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'short[]' value '[S@74650e52' to type 'short[]'
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a short[]
20:06:04.432 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigDecimal;@6acdbdf5
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigDecimal[]' value '[Ljava.math.BigDecimal;@6acdbdf5' to type 'BigDecimal[]'
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a BigDecimal[]
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigInteger;@17579e0f
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigInteger[]' value '[Ljava.math.BigInteger;@17579e0f' to type 'BigInteger[]'
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a BigInteger[]
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Boolean;@3712b94
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Boolean[]' value '[Ljava.lang.Boolean;@3712b94' to type 'Boolean[]'
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Boolean[]
20:06:04.442 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Byte;@33f88ab
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Byte[]' value '[Ljava.lang.Byte;@33f88ab' to type 'Byte[]'
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Byte[]
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Character;@2d8f65a4
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Character[]' value '[Ljava.lang.Character;@2d8f65a4' to type 'Character[]'
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Character[]
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Double;@646d64ab
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Double[]' value '[Ljava.lang.Double;@646d64ab' to type 'Double[]'
20:06:04.452 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Double[]
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Float;@536aaa8d
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Float[]' value '[Ljava.lang.Float;@536aaa8d' to type 'Float[]'
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Float[]
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Integer;@1f57539
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Integer[]' value '[Ljava.lang.Integer;@1f57539' to type 'Integer[]'
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Integer[]
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Long;@704a52ec
20:06:04.462 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Long[]' value '[Ljava.lang.Long;@704a52ec' to type 'Long[]'
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Long[]
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Short;@4493d195
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Short[]' value '[Ljava.lang.Short;@4493d195' to type 'Short[]'
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Short[]
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.String;@57e1b0c
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'String[]' value '[Ljava.lang.String;@57e1b0c' to type 'String[]'
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a String[]
20:06:04.472 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Class;@1877ab81
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Class[]' value '[Ljava.lang.Class;@1877ab81' to type 'Class[]'
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Class[]
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Date;@458c1321
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Date[]' value '[Ljava.util.Date;@458c1321' to type 'Date[]'
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Date[]
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Calendar;@34cd072c
20:06:04.482 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Calendar[]' value '[Ljava.util.Calendar;@34cd072c' to type 'Calendar[]'
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Calendar[]
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.io.File;@5faeada1
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.io.File[]' value '[Ljava.io.File;@5faeada1' to type 'java.io.File[]'
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.io.File[]
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Date;@ea1a8d5
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Date[]' value '[Ljava.sql.Date;@ea1a8d5' to type 'java.sql.Date[]'
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Date[]
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Time;@2bbf4b8b
20:06:04.492 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Time[]' value '[Ljava.sql.Time;@2bbf4b8b' to type 'java.sql.Time[]'
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Time[]
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Timestamp;@33c7e1bb
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Timestamp[]' value '[Ljava.sql.Timestamp;@33c7e1bb' to type 'java.sql.Timestamp[]'
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Timestamp[]
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.net.URL;@52feb982
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.net.URL[]' value '[Ljava.net.URL;@52feb982' to type 'java.net.URL[]'
20:06:04.502 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.net.URL[]
20:06:04.532 [main] INFO  o.a.c.b.FluentPropertyBeanIntrospector - Error when creating PropertyDescriptor for public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)! Ignoring this property.
