ATA and DataType.SERIALIZED_BINARY 16:31:32,806 DEBUG DefaultCoreRegistryBuilder:150 - Processing 1 RecordFields for RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,806 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.SERIALIZED_APPLICATION_DATA : RecordField.NUMBER_OF_BYTES 16:31:32,807 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,807 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,807 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,808 INFO DefaultCoreRegistry:472 - Registered RecordType.SERIALIZED_APPLICATION_DATA has EntityType.APPLICATION_DATA has DataType.SERIALIZED_BINARY 16:31:32,808 INFO DefaultCoreRegistry:478 - Registered RecordType.SERIALIZED_APPLICATION_DATA has RecordField.NUMBER_OF_BYTES with FieldType.INTEGER 16:31:32,809 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.DISCRETE_CHARACTER_MATRIX: EntityType.DISCRETE_CHARACTER and DataType.MATRIX 16:31:32,809 DEBUG DefaultCoreRegistryBuilder:150 - Processing 1 RecordFields for RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,810 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.DISCRETE_CHARACTER_MATRIX : RecordField.NUMBER_OF_BYTES 16:31:32,810 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,811 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,811 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,812 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,812 INFO DefaultCoreRegistry:472 - Registered RecordType.DISCRETE_CHARACTER_MATRIX has EntityType.DISCRETE_CHARACTER has DataType.MATRIX 16:31:32,812 INFO DefaultCoreRegistry:478 - Registered RecordType.DISCRETE_CHARACTER_MATRIX has RecordField.NUMBER_OF_BYTES with FieldType.INTEGER 16:31:32,813 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.CONTINUOUS_CHARACTER_MATRIX: EntityType.CONTINUOUS_CHARACTER and DataType.MATRIX 16:31:32,814 DEBUG DefaultCoreRegistryBuilder:150 - Processing 1 RecordFields for RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,814 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.CONTINUOUS_CHARACTER_MATRIX : RecordField.NUMBER_OF_BYTES 16:31:32,815 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,816 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,818 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,820 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,820 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,823 INFO DefaultCoreRegistry:472 - Registered RecordType.CONTINUOUS_CHARACTER_MATRIX has EntityType.CONTINUOUS_CHARACTER has DataType.MATRIX 16:31:32,823 INFO DefaultCoreRegistry:478 - Registered RecordType.CONTINUOUS_CHARACTER_MATRIX has RecordField.NUMBER_OF_BYTES with FieldType.INTEGER 16:31:32,823 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.TAXON_PHYLOGENETIC_TREE: EntityType.TAXON and DataType.PHYLOGENETIC_TREE 16:31:32,824 DEBUG DefaultCoreRegistryBuilder:150 - Processing 1 RecordFields for RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,824 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.TAXON_PHYLOGENETIC_TREE : RecordField.NUMBER_OF_BYTES 16:31:32,825 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,826 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,826 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,826 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,827 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,827 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,827 INFO DefaultCoreRegistry:472 - Registered RecordType.TAXON_PHYLOGENETIC_TREE has EntityType.TAXON has DataType.PHYLOGENETIC_TREE 16:31:32,828 INFO DefaultCoreRegistry:478 - Registered RecordType.TAXON_PHYLOGENETIC_TREE has RecordField.NUMBER_OF_BYTES with FieldType.INTEGER 16:31:32,828 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.MACROMOLECULE_SEQUENCE: EntityType.MACROMOLECULE and DataType.SEQUENCE 16:31:32,829 DEBUG DefaultCoreRegistryBuilder:129 - RecordType.MACROMOLECULE_SEQUENCE has abstract attribute set to true 16:31:32,829 DEBUG DefaultCoreRegistryBuilder:150 - Processing 5 RecordFields for RecordType.MACROMOLECULE_SEQUENCE 16:31:32,829 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE : RecordField.PRIMARY_ID 16:31:32,829 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE : RecordField.ALTERNATIVE_ID 16:31:32,830 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE : RecordField.NAME 16:31:32,830 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE : RecordField.ORGANISM 16:31:32,830 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE : RecordField.VERSION 16:31:32,831 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,831 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,831 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,832 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,832 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,832 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,833 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,833 INFO DefaultCoreRegistry:472 - Registered RecordType.MACROMOLECULE_SEQUENCE has EntityType.MACROMOLECULE has DataType.SEQUENCE is abstract 16:31:32,833 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE has RecordField.ALTERNATIVE_ID with FieldType.STRING 16:31:32,834 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE has RecordField.PRIMARY_ID with FieldType.STRING 16:31:32,834 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE has RecordField.ORGANISM with FieldType.STRING 16:31:32,834 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE has RecordField.NAME with FieldType.STRING 16:31:32,834 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE has RecordField.VERSION with FieldType.STRING 16:31:32,835 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.NUCLEIC_ACID_SEQUENCE: EntityType.NUCLEIC_ACID and DataType.SEQUENCE 16:31:32,835 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.NUCLEIC_ACID_SEQUENCE extends MACROMOLECULE_SEQUENCE 16:31:32,835 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,836 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,836 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,836 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,837 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,837 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,839 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,839 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,840 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,841 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,842 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,842 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,843 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,843 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,843 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,844 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,844 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,844 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,844 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,845 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,845 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,845 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,846 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,846 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,846 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,846 INFO DefaultCoreRegistry:472 - Registered RecordType.NUCLEIC_ACID_SEQUENCE has EntityType.NUCLEIC_ACID has DataType.SEQUENCE extends RecordType.MACROMOLECULE_SEQUENCE 16:31:32,847 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE has RecordField.ALTERNATIVE_ID with FieldType.STRING 16:31:32,847 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE has RecordField.PRIMARY_ID with FieldType.STRING 16:31:32,848 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE has RecordField.ORGANISM with FieldType.STRING 16:31:32,848 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE has RecordField.NAME with FieldType.STRING 16:31:32,848 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE has RecordField.VERSION with FieldType.STRING 16:31:32,848 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_SEQUENCE: EntityType.PROTEIN and DataType.SEQUENCE 16:31:32,849 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_SEQUENCE extends MACROMOLECULE_SEQUENCE 16:31:32,849 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.PROTEIN_SEQUENCE 16:31:32,849 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,850 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,850 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,850 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,850 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,851 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,851 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,851 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,851 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,852 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,852 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,852 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,852 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,853 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,853 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,854 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,854 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,854 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,855 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,855 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,855 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,855 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,855 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,856 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,856 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,856 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,856 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,857 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_SEQUENCE has EntityType.PROTEIN has DataType.SEQUENCE extends RecordType.MACROMOLECULE_SEQUENCE 16:31:32,857 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE has RecordField.ALTERNATIVE_ID with FieldType.STRING 16:31:32,857 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE has RecordField.PRIMARY_ID with FieldType.STRING 16:31:32,858 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE has RecordField.ORGANISM with FieldType.STRING 16:31:32,858 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE has RecordField.NAME with FieldType.STRING 16:31:32,858 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE has RecordField.VERSION with FieldType.STRING 16:31:32,859 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.COMPOUND_STRUCTURE: EntityType.COMPOUND and DataType.STRUCTURE 16:31:32,859 DEBUG DefaultCoreRegistryBuilder:150 - Processing 9 RecordFields for RecordType.COMPOUND_STRUCTURE 16:31:32,859 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.PRIMARY_ID 16:31:32,859 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.TYPE 16:31:32,860 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.RESOLUTION 16:31:32,860 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.NAME 16:31:32,860 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.AUTHOR 16:31:32,860 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.MOLECULE 16:31:32,861 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.ORGANISM 16:31:32,861 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.DEPOSITION_DATE 16:31:32,861 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.COMPOUND_STRUCTURE : RecordField.MODIFICATION_DATE 16:31:32,862 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,862 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,862 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,862 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,863 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,865 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,866 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,866 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,867 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,867 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,867 INFO DefaultCoreRegistry:472 - Registered RecordType.COMPOUND_STRUCTURE has EntityType.COMPOUND has DataType.STRUCTURE 16:31:32,868 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.TYPE with FieldType.STRING 16:31:32,868 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.MOLECULE with FieldType.STRING 16:31:32,869 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.ORGANISM with FieldType.STRING 16:31:32,869 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.AUTHOR with FieldType.STRING 16:31:32,869 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.DEPOSITION_DATE with FieldType.DATE 16:31:32,869 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.PRIMARY_ID with FieldType.STRING 16:31:32,870 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.RESOLUTION with FieldType.FLOAT 16:31:32,870 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.NAME with FieldType.STRING 