20:06:04.542 [main] DEBUG o.a.c.b.FluentPropertyBeanIntrospector - Exception is:
java.beans.IntrospectionException: bad write method arg count: public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)
        at java.beans.PropertyDescriptor.findPropertyType(Unknown Source) ~[na:1.8.0_231]
        at java.beans.PropertyDescriptor.setWriteMethod(Unknown Source) ~[na:1.8.0_231]
        at java.beans.PropertyDescriptor.<init>(Unknown Source) ~[na:1.8.0_231]
        at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.createFluentPropertyDescritor(FluentPropertyBeanIntrospector.java:178) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.introspect(FluentPropertyBeanIntrospector.java:141) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.fetchIntrospectionData(PropertyUtilsBean.java:2245) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.getIntrospectionData(PropertyUtilsBean.java:2226) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.getPropertyDescriptor(PropertyUtilsBean.java:954) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.isWriteable(PropertyUtilsBean.java:1478) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.configuration2.beanutils.BeanHelper.isPropertyWriteable(BeanHelper.java:521) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.initProperty(BeanHelper.java:357) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.initBeanProperties(BeanHelper.java:273) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.initBean(BeanHelper.java:192) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper$BeanCreationContextImpl.initBean(BeanHelper.java:669) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.initBeanInstance(DefaultBeanFactory.java:162) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.createBean(DefaultBeanFactory.java:116) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:459) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:479) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:492) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResultInstance(BasicConfigurationBuilder.java:447) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResult(BasicConfigurationBuilder.java:417) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.getConfiguration(BasicConfigurationBuilder.java:285) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at utilities.Configuration.setConfiguration(Configuration.java:215) [aptasuite.jar:na]
        at aptasuite.CLI.<init>(CLI.java:104) [aptasuite.jar:na]
        at aptasuite.Aptasuite.main(Aptasuite.java:70) [aptasuite.jar:na]
E:\AST\HE4
Using the following parameters:
Experiment.name : HE4Analysis
Experiment.description : HE4-CE-IPPC-SELEX
Experiment.primer5 : AGCAGCACAGAGGTCAGATG
Experiment.primer3 : CCTATGCGTGCTACCGTGAA
AptaplexParser.randomizedRegionSizeLowerBound : 17
AptaplexParser.randomizedRegionSizeUpperBound : 28
AptaplexParser.isPerFile : true
AptaplexParser.reader : FastqReader
SelectionCycle.name : [HE4-IPPC-AptaLib, HE4-IPPC-CSL, HE4-IPPC-SR1, HE4-IPPC-SR2, HE4-IPPC-SR3, HE4-IPPC-SR4]
SelectionCycle.round : [0, 1, 2, 3, 4, 5]
SelectionCycle.isControlSelection : [True, False, False, False, False, False]
SelectionCycle.isCounterSelection : [False, False, False, False, False, False]
AptaplexParser.forwardFiles : [E:\AST\HE4\HE4_SELEX_FAMLib_S6_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_CSL_S5_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR1_S1_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR2_S2_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR3_S3_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR4_S4_R1_001.fastq.gz]
MapDBAptamerPool.maxTreeMapCapacity : 10000000
Aptatrace.KmerLength : 6
Aptatrace.FilterClusters : True
Aptatrace.OutputClusters : True
Aptatrace.Alpha : 13
Aptacluster.RandomizedRegionSize : 25
Aptacluster.EditDistance : 5
Aptacluster.LSHIterations : 5
Aptacluster.KmerSize : 3
Aptacluster.KmerCutoffIterations : 10000
Export.Cycles : [HE4-IPPC-AptaLib, HE4-IPPC-CSL, HE4-IPPC-SR1, HE4-IPPC-SR2, HE4-IPPC-SR3, HE4-IPPC-SR4]
Export.MinimalClusterSize : 1