16:31:32,870 INFO DefaultCoreRegistry:478 - Registered RecordType.COMPOUND_STRUCTURE has RecordField.MODIFICATION_DATE with FieldType.STRING 16:31:32,871 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_STRUCTURE: EntityType.PROTEIN and DataType.STRUCTURE 16:31:32,871 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_STRUCTURE extends COMPOUND_STRUCTURE 16:31:32,871 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.PROTEIN_STRUCTURE 16:31:32,872 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,872 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,872 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,873 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,873 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,873 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,874 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,874 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,874 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,875 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,875 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,875 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,875 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,876 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,876 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,876 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,877 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,877 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,877 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,878 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,878 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,878 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,879 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,879 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,879 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,880 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,880 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,880 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,881 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,881 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,881 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,882 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,882 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,882 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_STRUCTURE has EntityType.PROTEIN has DataType.STRUCTURE extends RecordType.COMPOUND_STRUCTURE 16:31:32,882 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.TYPE with FieldType.STRING 16:31:32,883 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.MOLECULE with FieldType.STRING 16:31:32,883 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.ORGANISM with FieldType.STRING 16:31:32,883 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.AUTHOR with FieldType.STRING 16:31:32,884 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.DEPOSITION_DATE with FieldType.DATE 16:31:32,884 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.PRIMARY_ID with FieldType.STRING 16:31:32,884 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.RESOLUTION with FieldType.FLOAT 16:31:32,885 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.NAME with FieldType.STRING 16:31:32,885 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE has RecordField.MODIFICATION_DATE with FieldType.STRING 16:31:32,885 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.NUCLEIC_ACID_STRUCTURE: EntityType.NUCLEIC_ACID and DataType.STRUCTURE 16:31:32,885 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.NUCLEIC_ACID_STRUCTURE extends COMPOUND_STRUCTURE 16:31:32,886 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,887 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,888 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,888 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,888 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,889 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,889 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,889 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,890 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,890 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,890 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,891 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,891 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,892 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,892 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,892 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,893 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,893 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,893 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,896 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,896 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,896 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,897 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,897 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,898 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,898 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,899 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,899 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,899 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,900 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,900 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,900 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,900 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,901 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,901 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,901 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,902 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,902 INFO DefaultCoreRegistry:472 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has EntityType.NUCLEIC_ACID has DataType.STRUCTURE extends RecordType.COMPOUND_STRUCTURE 16:31:32,902 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.TYPE with FieldType.STRING 16:31:32,903 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.MOLECULE with FieldType.STRING 16:31:32,903 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.ORGANISM with FieldType.STRING 16:31:32,903 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.AUTHOR with FieldType.STRING 16:31:32,904 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.DEPOSITION_DATE with FieldType.DATE 16:31:32,904 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.PRIMARY_ID with FieldType.STRING 16:31:32,906 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.RESOLUTION with FieldType.FLOAT 16:31:32,906 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.NAME with FieldType.STRING 16:31:32,906 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_STRUCTURE has RecordField.MODIFICATION_DATE with FieldType.STRING 16:31:32,907 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.MACROMOLECULE_BLAST_OUTPUT: EntityType.MACROMOLECULE and DataType.BLAST_OUTPUT 16:31:32,907 DEBUG DefaultCoreRegistryBuilder:129 - RecordType.MACROMOLECULE_BLAST_OUTPUT has abstract attribute set to true 16:31:32,907 DEBUG DefaultCoreRegistryBuilder:150 - Processing 10 RecordFields for RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,908 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.DATASET 16:31:32,908 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.PROGRAM 16:31:32,908 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.SCORING_MATRIX 16:31:32,909 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.PROGRAM_VERSION 16:31:32,909 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.NUMBER_OF_HITS 16:31:32,909 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.NUMBER_OF_LETTERS 16:31:32,909 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.NUMBER_OF_SEQUENCES 16:31:32,910 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.GAP_PENALTY 16:31:32,910 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.GAP_EXTENSION_PENALTY 16:31:32,910 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_BLAST_OUTPUT : RecordField.QUERY 16:31:32,911 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,911 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,912 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,912 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,912 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,913 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,913 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,913 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,913 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,914 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,914 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,914 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,915 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,915 INFO DefaultCoreRegistry:472 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has EntityType.MACROMOLECULE has DataType.BLAST_OUTPUT is abstract 16:31:32,915 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.QUERY with FieldType.STRING 16:31:32,915 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.PROGRAM with FieldType.STRING 16:31:32,916 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.NUMBER_OF_SEQUENCES with FieldType.LONG 16:31:32,916 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.GAP_EXTENSION_PENALTY with FieldType.FLOAT 16:31:32,916 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.SCORING_MATRIX with FieldType.STRING 16:31:32,917 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.NUMBER_OF_HITS with FieldType.INTEGER 16:31:32,917 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.PROGRAM_VERSION with FieldType.STRING 16:31:32,917 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.NUMBER_OF_LETTERS with FieldType.LONG 16:31:32,917 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.GAP_PENALTY with FieldType.FLOAT 16:31:32,918 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_BLAST_OUTPUT has RecordField.DATASET with FieldType.DATASET 16:31:32,918 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT: EntityType.NUCLEIC_ACID and DataType.BLAST_OUTPUT 16:31:32,918 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT extends MACROMOLECULE_BLAST_OUTPUT 16:31:32,919 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,919 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,920 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,920 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,920 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,921 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,921 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,921 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,921 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,922 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,923 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,923 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,924 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,925 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,925 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,926 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,926 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,927 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,927 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,927 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,928 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,928 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,929 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,929 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,929 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,929 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,930 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,931 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,931 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,931 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,932 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,932 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,932 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,933 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,933 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,934 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,934 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,934 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,935 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,935 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,935 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,936 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,936 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,936 INFO DefaultCoreRegistry:472 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has EntityType.NUCLEIC_ACID has DataType.BLAST_OUTPUT extends RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,936 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.QUERY with FieldType.STRING 16:31:32,937 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.PROGRAM with FieldType.STRING 16:31:32,937 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.NUMBER_OF_SEQUENCES with FieldType.LONG 16:31:32,937 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.GAP_EXTENSION_PENALTY with FieldType.FLOAT 16:31:32,938 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.SCORING_MATRIX with FieldType.STRING 16:31:32,938 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.NUMBER_OF_HITS with FieldType.INTEGER 16:31:32,938 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.PROGRAM_VERSION with FieldType.STRING 16:31:32,939 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.NUMBER_OF_LETTERS with FieldType.LONG 16:31:32,939 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.GAP_PENALTY with FieldType.FLOAT 16:31:32,939 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT has RecordField.DATASET with FieldType.DATASET 16:31:32,939 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_BLAST_OUTPUT: EntityType.PROTEIN and DataType.BLAST_OUTPUT 16:31:32,940 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_BLAST_OUTPUT extends MACROMOLECULE_BLAST_OUTPUT 16:31:32,940 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,941 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,941 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,941 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,942 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,942 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,942 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,942 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,943 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,943 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,944 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,944 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,944 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,944 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,945 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,945 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,945 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,946 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,946 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,946 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,946 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,947 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,947 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,947 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,947 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,948 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,948 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,948 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,948 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,949 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,952 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,952 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,953 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,953 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,953 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,954 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,954 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,954 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,955 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,955 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,956 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,956 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,956 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,957 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,957 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,957 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,958 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_BLAST_OUTPUT has EntityType.PROTEIN has DataType.BLAST_OUTPUT extends RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,958 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.QUERY with FieldType.STRING 16:31:32,958 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.PROGRAM with FieldType.STRING 16:31:32,959 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.NUMBER_OF_SEQUENCES with FieldType.LONG 16:31:32,959 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.GAP_EXTENSION_PENALTY with FieldType.FLOAT 16:31:32,959 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.SCORING_MATRIX with FieldType.STRING 16:31:32,960 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.NUMBER_OF_HITS with FieldType.INTEGER 16:31:32,960 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.PROGRAM_VERSION with FieldType.STRING 16:31:32,960 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.NUMBER_OF_LETTERS with FieldType.LONG 16:31:32,961 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.GAP_PENALTY with FieldType.FLOAT 16:31:32,961 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_BLAST_OUTPUT has RecordField.DATASET with FieldType.DATASET 16:31:32,961 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.MACROMOLECULE_FASTA_OUTPUT: EntityType.MACROMOLECULE and DataType.FASTA_OUTPUT 16:31:32,962 DEBUG DefaultCoreRegistryBuilder:129 - RecordType.MACROMOLECULE_FASTA_OUTPUT has abstract attribute set to true 16:31:32,962 DEBUG DefaultCoreRegistryBuilder:150 - Processing 7 RecordFields for RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:32,962 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.DATASET 16:31:32,963 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.PROGRAM 16:31:32,963 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.PROGRAM_VERSION 16:31:32,963 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.NUMBER_OF_HITS 16:31:32,963 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.NUMBER_OF_LETTERS 16:31:32,964 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.NUMBER_OF_SEQUENCES 16:31:32,964 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_FASTA_OUTPUT : RecordField.QUERY 16:31:32,965 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,965 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,965 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,966 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,966 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,966 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,966 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,967 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,967 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,967 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,968 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,968 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,968 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,969 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:32,969 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,969 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,970 INFO DefaultCoreRegistry:472 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has EntityType.MACROMOLECULE has DataType.FASTA_OUTPUT is abstract 16:31:32,970 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.QUERY with FieldType.STRING 16:31:32,970 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.PROGRAM with FieldType.STRING 16:31:32,970 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.NUMBER_OF_SEQUENCES with FieldType.LONG 16:31:32,971 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.NUMBER_OF_HITS with FieldType.INTEGER 16:31:32,971 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.PROGRAM_VERSION with FieldType.STRING 16:31:32,971 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.NUMBER_OF_LETTERS with FieldType.LONG 16:31:32,972 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_FASTA_OUTPUT has RecordField.DATASET with FieldType.DATASET 16:31:32,972 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT: EntityType.NUCLEIC_ACID and DataType.FASTA_OUTPUT 16:31:32,972 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT extends MACROMOLECULE_FASTA_OUTPUT 16:31:32,973 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:32,973 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,973 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,974 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,974 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,974 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,975 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,975 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,976 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,976 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,976 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,979 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,980 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,980 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,981 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:32,981 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,982 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:32,982 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,983 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,983 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,984 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,984 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,984 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,984 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,985 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,985 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,986 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,986 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,986 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,986 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,987 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,987 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:32,987 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,988 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:32,988 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,989 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,989 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,989 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,990 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,990 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,990 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,990 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:32,991 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:32,991 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:32,991 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:32,992 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:32,992 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:32,992 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:32,993 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:32,993 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:32,993 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:32,994 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:32,994 INFO DefaultCoreRegistry:472 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has EntityType.NUCLEIC_ACID has DataType.FASTA_OUTPUT extends RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:32,994 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.QUERY with FieldType.STRING 16:31:32,995 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.PROGRAM with FieldType.STRING 16:31:32,995 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.NUMBER_OF_SEQUENCES with FieldType.LONG 16:31:32,995 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.NUMBER_OF_HITS with FieldType.INTEGER 16:31:32,995 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.PROGRAM_VERSION with FieldType.STRING 16:31:32,996 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.NUMBER_OF_LETTERS with FieldType.LONG 16:31:32,996 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT has RecordField.DATASET with FieldType.DATASET 16:31:32,996 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_FASTA_OUTPUT: EntityType.PROTEIN and DataType.FASTA_OUTPUT 16:31:32,997 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_FASTA_OUTPUT extends MACROMOLECULE_FASTA_OUTPUT 16:31:32,997 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.PROTEIN_FASTA_OUTPUT 16:31:32,997 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:32,998 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:32,998 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:32,998 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:32,999 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:32,999 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:32,999 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,000 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,000 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,000 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,000 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,001 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,001 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,001 