Export.ClusterFilterCriteria : ClusterSize
Export.compress : true
Export.SequenceFormat : fastq
Aptacluster.LSHDimension : 18
Performance.maxNumberOfCores : 20
Experiment.projectPath : E:\AST\HE4
AptamerPool.backend : MapDBAptamerPool
Aptasim.AmplificationEfficiency : 0.995
Export.IncludePrimerRegions : true
AptaplexParser.OnlyRandomizedRegionInData : false
AptaplexParser.BlockingQueueSize : 5000
MapDBAptamerPool.bloomFilterCollisionProbability : 0.001
MapDBStructurePool.bloomFilterCollisionProbability : 0.001
StructurePool.backend : MapDBStructurePool
Aptasim.NucleotideDistribution : [0.25, 0.25, 0.25, 0.25]
Aptasim.MinSeedAffinity : 80
AptaplexParser.CheckReverseComplement : false
Aptasim.BaseMutationRates : [0.25, 0.25, 0.25, 0.25]
Aptasim.HmmDegree : 2
Aptasim.MaxSequenceAffinity : 25
Aptasim.SelectionPercentage : 0.2
Aptasim.MutationProbability : 0.05
AptaplexParser.PairedEndMaxScoreValue : 55
AptaplexParser.PairedEndMinOverlap : 15
MapDBSelectionCycle.bloomFilterCollisionProbability : 0.001
Export.PoolCardinalityFormat : frequencies
AptaplexParser.StoreReverseComplement : false
ClusterContainer.backend : MapDBClusterContainer
AptaplexParser.UndeterminedToFile : false
SelectionCycle.backend : MapDBSelectionCycle
Aptasim.NumberOfSeeds : 100
MapDBStructurePool.maxTreeMapCapacityBppm : 150000
Aptasim.NumberOfSequences : 1000000
Parser.backend : AptaplexParser
AptaplexParser.BarcodeTolerance : 1
MapDBAptamerPool.bloomFilterCapacity : 250000000
Aptasim.MaxSequenceCount : 10
AptaplexParser.PrimerTolerance : 3
AptaplexParser.PairedEndMaxMutations : 5
MapDBAllocateStartSize : 1073741824
MapDBAllocateIncrement : 104857600
MapDBStructurePool.maxTreeMapCapacity : 500000
Aptasim.RandomizedRegionSize : 40

Starting Structure Predition
Loading data from disk
Instantiating MapDBAptamerPool
Searching for existing datasets in E:\AST\HE4\pooldata
Found a total of 14 files on disk.
Processing E:\AST\HE4\pooldata\data0000.mapdb
Processing E:\AST\HE4\pooldata\data0001.mapdb
Processing E:\AST\HE4\pooldata\data0002.mapdb
Processing E:\AST\HE4\pooldata\data0003.mapdb
Processing E:\AST\HE4\pooldata\data0004.mapdb
Processing E:\AST\HE4\pooldata\data0005.mapdb
Processing E:\AST\HE4\pooldata\data0006.mapdb
Processing E:\AST\HE4\pooldata\data0007.mapdb
Processing E:\AST\HE4\pooldata\data0008.mapdb
Processing E:\AST\HE4\pooldata\data0009.mapdb
Processing E:\AST\HE4\pooldata\data0010.mapdb
Processing E:\AST\HE4\pooldata\data0011.mapdb
Processing E:\AST\HE4\pooldata\data0012.mapdb
Processing E:\AST\HE4\pooldata\data0013.mapdb
Found and loaded a total of 133551145 aptamers from disk.
Processing selection cycle HE4-IPPC-AptaLib
Processing selection cycle HE4-IPPC-CSL
Processing selection cycle HE4-IPPC-SR1
Processing selection cycle HE4-IPPC-SR2
Processing selection cycle HE4-IPPC-SR3
Processing selection cycle HE4-IPPC-SR4
Loading took 2937681 milliseconds
Instantiating MapDBStructurePool
Starting Structure Prediction using 20 threads:
Predicting...
Completed: 133551145/133551145                                            Structure prediction completed in 949113.121 seconds.

If you use this software in your research, please cite AptaCLUSTER as
Hoinka, J., Berezhnoy, A., Sauna, Z. E., Gilboa, E., & Przytycka, T. M. (2014).
AptaCluster - A method to cluster HT-SELEX aptamer pools and lessons from its application.
In Lecture Notes in Computer Science  (Vol. 8394 LNBI, pp. 115?128). http://doi.org/10.1007/978-3-319-05269-4_9
Starting AptaCluster
Using existing data
Starting AptaCluster
Initiallizing auxilliary datastructures
Finished initialization in 1839.252 seconds
Computing kmer cutoff for cluster generation
Finished cutoff computation in 119.01 seconds. Using cutoff 0.005051113026575192
Starting LSH Iteration 1
Generating LSH Buckets
Processed 95535000/133551145 items
E:\AST\HE4>
E:\AST\HE4>
E:\AST\HE4>^P^P^P^P
'????' is not recognized as an internal or external command,
operable program or batch file.

E:\AST\HE4>
E:\AST\HE4>
E:\AST\HE4>^P
'?' is not recognized as an internal or external command,
operable program or batch file.