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,002 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,002 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,002 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,003 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,003 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,003 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,004 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,004 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,004 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,008 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,008 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,009 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,009 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,009 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,010 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,010 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,010 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,011 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,011 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,011 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,011 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,012 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,012 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,012 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,013 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,013 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,013 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,014 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,014 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,014 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,015 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,015 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,015 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,016 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,016 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,016 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,016 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,017 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,017 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,017 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,018 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_FASTA_OUTPUT has EntityType.PROTEIN has DataType.FASTA_OUTPUT extends RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,018 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.QUERY with FieldType.STRING 16:31:33,018 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.PROGRAM with FieldType.STRING 16:31:33,018 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.NUMBER_OF_SEQUENCES with FieldType.LONG 16:31:33,019 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.NUMBER_OF_HITS with FieldType.INTEGER 16:31:33,019 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.PROGRAM_VERSION with FieldType.STRING 16:31:33,019 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.NUMBER_OF_LETTERS with FieldType.LONG 16:31:33,020 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_FASTA_OUTPUT has RecordField.DATASET with FieldType.DATASET 16:31:33,020 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT: EntityType.NUCLEIC_ACID and DataType.SIMILARITY_SEARCH_HIT 16:31:33,020 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT extends NUCLEIC_ACID_SEQUENCE 16:31:33,020 DEBUG DefaultCoreRegistryBuilder:150 - Processing 4 RecordFields for RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,021 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT : RecordField.DATASET 16:31:33,021 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT : RecordField.E_VALUE 16:31:33,022 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT : RecordField.SCORE 16:31:33,022 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT : RecordField.QUERY 16:31:33,023 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,023 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,023 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,024 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,024 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,024 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,024 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,025 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,025 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,026 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,026 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,026 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,027 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,027 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,027 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,028 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,028 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,028 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,029 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,029 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,030 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,030 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,030 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,030 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,031 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,031 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,034 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,034 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,035 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,035 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,035 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,036 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,036 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,036 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,036 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,037 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,038 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,038 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,039 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,039 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,039 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,040 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,040 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,040 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,041 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,041 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,041 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,041 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,042 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,042 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,042 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,043 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,043 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,043 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,043 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,044 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,044 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,044 INFO DefaultCoreRegistry:472 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has EntityType.NUCLEIC_ACID has DataType.SIMILARITY_SEARCH_HIT extends RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,045 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.QUERY with FieldType.STRING 16:31:33,045 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.SCORE with FieldType.FLOAT 16:31:33,045 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.ORGANISM with FieldType.STRING 16:31:33,046 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.E_VALUE with FieldType.DOUBLE 16:31:33,046 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.ALTERNATIVE_ID with FieldType.STRING 16:31:33,046 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.PRIMARY_ID with FieldType.STRING 16:31:33,047 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.NAME with FieldType.STRING 16:31:33,047 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.DATASET with FieldType.DATASET 16:31:33,047 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT has RecordField.VERSION with FieldType.STRING 16:31:33,048 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT: EntityType.PROTEIN and DataType.SIMILARITY_SEARCH_HIT 16:31:33,048 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT extends PROTEIN_SEQUENCE 16:31:33,048 DEBUG DefaultCoreRegistryBuilder:150 - Processing 4 RecordFields for RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,049 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT : RecordField.DATASET 16:31:33,049 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT : RecordField.E_VALUE 16:31:33,049 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT : RecordField.SCORE 16:31:33,049 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT : RecordField.QUERY 16:31:33,051 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,051 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,051 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,051 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,052 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,052 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,052 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,053 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,053 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,053 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,053 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,054 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,054 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,054 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,055 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,055 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,055 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,056 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,056 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,056 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,057 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,057 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,057 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,058 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,058 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,058 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,059 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,059 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,059 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,060 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,060 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,060 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,060 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,061 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,062 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,063 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,063 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,064 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,064 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,065 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,065 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,065 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,066 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,067 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,067 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,067 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,068 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,068 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,068 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,068 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,069 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,069 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,069 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,071 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,072 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,072 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,073 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,073 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,073 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,074 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,074 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has EntityType.PROTEIN has DataType.SIMILARITY_SEARCH_HIT extends RecordType.PROTEIN_SEQUENCE 16:31:33,074 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.QUERY with FieldType.STRING 16:31:33,074 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.SCORE with FieldType.FLOAT 16:31:33,075 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.ORGANISM with FieldType.STRING 16:31:33,075 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.E_VALUE with FieldType.DOUBLE 16:31:33,076 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.ALTERNATIVE_ID with FieldType.STRING 16:31:33,076 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.PRIMARY_ID with FieldType.STRING 16:31:33,076 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.NAME with FieldType.STRING 16:31:33,077 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.DATASET with FieldType.DATASET 16:31:33,077 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SIMILARITY_SEARCH_HIT has RecordField.VERSION with FieldType.STRING 16:31:33,078 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT: EntityType.COMPOUND and DataType.SIMILARITY_SEARCH_HIT 16:31:33,078 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT extends COMPOUND_STRUCTURE 16:31:33,078 DEBUG DefaultCoreRegistryBuilder:150 - Processing 5 RecordFields for RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,079 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT : RecordField.DATASET 16:31:33,079 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT : RecordField.E_VALUE 16:31:33,079 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT : RecordField.SCORE 16:31:33,079 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT : RecordField.CHAIN 16:31:33,080 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT : RecordField.QUERY 16:31:33,081 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,081 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,081 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,082 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,082 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,082 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,083 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,083 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,083 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,084 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,084 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,084 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,085 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,085 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,085 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,085 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,086 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,086 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,086 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,087 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,087 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,087 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,088 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,088 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,088 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,088 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,089 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,089 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,089 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,090 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,090 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,090 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,091 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,091 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,094 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,094 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,095 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,095 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,096 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,096 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,096 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,096 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,097 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,097 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,097 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,098 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,098 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,098 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,098 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,099 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,099 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,099 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,100 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,100 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,100 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,100 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,101 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,101 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,101 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,102 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,102 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,102 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,102 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,103 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has EntityType.COMPOUND has DataType.SIMILARITY_SEARCH_HIT extends RecordType.COMPOUND_STRUCTURE 16:31:33,103 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.QUERY with FieldType.STRING 16:31:33,103 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.TYPE with FieldType.STRING 16:31:33,104 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.MOLECULE with FieldType.STRING 16:31:33,104 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.E_VALUE with FieldType.DOUBLE 16:31:33,104 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.DEPOSITION_DATE with FieldType.DATE 16:31:33,105 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.NAME with FieldType.STRING 16:31:33,105 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.MODIFICATION_DATE with FieldType.STRING 16:31:33,105 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.SCORE with FieldType.FLOAT 16:31:33,105 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.ORGANISM with FieldType.STRING 16:31:33,106 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.CHAIN with FieldType.STRING 16:31:33,106 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.AUTHOR with FieldType.STRING 16:31:33,106 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.PRIMARY_ID with FieldType.STRING 16:31:33,107 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.RESOLUTION with FieldType.FLOAT 16:31:33,107 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT has RecordField.DATASET with FieldType.DATASET 16:31:33,107 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT: EntityType.MACROMOLECULE and DataType.SEQUENCE_ALIGNMENT 16:31:33,108 DEBUG DefaultCoreRegistryBuilder:129 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT has abstract attribute set to true 16:31:33,108 DEBUG DefaultCoreRegistryBuilder:150 - Processing 2 RecordFields for RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,108 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT : RecordField.NUMBER_OF_ALIGNED_SEQUENCES 16:31:33,109 DEBUG DefaultCoreRegistryBuilder:161 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT : RecordField.LENGTH 16:31:33,109 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,109 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,110 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,110 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,110 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,110 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,111 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,111 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,111 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,112 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,112 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,112 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,112 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,113 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,113 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,114 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,114 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,114 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,114 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,115 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,115 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,115 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,116 INFO DefaultCoreRegistry:472 - Registered RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT has EntityType.MACROMOLECULE has DataType.SEQUENCE_ALIGNMENT is abstract 16:31:33,116 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT has RecordField.LENGTH with FieldType.INTEGER 16:31:33,116 INFO DefaultCoreRegistry:478 - Registered RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT has RecordField.NUMBER_OF_ALIGNED_SEQUENCES with FieldType.INTEGER 16:31:33,118 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT: EntityType.PROTEIN and DataType.SEQUENCE_ALIGNMENT 16:31:33,118 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT extends MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,118 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,119 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,119 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,119 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,120 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,120 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,120 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,121 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,121 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,121 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,121 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,122 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,122 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,122 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,123 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,123 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,123 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,123 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,124 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,124 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,124 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,124 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,125 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,125 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,125 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,126 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,126 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,126 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,127 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,127 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,128 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,128 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,128 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,128 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,129 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,129 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,129 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,129 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,130 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,130 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,130 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,130 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,130 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,131 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,131 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,131 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,131 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,132 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,132 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,132 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,133 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,133 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,133 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,133 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,134 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,134 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,134 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,134 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,135 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,135 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,135 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,135 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,136 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,136 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,136 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,136 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,137 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,137 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,137 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,137 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,138 INFO DefaultCoreRegistry:472 - Registered RecordType.PROTEIN_SEQUENCE_ALIGNMENT