E:\AST\HE4>java -Xmx400G -jar aptasuite.jar -cluster -trace -export pool,cycles,structures,clusters,clustertables -config E:\AST\HE4\configuration.aptasuite
Reading configuration from file.
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/E:/AST/HE4/lib/ch.qos.logback.logback-classic-1.1.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/E:/AST/HE4/lib/org.slf4j.slf4j-simple-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
21:19:02.689 [main] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false
21:19:02.729 [main] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean'
21:19:02.729 [main] DEBUG o.a.c.b.converters.BooleanConverter -     No conversion required, value is already a Boolean
21:19:02.739 [main] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0
21:19:02.739 [main] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte'
21:19:02.739 [main] DEBUG o.a.c.b.converters.ByteConverter -     Converted to Byte value '0'
21:19:02.739 [main] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
21:19:02.739 [main] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character'
21:19:02.739 [main] DEBUG o.a.c.b.c.CharacterConverter -     No conversion required, value is already a Character
21:19:02.749 [main] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0
21:19:02.749 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double'
21:19:02.749 [main] DEBUG o.a.c.b.converters.DoubleConverter -     Converted to Double value '0.0'
21:19:02.749 [main] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0
21:19:02.749 [main] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float'
21:19:02.759 [main] DEBUG o.a.c.b.converters.FloatConverter -     Converted to Float value '0.0'
21:19:02.759 [main] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0
21:19:02.759 [main] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer'
21:19:02.759 [main] DEBUG o.a.c.b.converters.IntegerConverter -     No conversion required, value is already a Integer
21:19:02.759 [main] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0
21:19:02.759 [main] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long'
21:19:02.769 [main] DEBUG o.a.c.b.converters.LongConverter -     Converted to Long value '0'
21:19:02.769 [main] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0
21:19:02.769 [main] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short'
21:19:02.769 [main] DEBUG o.a.c.b.converters.ShortConverter -     Converted to Short value '0'
21:19:02.769 [main] DEBUG o.a.c.b.c.BigDecimalConverter - Setting default value: 0.0
21:19:02.769 [main] DEBUG o.a.c.b.c.BigDecimalConverter - Converting 'BigDecimal' value '0.0' to type 'BigDecimal'
21:19:02.779 [main] DEBUG o.a.c.b.c.BigDecimalConverter -     No conversion required, value is already a BigDecimal
21:19:02.779 [main] DEBUG o.a.c.b.c.BigIntegerConverter - Setting default value: 0
21:19:02.779 [main] DEBUG o.a.c.b.c.BigIntegerConverter - Converting 'BigInteger' value '0' to type 'BigInteger'
21:19:02.779 [main] DEBUG o.a.c.b.c.BigIntegerConverter -     No conversion required, value is already a BigInteger
21:19:02.779 [main] DEBUG o.a.c.b.converters.BooleanConverter - Setting default value: false
21:19:02.789 [main] DEBUG o.a.c.b.converters.BooleanConverter - Converting 'Boolean' value 'false' to type 'Boolean'
21:19:02.789 [main] DEBUG o.a.c.b.converters.BooleanConverter -     No conversion required, value is already a Boolean
21:19:02.789 [main] DEBUG o.a.c.b.converters.ByteConverter - Setting default value: 0
21:19:02.789 [main] DEBUG o.a.c.b.converters.ByteConverter - Converting 'Integer' value '0' to type 'Byte'
21:19:02.789 [main] DEBUG o.a.c.b.converters.ByteConverter -     Converted to Byte value '0'
21:19:02.789 [main] DEBUG o.a.c.b.c.CharacterConverter - Setting default value:
21:19:02.799 [main] DEBUG o.a.c.b.c.CharacterConverter - Converting 'Character' value ' ' to type 'Character'
21:19:02.799 [main] DEBUG o.a.c.b.c.CharacterConverter -     No conversion required, value is already a Character
21:19:02.799 [main] DEBUG o.a.c.b.converters.DoubleConverter - Setting default value: 0
21:19:02.799 [main] DEBUG o.a.c.b.converters.DoubleConverter - Converting 'Integer' value '0' to type 'Double'
21:19:02.799 [main] DEBUG o.a.c.b.converters.DoubleConverter -     Converted to Double value '0.0'
21:19:02.799 [main] DEBUG o.a.c.b.converters.FloatConverter - Setting default value: 0
21:19:02.809 [main] DEBUG o.a.c.b.converters.FloatConverter - Converting 'Integer' value '0' to type 'Float'