has EntityType.PROTEIN has DataType.SEQUENCE_ALIGNMENT extends RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,138 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE_ALIGNMENT has RecordField.LENGTH with FieldType.INTEGER 16:31:33,138 INFO DefaultCoreRegistry:478 - Registered RecordType.PROTEIN_SEQUENCE_ALIGNMENT has RecordField.NUMBER_OF_ALIGNED_SEQUENCES with FieldType.INTEGER 16:31:33,141 DEBUG DefaultCoreRegistryBuilder:115 - RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT: EntityType.NUCLEIC_ACID and DataType.SEQUENCE_ALIGNMENT 16:31:33,142 DEBUG DefaultCoreRegistryBuilder:122 - RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT extends MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,142 DEBUG DefaultCoreRegistryBuilder:150 - Processing 0 RecordFields for RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT 16:31:33,144 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,144 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,144 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,145 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,145 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,145 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,146 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,146 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,146 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,147 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,147 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,147 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,147 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,148 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,148 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,148 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,149 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,149 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,149 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,149 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT 16:31:33,150 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,150 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,150 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,151 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,151 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,151 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,152 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,152 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,152 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,152 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,153 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,153 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,153 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,154 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,154 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,154 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,154 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,155 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,155 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,155 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,156 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,156 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,156 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,156 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT 16:31:33,157 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,157 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,157 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,158 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,158 DEBUG DefaultCoreRegistry:220 - getRecordTypes() returns: 16:31:33,158 DEBUG DefaultCoreRegistry:222 - RecordType.DISCRETE_CHARACTER_MATRIX 16:31:33,159 DEBUG DefaultCoreRegistry:222 - RecordType.COMPOUND_STRUCTURE 16:31:33,159 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SIMILARITY_SEARCH_HIT 16:31:33,159 DEBUG DefaultCoreRegistry:222 - RecordType.UNKNOWN 16:31:33,160 DEBUG DefaultCoreRegistry:222 - RecordType.TAXON_PHYLOGENETIC_TREE 16:31:33,160 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE_CHAIN_SIMILARITY_SEARCH_HIT 16:31:33,160 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SIMILARITY_SEARCH_HIT 16:31:33,160 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_BLAST_OUTPUT 16:31:33,161 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_STRUCTURE 16:31:33,161 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,161 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_BLAST_OUTPUT 16:31:33,162 DEBUG DefaultCoreRegistry:222 - RecordType.CONTINUOUS_CHARACTER_MATRIX 16:31:33,162 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_SEQUENCE 16:31:33,162 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE_ALIGNMENT 16:31:33,163 DEBUG DefaultCoreRegistry:222 - RecordType.SERIALIZED_APPLICATION_DATA 16:31:33,163 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_BLAST_OUTPUT 16:31:33,163 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_STRUCTURE 16:31:33,164 DEBUG DefaultCoreRegistry:222 - RecordType.MACROMOLECULE_FASTA_OUTPUT 16:31:33,164 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT 16:31:33,165 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_FASTA_OUTPUT 16:31:33,165 DEBUG DefaultCoreRegistry:222 - RecordType.PROTEIN_SEQUENCE 16:31:33,165 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_FASTA_OUTPUT 16:31:33,167 DEBUG DefaultCoreRegistry:222 - RecordType.NUCLEIC_ACID_SEQUENCE 16:31:33,167 INFO DefaultCoreRegistry:472 - Registered RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT has EntityType.NUCLEIC_ACID has DataType.SEQUENCE_ALIGNMENT extends RecordType.MACROMOLECULE_SEQUENCE_ALIGNMENT 16:31:33,168 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT has RecordField.LENGTH with FieldType.INTEGER 16:31:33,168 INFO DefaultCoreRegistry:478 - Registered RecordType.NUCLEIC_ACID_SEQUENCE_ALIGNMENT has RecordField.NUMBER_OF_ALIGNED_SEQUENCES with FieldType.INTEGER 16:31:33,168 DEBUG DefaultCoreRegistryBuilder:175 - Processing 6 Transformations 16:31:33,173 DEBUG DefaultCoreRegistryBuilder:202 - Registered RecordType.NUCLEIC_ACID_BLAST_OUTPUT transformation to RecordType.class org.ngbw.sdk.core.transformation.BlastOutput2SequenceBlastHitTransformer 16:31:33,174 DEBUG DefaultCoreRegistryBuilder:202 - Registered RecordType.PROTEIN_BLAST_OUTPUT transformation to RecordType.class org.ngbw.sdk.core.transformation.BlastOutput2SequenceBlastHitTransformer 16:31:33,176 DEBUG DefaultCoreRegistryBuilder:202 - Registered RecordType.PROTEIN_BLAST_OUTPUT transformation to RecordType.class org.ngbw.sdk.core.transformation.BlastOutput2StructureBlastHitTransformer 16:31:33,177 DEBUG DefaultCoreRegistryBuilder:202 - Registered RecordType.NUCLEIC_ACID_FASTA_OUTPUT transformation to RecordType.class org.ngbw.sdk.core.transformation.FastaOutput2SequenceFastaHitTransformer 16:31:33,177 DEBUG DefaultCoreRegistryBuilder:202 - Registered RecordType.PROTEIN_FASTA_OUTPUT transformation to RecordType.class org.ngbw.sdk.core.transformation.FastaOutput2SequenceFastaHitTransformer 16:31:33,179 DEBUG DefaultCoreRegistryBuilder:202 - Registered RecordType.PROTEIN_FASTA_OUTPUT transformation to RecordType.class org.ngbw.sdk.core.transformation.FastaOutput2StructureFastaHitTransformer 16:31:33,189 DEBUG DefaultDatasetRegistryBuilder:55 - Processing 1 DataResources 16:31:33,189 DEBUG DefaultDatasetRegistryBuilder:60 - Dispatching DataResource LUCENE_INDEX 16:31:33,189 DEBUG DefaultDatasetRegistryBuilder:96 - Handling node DataResource 16:31:33,206 INFO LuceneDataResourceConfig:48 - JVM host is: 0-19-e3-1-3a-b8.dynamic.ucsd.edu 16:31:33,222 INFO LuceneDataResourceConfig:73 - DATARESOURCE_ID: LUCENE_INDEX 16:31:33,222 INFO LuceneDataResourceConfig:78 - INDEX_ROOT_DIRECTORY: /projects/ngbw_db1/data/databases/lucene/ 16:31:33,222 INFO LuceneDataResourceConfig:319 - setHost:localhost 16:31:33,223 DEBUG LuceneDataResourceConfig:93 - Processing 4 RecordField Mappings 16:31:33,224 INFO LuceneDataResourceConfig:343 - Register index type mapping for PROTEIN_SEQUENCE 16:31:33,224 INFO LuceneDataResourceConfig:345 - VERSION : KEYWORD 16:31:33,225 INFO LuceneDataResourceConfig:345 - ALTERNATIVE_ID : KEYWORD 16:31:33,225 INFO LuceneDataResourceConfig:345 - ORGANISM : TEXT 16:31:33,225 INFO LuceneDataResourceConfig:345 - NAME : TEXT 16:31:33,225 INFO LuceneDataResourceConfig:345 - PRIMARY_ID : ID 16:31:33,226 INFO LuceneDataResourceConfig:343 - Register index type mapping for NUCLEIC_ACID_SEQUENCE 16:31:33,226 INFO LuceneDataResourceConfig:345 - VERSION : KEYWORD 16:31:33,227 INFO LuceneDataResourceConfig:345 - ALTERNATIVE_ID : KEYWORD 16:31:33,227 INFO LuceneDataResourceConfig:345 - ORGANISM : TEXT 16:31:33,227 INFO LuceneDataResourceConfig:345 - NAME : TEXT 16:31:33,228 INFO LuceneDataResourceConfig:345 - PRIMARY_ID : ID 16:31:33,228 INFO LuceneDataResourceConfig:343 - Register index type mapping for PROTEIN_STRUCTURE 16:31:33,228 INFO LuceneDataResourceConfig:345 - TYPE : KEYWORD 16:31:33,229 INFO LuceneDataResourceConfig:345 - ORGANISM : TEXT 16:31:33,229 INFO LuceneDataResourceConfig:345 - MOLECULE : TEXT 16:31:33,229 INFO LuceneDataResourceConfig:345 - AUTHOR : TEXT 16:31:33,230 INFO LuceneDataResourceConfig:345 - RESOLUTION : KEYWORD 16:31:33,230 INFO LuceneDataResourceConfig:345 - NAME : TEXT 16:31:33,230 INFO LuceneDataResourceConfig:345 - MODIFICATION_DATE : TEXT 16:31:33,230 INFO LuceneDataResourceConfig:345 - PRIMARY_ID : ID 16:31:33,233 INFO LuceneDataResourceConfig:345 - DEPOSITION_DATE : DATE 16:31:33,234 INFO LuceneDataResourceConfig:343 - Register index type mapping for NUCLEIC_ACID_STRUCTURE 16:31:33,235 INFO LuceneDataResourceConfig:345 - TYPE : KEYWORD 16:31:33,235 INFO LuceneDataResourceConfig:345 - ORGANISM : TEXT 16:31:33,236 INFO LuceneDataResourceConfig:345 - MOLECULE : TEXT 16:31:33,236 INFO LuceneDataResourceConfig:345 - AUTHOR : TEXT 16:31:33,236 INFO LuceneDataResourceConfig:345 - RESOLUTION : KEYWORD 16:31:33,237 INFO LuceneDataResourceConfig:345 - NAME : TEXT 16:31:33,237 INFO LuceneDataResourceConfig:345 - MODIFICATION_DATE : TEXT 16:31:33,238 INFO LuceneDataResourceConfig:345 - PRIMARY_ID : ID 16:31:33,238 INFO LuceneDataResourceConfig:345 - DEPOSITION_DATE : DATE 16:31:33,238 DEBUG LuceneDataResourceConfig:128 - Processing 4 Filter Patterns 16:31:33,239 INFO LuceneDataResourceConfig:356 - GENBANK start pattern "^LOCUS\s+" end pattern "^\s+/translation=|^ORIGIN" 16:31:33,239 INFO LuceneDataResourceConfig:356 - GENPEPT start pattern "^LOCUS\s+" end pattern "^\s+/translation=|^ORIGIN" 16:31:33,240 INFO LuceneDataResourceConfig:356 - PDB start pattern "^HEADER\s+" end pattern "^(SEQRES)|(SEQADV)|(ATOM)" 16:31:33,240 INFO LuceneDataResourceConfig:356 - UNIPROT start pattern "^ID\s+" end pattern "^CC\s+-+$" 16:31:33,241 DEBUG LuceneDataResourceConfig:145 - Processing 23 Datasets 16:31:33,242 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: PDB : true 16:31:33,242 INFO LuceneDataResourceConfig:260 - index subdirectory: PDB : PDB 16:31:33,243 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: PDBSEQ : false 16:31:33,244 INFO LuceneDataResourceConfig:260 - index subdirectory: PDBSEQ : PDBSEQ 16:31:33,246 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: NDB : true 16:31:33,246 INFO LuceneDataResourceConfig:260 - index subdirectory: NDB : NDB 16:31:33,247 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: SWISSPROT : false 16:31:33,247 INFO LuceneDataResourceConfig:260 - index subdirectory: SWISSPROT : SWISSPROT 16:31:33,247 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: TREMBL : false 16:31:33,248 INFO LuceneDataResourceConfig:260 - index subdirectory: TREMBL : TREMBL 16:31:33,248 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBBCT : true 16:31:33,248 INFO LuceneDataResourceConfig:260 - index subdirectory: GBBCT : GBBCT 16:31:33,249 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBENV : true 16:31:33,249 INFO LuceneDataResourceConfig:260 - index subdirectory: GBENV : GBENV 16:31:33,249 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBEST : true 16:31:33,250 INFO LuceneDataResourceConfig:260 - index subdirectory: GBEST : GBEST 16:31:33,250 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBGSS : true 16:31:33,251 INFO LuceneDataResourceConfig:260 - index subdirectory: GBGSS : GBGSS 16:31:33,251 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBHTC : true 16:31:33,251 INFO LuceneDataResourceConfig:260 - index subdirectory: GBHTC : GBHTC 16:31:33,252 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBHTG : true 16:31:33,252 INFO LuceneDataResourceConfig:260 - index subdirectory: GBHTG : GBHTG 16:31:33,253 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBINV : true 16:31:33,254 INFO LuceneDataResourceConfig:260 - index subdirectory: GBINV : GBINV 16:31:33,254 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBMAM : true 16:31:33,254 INFO LuceneDataResourceConfig:260 - index subdirectory: GBMAM : GBMAM 16:31:33,255 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBPAT : true 16:31:33,255 INFO LuceneDataResourceConfig:260 - index subdirectory: GBPAT : GBPAT 16:31:33,256 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBPHG : true 16:31:33,256 INFO LuceneDataResourceConfig:260 - index subdirectory: GBPHG : GBPHG 16:31:33,257 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBPLN : true 16:31:33,257 INFO LuceneDataResourceConfig:260 - index subdirectory: GBPLN : GBPLN 16:31:33,258 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBPRI : true 16:31:33,258 INFO LuceneDataResourceConfig:260 - index subdirectory: GBPRI : GBPRI 16:31:33,258 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBROD : true 16:31:33,259 INFO LuceneDataResourceConfig:260 - index subdirectory: GBROD : GBROD 16:31:33,259 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBSTS : true 16:31:33,260 INFO LuceneDataResourceConfig:260 - index subdirectory: GBSTS : GBSTS 16:31:33,260 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBSYN : true 16:31:33,261 INFO LuceneDataResourceConfig:260 - index subdirectory: GBSYN : GBSYN 16:31:33,261 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBUNA : true 16:31:33,262 INFO LuceneDataResourceConfig:260 - index subdirectory: GBUNA : GBUNA 16:31:33,263 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBVRL : true 16:31:33,263 INFO LuceneDataResourceConfig:260 - index subdirectory: GBVRL : GBVRL 16:31:33,264 INFO LuceneDataResourceConfig:250 - setMultipleFilesFlag: GBVRT : true 16:31:33,264 INFO LuceneDataResourceConfig:260 - index subdirectory: GBVRT : GBVRT 16:31:33,264 DEBUG DefaultDatasetRegistryBuilder:108 - Registered DataResource LUCENE_INDEX 16:31:33,265 DEBUG DefaultDatasetRegistryBuilder:66 - Processing 5 SourceDocumentTypes 16:31:33,265 DEBUG DefaultDatasetRegistryBuilder:73 - SourceDocumentType GENBANK: EntityType.NUCLEIC_ACID | DataType.SEQUENCE | DataFormat.GENBANK 16:31:33,266 DEBUG DefaultDatasetRegistryBuilder:73 - SourceDocumentType UNIPROT: EntityType.PROTEIN | DataType.SEQUENCE | DataFormat.UNIPROT 16:31:33,266 DEBUG DefaultDatasetRegistryBuilder:73 - SourceDocumentType PDB: EntityType.PROTEIN | DataType.STRUCTURE | DataFormat.PDB 16:31:33,266 DEBUG DefaultDatasetRegistryBuilder:73 - SourceDocumentType PDBSEQ: EntityType.PROTEIN | DataType.SEQUENCE | DataFormat.PDB_FINDER 16:31:33,267 DEBUG DefaultDatasetRegistryBuilder:73 - SourceDocumentType NDB: EntityType.NUCLEIC_ACID | DataType.STRUCTURE | DataFormat.PDB 16:31:33,267 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset PDB 16:31:33,267 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,267 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: PDB 16:31:33,268 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: The Protein Data Bank 16:31:33,269 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: PDB 16:31:33,269 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: The Protein Data Bank 16:31:33,269 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset PDBSEQ 16:31:33,269 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,270 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: PDBSEQ 16:31:33,270 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: The Protein Data Bank - Sequences 16:31:33,270 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: PDBSEQ 16:31:33,270 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: The Protein Data Bank - Sequences 16:31:33,271 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset NDB 16:31:33,271 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,271 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: NDB 16:31:33,271 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: The Nucleotide Data Bank 16:31:33,272 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: NDB 16:31:33,272 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: The Nucleotide Data Bank 16:31:33,272 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset SWISSPROT 16:31:33,272 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,273 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: SWISSPROT 16:31:33,273 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: The Universal Protein Resource - Swissprot 16:31:33,274 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: UNIPROT 16:31:33,274 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: The Universal Protein Resource - Swissprot 16:31:33,274 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset TREMBL 16:31:33,274 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,275 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: TREMBL 16:31:33,275 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: The Universal Protein Resource - Trembl 16:31:33,275 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: UNIPROT 16:31:33,276 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: The Universal Protein Resource - Trembl 16:31:33,276 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBBCT 16:31:33,276 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,276 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBBCT 16:31:33,277 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Bacterial Sequences 16:31:33,277 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,277 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Bacterial Sequences 16:31:33,277 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBENV 16:31:33,277 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,278 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBENV 16:31:33,278 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Environmental Sampling Sequences 16:31:33,278 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,278 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Environmental Sampling Sequences 16:31:33,279 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBEST 16:31:33,279 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,279 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBEST 16:31:33,279 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank EST Sequences 16:31:33,280 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,280 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank EST Sequences 16:31:33,281 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBGSS 16:31:33,281 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,282 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBGSS 16:31:33,282 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Genome Survey Sequences 16:31:33,282 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,282 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Genome Survey Sequences 16:31:33,283 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBHTC 16:31:33,283 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,283 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBHTC 16:31:33,283 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank High Throughput cDNA Sequences 16:31:33,284 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,284 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank High Throughput cDNA Sequences 16:31:33,284 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBHTG 16:31:33,284 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,285 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBHTG 16:31:33,285 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank High Throughput Genomic Sequencing 16:31:33,285 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,285 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank High Throughput Genomic Sequencing 16:31:33,286 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBINV 16:31:33,286 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,286 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBINV 16:31:33,289 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Invertebrate Sequences 16:31:33,289 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,290 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Invertebrate Sequences 16:31:33,291 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBMAM 16:31:33,291 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,291 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBMAM 16:31:33,292 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Other Mammalian Sequences 16:31:33,292 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,292 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Other Mammalian Sequences 16:31:33,293 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBPAT 16:31:33,293 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,293 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBPAT 16:31:33,293 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Patent Sequences 16:31:33,294 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,294 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Patent Sequences 16:31:33,294 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBPHG 16:31:33,295 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,295 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBPHG 16:31:33,296 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Phage Sequences 16:31:33,296 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,296 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Phage Sequences 16:31:33,297 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBPLN 16:31:33,297 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,297 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBPLN 16:31:33,297 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Plant Sequences 16:31:33,298 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,298 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Plant Sequences 16:31:33,298 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBPRI 16:31:33,299 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,299 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBPRI 16:31:33,299 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Primate Sequences 16:31:33,299 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,300 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Primate Sequences 16:31:33,300 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBROD 16:31:33,300 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,301 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBROD 16:31:33,301 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Rodent Sequences 16:31:33,301 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,301 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Rodent Sequences 16:31:33,302 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBSTS 16:31:33,302 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,303 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBSTS 16:31:33,303 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Sequence Tagged Site Entries 16:31:33,303 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,303 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Sequence Tagged Site Entries 16:31:33,304 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBSYN 16:31:33,304 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,304 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBSYN 16:31:33,305 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Synthetic Sequences 16:31:33,305 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,305 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Synthetic Sequences 16:31:33,305 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBUNA 16:31:33,306 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,306 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBUNA 16:31:33,306 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Unannotated Sequences 16:31:33,307 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,307 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Unannotated Sequences 16:31:33,307 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBVRL 16:31:33,307 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,308 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBVRL 16:31:33,308 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Viral Sequences 16:31:33,308 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,309 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Viral Sequences 16:31:33,309 DEBUG DefaultDatasetRegistryBuilder:86 - Dispatching Dataset GBVRT 16:31:33,309 DEBUG DefaultDatasetRegistryBuilder:114 - Handling node Dataset 16:31:33,310 DEBUG DefaultDatasetRegistryBuilder:119 - Dataset: GBVRT 16:31:33,310 DEBUG DefaultDatasetRegistryBuilder:124 - Dataset name: GenBank Other Vertebrate Sequences 16:31:33,310 DEBUG DefaultDatasetRegistryBuilder:129 - Dataset sourceDocumentType attribute: GENBANK 16:31:33,311 DEBUG DefaultDatasetRegistryBuilder:137 - Dataset dataResource: GenBank Other Vertebrate Sequences 16:31:33,314 DEBUG Configuration:102 - ExtraTools is tool/.