21:19:02.809 [main] DEBUG o.a.c.b.converters.FloatConverter -     Converted to Float value '0.0'
21:19:02.809 [main] DEBUG o.a.c.b.converters.IntegerConverter - Setting default value: 0
21:19:02.809 [main] DEBUG o.a.c.b.converters.IntegerConverter - Converting 'Integer' value '0' to type 'Integer'
21:19:02.809 [main] DEBUG o.a.c.b.converters.IntegerConverter -     No conversion required, value is already a Integer
21:19:02.809 [main] DEBUG o.a.c.b.converters.LongConverter - Setting default value: 0
21:19:02.819 [main] DEBUG o.a.c.b.converters.LongConverter - Converting 'Integer' value '0' to type 'Long'
21:19:02.819 [main] DEBUG o.a.c.b.converters.LongConverter -     Converted to Long value '0'
21:19:02.819 [main] DEBUG o.a.c.b.converters.ShortConverter - Setting default value: 0
21:19:02.819 [main] DEBUG o.a.c.b.converters.ShortConverter - Converting 'Integer' value '0' to type 'Short'
21:19:02.819 [main] DEBUG o.a.c.b.converters.ShortConverter -     Converted to Short value '0'
21:19:02.829 [main] DEBUG o.a.c.b.converters.StringConverter - Setting default value:
21:19:02.829 [main] DEBUG o.a.c.b.converters.StringConverter - Converting 'String' value '' to type 'String'
21:19:02.849 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Z@56aac163
21:19:02.849 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'boolean[]' value '[Z@56aac163' to type 'boolean[]'
21:19:02.849 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a boolean[]
21:19:02.849 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [B@5a1c0542
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'byte[]' value '[B@5a1c0542' to type 'byte[]'
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a byte[]
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [C@394e1a0f
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'char[]' value '[C@394e1a0f' to type 'char[]'
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a char[]
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [D@1d29cf23
21:19:02.859 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'double[]' value '[D@1d29cf23' to type 'double[]'
21:19:02.869 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a double[]
21:19:02.869 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [F@167fdd33
21:19:02.869 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'float[]' value '[F@167fdd33' to type 'float[]'
21:19:02.869 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a float[]
21:19:02.869 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [I@4d95d2a2
21:19:02.879 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'int[]' value '[I@4d95d2a2' to type 'int[]'
21:19:02.879 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a int[]
21:19:02.879 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [J@3b088d51
21:19:02.879 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'long[]' value '[J@3b088d51' to type 'long[]'
21:19:02.879 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a long[]
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [S@74650e52
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'short[]' value '[S@74650e52' to type 'short[]'
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a short[]
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigDecimal;@6acdbdf5
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigDecimal[]' value '[Ljava.math.BigDecimal;@6acdbdf5' to type 'BigDecimal[]'
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a BigDecimal[]
21:19:02.889 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.math.BigInteger;@17579e0f
21:19:02.899 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'BigInteger[]' value '[Ljava.math.BigInteger;@17579e0f' to type 'BigInteger[]'
21:19:02.899 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a BigInteger[]
21:19:02.899 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Boolean;@3712b94
21:19:02.899 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Boolean[]' value '[Ljava.lang.Boolean;@3712b94' to type 'Boolean[]'
21:19:02.899 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Boolean[]
21:19:02.909 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Byte;@33f88ab
21:19:02.909 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Byte[]' value '[Ljava.lang.Byte;@33f88ab' to type 'Byte[]'
21:19:02.909 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Byte[]
21:19:02.909 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Character;@2d8f65a4
21:19:02.909 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Character[]' value '[Ljava.lang.Character;@2d8f65a4' to type 'Character[]'
21:19:02.909 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Character[]
21:19:02.919 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Double;@646d64ab
21:19:02.919 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Double[]' value '[Ljava.lang.Double;@646d64ab' to type 'Double[]'
21:19:02.919 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Double[]
21:19:02.919 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Float;@536aaa8d
21:19:02.919 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Float[]' value '[Ljava.lang.Float;@536aaa8d' to type 'Float[]'
21:19:02.929 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Float[]
21:19:02.929 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Integer;@1f57539
21:19:02.929 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Integer[]' value '[Ljava.lang.Integer;@1f57539' to type 'Integer[]'
21:19:02.929 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Integer[]
21:19:02.929 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Long;@704a52ec
21:19:02.929 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Long[]' value '[Ljava.lang.Long;@704a52ec' to type 'Long[]'
21:19:02.939 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Long[]
21:19:02.939 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Short;@4493d195
21:19:02.939 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Short[]' value '[Ljava.lang.Short;@4493d195' to type 'Short[]'
21:19:02.939 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Short[]
21:19:02.939 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.String;@57e1b0c
21:19:02.939 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'String[]' value '[Ljava.lang.String;@57e1b0c' to type 'String[]'
21:19:02.949 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a String[]
21:19:02.949 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.lang.Class;@1877ab81
21:19:02.949 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Class[]' value '[Ljava.lang.Class;@1877ab81' to type 'Class[]'
21:19:02.949 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Class[]
21:19:02.949 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Date;@458c1321
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Date[]' value '[Ljava.util.Date;@458c1321' to type 'Date[]'
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Date[]
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.util.Calendar;@34cd072c
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'Calendar[]' value '[Ljava.util.Calendar;@34cd072c' to type 'Calendar[]'
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a Calendar[]
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.io.File;@5faeada1
21:19:02.959 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.io.File[]' value '[Ljava.io.File;@5faeada1' to type 'java.io.File[]'
21:19:02.969 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.io.File[]
21:19:02.969 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Date;@ea1a8d5
21:19:02.969 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Date[]' value '[Ljava.sql.Date;@ea1a8d5' to type 'java.sql.Date[]'
21:19:02.969 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Date[]
21:19:02.969 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Time;@2bbf4b8b
21:19:02.979 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Time[]' value '[Ljava.sql.Time;@2bbf4b8b' to type 'java.sql.Time[]'
21:19:02.979 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Time[]
21:19:02.979 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.sql.Timestamp;@33c7e1bb
21:19:02.979 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.sql.Timestamp[]' value '[Ljava.sql.Timestamp;@33c7e1bb' to type 'java.sql.Timestamp[]'
21:19:02.979 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.sql.Timestamp[]
21:19:02.979 [main] DEBUG o.a.c.b.converters.ArrayConverter - Setting default value: [Ljava.net.URL;@52feb982
21:19:02.989 [main] DEBUG o.a.c.b.converters.ArrayConverter - Converting 'java.net.URL[]' value '[Ljava.net.URL;@52feb982' to type 'java.net.URL[]'
21:19:02.989 [main] DEBUG o.a.c.b.converters.ArrayConverter -     No conversion required, value is already a java.net.URL[]
21:19:03.139 [main] INFO  o.a.c.b.FluentPropertyBeanIntrospector - Error when creating PropertyDescriptor for public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)! Ignoring this property.
21:19:03.149 [main] DEBUG o.a.c.b.FluentPropertyBeanIntrospector - Exception is:
java.beans.IntrospectionException: bad write method arg count: public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)
        at java.beans.PropertyDescriptor.findPropertyType(Unknown Source) ~[na:1.8.0_231]
        at java.beans.PropertyDescriptor.setWriteMethod(Unknown Source) ~[na:1.8.0_231]
        at java.beans.PropertyDescriptor.<init>(Unknown Source) ~[na:1.8.0_231]
        at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.createFluentPropertyDescritor(FluentPropertyBeanIntrospector.java:178) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.FluentPropertyBeanIntrospector.introspect(FluentPropertyBeanIntrospector.java:141) ~[commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.fetchIntrospectionData(PropertyUtilsBean.java:2245) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.getIntrospectionData(PropertyUtilsBean.java:2226) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.getPropertyDescriptor(PropertyUtilsBean.java:954) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.beanutils.PropertyUtilsBean.isWriteable(PropertyUtilsBean.java:1478) [commons-beanutils.commons-beanutils-1.9.3.jar:1.9.3]
        at org.apache.commons.configuration2.beanutils.BeanHelper.isPropertyWriteable(BeanHelper.java:521) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.initProperty(BeanHelper.java:357) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.initBeanProperties(BeanHelper.java:273) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.initBean(BeanHelper.java:192) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper$BeanCreationContextImpl.initBean(BeanHelper.java:669) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.initBeanInstance(DefaultBeanFactory.java:162) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.DefaultBeanFactory.createBean(DefaultBeanFactory.java:116) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:459) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:479) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.beanutils.BeanHelper.createBean(BeanHelper.java:492) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResultInstance(BasicConfigurationBuilder.java:447) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.createResult(BasicConfigurationBuilder.java:417) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at org.apache.commons.configuration2.builder.BasicConfigurationBuilder.getConfiguration(BasicConfigurationBuilder.java:285) [org.apache.commons.commons-configuration2-2.2.jar:2.2]
        at utilities.Configuration.setConfiguration(Configuration.java:215) [aptasuite.jar:na]
        at aptasuite.CLI.<init>(CLI.java:104) [aptasuite.jar:na]
        at aptasuite.Aptasuite.main(Aptasuite.java:70) [aptasuite.jar:na]
E:\AST\HE4
Using the following parameters:
Experiment.name : HE4Analysis
Experiment.description : HE4-CE-IPPC-SELEX
Experiment.primer5 : AGCAGCACAGAGGTCAGATG
Experiment.primer3 : CCTATGCGTGCTACCGTGAA
AptaplexParser.randomizedRegionSizeLowerBound : 17
AptaplexParser.randomizedRegionSizeUpperBound : 28
AptaplexParser.isPerFile : true
AptaplexParser.reader : FastqReader
SelectionCycle.name : [HE4-IPPC-AptaLib, HE4-IPPC-CSL, HE4-IPPC-SR1, HE4-IPPC-SR2, HE4-IPPC-SR3, HE4-IPPC-SR4]
SelectionCycle.round : [0, 1, 2, 3, 4, 5]
SelectionCycle.isControlSelection : [True, False, False, False, False, False]
SelectionCycle.isCounterSelection : [False, False, False, False, False, False]
AptaplexParser.forwardFiles : [E:\AST\HE4\HE4_SELEX_FAMLib_S6_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_CSL_S5_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR1_S1_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR2_S2_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR3_S3_R1_001.fastq.gz, E:\AST\HE4\HE4_SELEX_SR4_S4_R1_001.fastq.gz]
MapDBAptamerPool.maxTreeMapCapacity : 10000000
Aptatrace.KmerLength : 6
Aptatrace.FilterClusters : True
Aptatrace.OutputClusters : True
Aptatrace.Alpha : 13
Aptacluster.RandomizedRegionSize : 25
Aptacluster.EditDistance : 5
Aptacluster.LSHIterations : 5
Aptacluster.KmerSize : 3
Aptacluster.KmerCutoffIterations : 10000
Export.Cycles : [HE4-IPPC-AptaLib, HE4-IPPC-CSL, HE4-IPPC-SR1, HE4-IPPC-SR2, HE4-IPPC-SR3, HE4-IPPC-SR4]
Export.MinimalClusterSize : 1
Export.ClusterFilterCriteria : ClusterSize
Export.compress : true
Export.SequenceFormat : fastq
Aptacluster.LSHDimension : 18
Performance.maxNumberOfCores : 20
Experiment.projectPath : E:\AST\HE4
AptamerPool.backend : MapDBAptamerPool
Aptasim.AmplificationEfficiency : 0.995
Export.IncludePrimerRegions : true
AptaplexParser.OnlyRandomizedRegionInData : false
AptaplexParser.BlockingQueueSize : 5000
MapDBAptamerPool.bloomFilterCollisionProbability : 0.001
MapDBStructurePool.bloomFilterCollisionProbability : 0.001
StructurePool.backend : MapDBStructurePool
Aptasim.NucleotideDistribution : [0.25, 0.25, 0.25, 0.25]
Aptasim.MinSeedAffinity : 80
AptaplexParser.CheckReverseComplement : false
Aptasim.BaseMutationRates : [0.25, 0.25, 0.25, 0.25]
Aptasim.HmmDegree : 2
Aptasim.MaxSequenceAffinity : 25
Aptasim.SelectionPercentage : 0.2
Aptasim.MutationProbability : 0.05
AptaplexParser.PairedEndMaxScoreValue : 55
AptaplexParser.PairedEndMinOverlap : 15
MapDBSelectionCycle.bloomFilterCollisionProbability : 0.001
Export.PoolCardinalityFormat : frequencies
AptaplexParser.StoreReverseComplement : false
ClusterContainer.backend : MapDBClusterContainer
AptaplexParser.UndeterminedToFile : false
SelectionCycle.backend : MapDBSelectionCycle
Aptasim.NumberOfSeeds : 100
MapDBStructurePool.maxTreeMapCapacityBppm : 150000
Aptasim.NumberOfSequences : 1000000
Parser.backend : AptaplexParser
AptaplexParser.BarcodeTolerance : 1
MapDBAptamerPool.bloomFilterCapacity : 250000000
Aptasim.MaxSequenceCount : 10
AptaplexParser.PrimerTolerance : 3
AptaplexParser.PairedEndMaxMutations : 5
MapDBAllocateStartSize : 1073741824
MapDBAllocateIncrement : 104857600
MapDBStructurePool.maxTreeMapCapacity : 500000
Aptasim.RandomizedRegionSize : 40

If you use this software in your research, please cite AptaCLUSTER as
Hoinka, J., Berezhnoy, A., Sauna, Z. E., Gilboa, E., & Przytycka, T. M. (2014).
AptaCluster - A method to cluster HT-SELEX aptamer pools and lessons from its application.
In Lecture Notes in Computer Science  (Vol. 8394 LNBI, pp. 115?128). http://doi.org/10.1007/978-3-319-05269-4_9
Starting AptaCluster
Loading data from disk
Instantiating MapDBAptamerPool
Searching for existing datasets in E:\AST\HE4\pooldata
Found a total of 14 files on disk.
Processing E:\AST\HE4\pooldata\data0000.mapdb
Processing E:\AST\HE4\pooldata\data0001.mapdb
Processing E:\AST\HE4\pooldata\data0002.mapdb
Processing E:\AST\HE4\pooldata\data0003.mapdb
Processing E:\AST\HE4\pooldata\data0004.mapdb
Processing E:\AST\HE4\pooldata\data0005.mapdb
Processing E:\AST\HE4\pooldata\data0006.mapdb
Processing E:\AST\HE4\pooldata\data0007.mapdb
Processing E:\AST\HE4\pooldata\data0008.mapdb
Processing E:\AST\HE4\pooldata\data0009.mapdb
Processing E:\AST\HE4\pooldata\data0010.mapdb
Processing E:\AST\HE4\pooldata\data0011.mapdb
Processing E:\AST\HE4\pooldata\data0012.mapdb
Processing E:\AST\HE4\pooldata\data0013.mapdb
Found and loaded a total of 133551145 aptamers from disk.
Processing selection cycle HE4-IPPC-AptaLib
Processing selection cycle HE4-IPPC-CSL
Processing selection cycle HE4-IPPC-SR1
Processing selection cycle HE4-IPPC-SR2
Processing selection cycle HE4-IPPC-SR3
Processing selection cycle HE4-IPPC-SR4
Loading took 2647403 milliseconds
Starting AptaCluster
Initiallizing auxilliary datastructures
Finished initialization in 199.691 seconds
Computing kmer cutoff for cluster generation
Finished cutoff computation in 11.29 seconds. Using cutoff 0.005051141689421968
Starting LSH Iteration 1
Generating LSH Buckets
Processed 73096000/133551145 items