*-reg\.xml 16:31:33,372 DEBUG DefaultToolRegistryBuilder:93 - Processing 4 ToolResources 16:31:33,373 DEBUG DefaultToolRegistryBuilder:98 - Dispatching ToolResource SNOOKER 16:31:33,373 DEBUG DefaultToolRegistryBuilder:122 - Handling node ToolResource 16:31:33,373 DEBUG DefaultToolRegistryBuilder:135 - Set parameter host = snooker 16:31:33,373 DEBUG DefaultToolRegistryBuilder:135 - Set parameter workspace = /fs/swami-ws/ 16:31:33,374 DEBUG DefaultToolRegistryBuilder:135 - Set parameter blastdb = /isilon/ngbw/FASTA/ 16:31:33,384 DEBUG SSLConnectionManager:36 - poolName: 8ball 16:31:33,384 DEBUG SSLConnectionManager:46 - host: 8ball.sdsc.edu 16:31:33,384 DEBUG SSLConnectionManager:47 - username: bwbatch 16:31:33,385 DEBUG SSLConnectionManager:48 - minconn: 0 16:31:33,385 DEBUG SSLConnectionManager:49 - maxconn: 0 16:31:33,389 INFO SSLConnectionPool:127 - Initializing pool with 0 connection for bwbatch@8ball.sdsc.edu 16:31:33,389 INFO SSLConnectionManager:107 - Initialized pool for bwbatch@8ball.sdsc.edu 16:31:33,389 DEBUG SSLConnectionManager:36 - poolName: snooker 16:31:33,390 DEBUG SSLConnectionManager:46 - host: snooker.sdsc.edu 16:31:33,390 DEBUG SSLConnectionManager:47 - username: bwbatch 16:31:33,390 DEBUG SSLConnectionManager:48 - minconn: 0 16:31:33,391 DEBUG SSLConnectionManager:49 - maxconn: 0 16:31:33,391 INFO SSLConnectionPool:127 - Initializing pool with 0 connection for bwbatch@snooker.sdsc.edu 16:31:33,391 INFO SSLConnectionManager:107 - Initialized pool for bwbatch@snooker.sdsc.edu 16:31:33,392 DEBUG DefaultToolRegistryBuilder:307 - FileHandler set to org.ngbw.sdk.tool.SFTPFileHandler 16:31:33,396 DEBUG DefaultToolRegistryBuilder:296 - ProcessWorker set to org.ngbw.sdk.tool.SSHProcessWorker 16:31:33,396 DEBUG DefaultToolRegistryBuilder:141 - registerToolResource SNOOKER = org.ngbw.sdk.tool.DefaultToolResource@2bfdff 16:31:33,397 DEBUG DefaultToolRegistryBuilder:98 - Dispatching ToolResource 8BALL 16:31:33,397 DEBUG DefaultToolRegistryBuilder:122 - Handling node ToolResource 16:31:33,397 DEBUG DefaultToolRegistryBuilder:135 - Set parameter host = 8ball 16:31:33,398 DEBUG DefaultToolRegistryBuilder:135 - Set parameter workspace = /fs/swami-ws/ 16:31:33,398 DEBUG DefaultToolRegistryBuilder:135 - Set parameter blastdb = /isilon/ngbw/FASTA/ 16:31:33,398 DEBUG DefaultToolRegistryBuilder:307 - FileHandler set to org.ngbw.sdk.tool.SFTPFileHandler 16:31:33,398 DEBUG DefaultToolRegistryBuilder:296 - ProcessWorker set to org.ngbw.sdk.tool.SSHProcessWorker 16:31:33,399 DEBUG DefaultToolRegistryBuilder:141 - registerToolResource 8BALL = org.ngbw.sdk.tool.DefaultToolResource@309f9f 16:31:33,399 DEBUG DefaultToolRegistryBuilder:98 - Dispatching ToolResource CIPRES_CLUSTER 16:31:33,399 DEBUG DefaultToolRegistryBuilder:122 - Handling node ToolResource 16:31:33,399 DEBUG DefaultToolRegistryBuilder:135 - Set parameter host = cipres1 16:31:33,400 DEBUG DefaultToolRegistryBuilder:135 - Set parameter workspace = /projects/cipres/w30548/swami-ws/ 16:31:33,400 DEBUG DefaultToolRegistryBuilder:135 - Set parameter blastdb = /isilon/ngbw/FASTA/ 16:31:33,400 DEBUG DefaultToolRegistryBuilder:135 - Set parameter rc = /projects/cipres/ngbw/contrib/scripts/workbench_cluster.rc 16:31:33,402 DEBUG DefaultToolRegistryBuilder:307 - FileHandler set to org.ngbw.sdk.tool.LocalFileHandler 16:31:33,405 DEBUG DefaultToolRegistryBuilder:296 - ProcessWorker set to org.ngbw.sdk.tool.DrmaaProcessWorker 16:31:33,405 DEBUG DefaultToolRegistryBuilder:141 - registerToolResource CIPRES_CLUSTER = org.ngbw.sdk.tool.DefaultToolResource@a9876e 16:31:33,405 DEBUG DefaultToolRegistryBuilder:98 - Dispatching ToolResource LOCALHOST 16:31:33,406 DEBUG DefaultToolRegistryBuilder:122 - Handling node ToolResource 16:31:33,406 DEBUG DefaultToolRegistryBuilder:135 - Set parameter workspace = /fs/swami-ws/ 16:31:33,406 DEBUG DefaultToolRegistryBuilder:307 - FileHandler set to org.ngbw.sdk.tool.LocalFileHandler 16:31:33,410 DEBUG DefaultToolRegistryBuilder:296 - ProcessWorker set to org.ngbw.sdk.tool.LocalProcessWorker 16:31:33,412 DEBUG DefaultToolRegistryBuilder:141 - registerToolResource LOCALHOST = org.ngbw.sdk.tool.DefaultToolResource@706eb7 16:31:33,412 DEBUG DefaultToolRegistryBuilder:104 - Processing 2 ToolGroups 16:31:33,412 DEBUG DefaultToolRegistryBuilder:114 - Dispatching ToolGroup WEB 16:31:33,413 DEBUG DefaultToolRegistryBuilder:183 - Processing 79 Tools 16:31:33,413 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FORMATVALIDATOR to group: WEB 16:31:33,413 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FORMATVALIDATOR 16:31:33,414 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,414 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FORMATVALIDATOR 16:31:33,416 DEBUG DefaultToolRegistryBuilder:239 - FORMATVALIDATOR Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,416 DEBUG DefaultToolRegistryBuilder:264 - FORMATVALIDATOR Tool Name Check matrix format in Nexus, Phylip, and Fasta 16:31:33,417 DEBUG DefaultToolRegistryBuilder:266 - FORMATVALIDATOR toolResourceId 8BALL 16:31:33,417 DEBUG DefaultToolRegistryBuilder:268 - FORMATVALIDATOR inputParameters 1 16:31:33,417 DEBUG DefaultToolRegistryBuilder:270 - FORMATVALIDATOR outputParameters 0 16:31:33,418 DEBUG DefaultToolRegistryBuilder:271 - FORMATVALIDATOR configfile pisexml/formatvalidator.xml 16:31:33,418 DEBUG DefaultToolRegistryBuilder:275 - FORMATVALIDATOR configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/formatvalidator.xml 16:31:33,419 DEBUG DefaultToolRegistryBuilder:279 - FORMATVALIDATOR commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,420 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: GARLI to group: WEB 16:31:33,420 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool GARLI 16:31:33,420 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,421 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool GARLI 16:31:33,421 DEBUG DefaultToolRegistryBuilder:239 - GARLI Input parameter infile_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE_ALIGNMENT:UNKNOWN 16:31:33,422 DEBUG DefaultToolRegistryBuilder:264 - GARLI Tool Name Genetic algorithm, maximum likelihood inference for large datasets 16:31:33,422 DEBUG DefaultToolRegistryBuilder:266 - GARLI toolResourceId CIPRES_CLUSTER 16:31:33,423 DEBUG DefaultToolRegistryBuilder:268 - GARLI inputParameters 1 16:31:33,423 DEBUG DefaultToolRegistryBuilder:270 - GARLI outputParameters 0 16:31:33,423 DEBUG DefaultToolRegistryBuilder:271 - GARLI configfile pisexml/garli.xml 16:31:33,424 DEBUG DefaultToolRegistryBuilder:275 - GARLI configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/garli.xml 16:31:33,424 DEBUG DefaultToolRegistryBuilder:279 - GARLI commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,425 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MAFFT to group: WEB 16:31:33,425 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MAFFT 16:31:33,425 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,425 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MAFFT 16:31:33,426 DEBUG DefaultToolRegistryBuilder:239 - MAFFT Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,426 DEBUG DefaultToolRegistryBuilder:264 - MAFFT Tool Name Multiple sequence alignment based on fast Fourier transform 16:31:33,426 DEBUG DefaultToolRegistryBuilder:266 - MAFFT toolResourceId CIPRES_CLUSTER 16:31:33,426 DEBUG DefaultToolRegistryBuilder:268 - MAFFT inputParameters 1 16:31:33,427 DEBUG DefaultToolRegistryBuilder:270 - MAFFT outputParameters 0 16:31:33,427 DEBUG DefaultToolRegistryBuilder:271 - MAFFT configfile pisexml/mafft.xml 16:31:33,428 DEBUG DefaultToolRegistryBuilder:275 - MAFFT configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/mafft.xml 16:31:33,428 DEBUG DefaultToolRegistryBuilder:279 - MAFFT commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,428 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MRBAYES to group: WEB 16:31:33,429 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MRBAYES 16:31:33,429 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,430 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MRBAYES 16:31:33,430 DEBUG DefaultToolRegistryBuilder:239 - MRBAYES Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,430 DEBUG DefaultToolRegistryBuilder:264 - MRBAYES Tool Name Tree Inference Using Bayesian Analysis 16:31:33,430 DEBUG DefaultToolRegistryBuilder:266 - MRBAYES toolResourceId CIPRES_CLUSTER 16:31:33,431 DEBUG DefaultToolRegistryBuilder:268 - MRBAYES inputParameters 1 16:31:33,431 DEBUG DefaultToolRegistryBuilder:270 - MRBAYES outputParameters 0 16:31:33,431 DEBUG DefaultToolRegistryBuilder:271 - MRBAYES configfile pisexml/mrbayes.xml 16:31:33,431 DEBUG DefaultToolRegistryBuilder:275 - MRBAYES configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/mrbayes.xml 16:31:33,432 DEBUG DefaultToolRegistryBuilder:279 - MRBAYES commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,432 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MUSCLE to group: WEB 16:31:33,432 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MUSCLE 16:31:33,432 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,433 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MUSCLE 16:31:33,433 DEBUG DefaultToolRegistryBuilder:239 - MUSCLE Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,433 DEBUG DefaultToolRegistryBuilder:264 - MUSCLE Tool Name Create Multiple Alignments from Sequences or Profiles 16:31:33,433 DEBUG DefaultToolRegistryBuilder:266 - MUSCLE toolResourceId CIPRES_CLUSTER 16:31:33,434 DEBUG DefaultToolRegistryBuilder:268 - MUSCLE inputParameters 1 16:31:33,434 DEBUG DefaultToolRegistryBuilder:270 - MUSCLE outputParameters 0 16:31:33,434 DEBUG DefaultToolRegistryBuilder:271 - MUSCLE configfile pisexml/muscle.xml 16:31:33,434 DEBUG DefaultToolRegistryBuilder:275 - MUSCLE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/muscle.xml 16:31:33,435 DEBUG DefaultToolRegistryBuilder:279 - MUSCLE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,435 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PAUP to group: WEB 16:31:33,435 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PAUP 16:31:33,435 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,436 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PAUP 16:31:33,436 DEBUG DefaultToolRegistryBuilder:239 - PAUP Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,436 DEBUG DefaultToolRegistryBuilder:264 - PAUP Tool Name paup 16:31:33,436 DEBUG DefaultToolRegistryBuilder:266 - PAUP toolResourceId 8BALL 16:31:33,436 DEBUG DefaultToolRegistryBuilder:268 - PAUP inputParameters 1 16:31:33,437 DEBUG DefaultToolRegistryBuilder:270 - PAUP outputParameters 0 16:31:33,437 DEBUG DefaultToolRegistryBuilder:271 - PAUP configfile pisexml/paup.xml 16:31:33,438 DEBUG DefaultToolRegistryBuilder:275 - PAUP configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/paup.xml 16:31:33,440 DEBUG DefaultToolRegistryBuilder:279 - PAUP commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,440 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: POY to group: WEB 16:31:33,442 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool POY 16:31:33,443 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,443 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool POY 16:31:33,443 DEBUG DefaultToolRegistryBuilder:239 - POY Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,444 DEBUG DefaultToolRegistryBuilder:264 - POY Tool Name poy 16:31:33,444 DEBUG DefaultToolRegistryBuilder:266 - POY toolResourceId 8BALL 16:31:33,445 DEBUG DefaultToolRegistryBuilder:268 - POY inputParameters 1 16:31:33,445 DEBUG DefaultToolRegistryBuilder:270 - POY outputParameters 0 16:31:33,445 DEBUG DefaultToolRegistryBuilder:271 - POY configfile pisexml/poy.xml 16:31:33,447 DEBUG DefaultToolRegistryBuilder:275 - POY configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/poy.xml 16:31:33,447 DEBUG DefaultToolRegistryBuilder:279 - POY commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,447 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PROBALIGN to group: WEB 16:31:33,447 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PROBALIGN 16:31:33,448 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,448 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PROBALIGN 16:31:33,448 DEBUG DefaultToolRegistryBuilder:239 - PROBALIGN Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:SEQUENCE:FASTA 16:31:33,449 DEBUG DefaultToolRegistryBuilder:264 - PROBALIGN Tool Name Create Multiple Alignments from Nucleic Acid or Protein Sequences 16:31:33,449 DEBUG DefaultToolRegistryBuilder:266 - PROBALIGN toolResourceId 8BALL 16:31:33,449 DEBUG DefaultToolRegistryBuilder:268 - PROBALIGN inputParameters 1 16:31:33,450 DEBUG DefaultToolRegistryBuilder:270 - PROBALIGN outputParameters 0 16:31:33,450 DEBUG DefaultToolRegistryBuilder:271 - PROBALIGN configfile pisexml/probalign.xml 16:31:33,450 DEBUG DefaultToolRegistryBuilder:275 - PROBALIGN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/probalign.xml 16:31:33,451 DEBUG DefaultToolRegistryBuilder:279 - PROBALIGN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,451 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: RAXMLHPC to group: WEB 16:31:33,451 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool RAXMLHPC 16:31:33,451 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,452 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool RAXMLHPC 16:31:33,452 DEBUG DefaultToolRegistryBuilder:239 - RAXMLHPC Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:SEQUENCE_ALIGNMENT:PHYLIP 16:31:33,452 DEBUG DefaultToolRegistryBuilder:264 - RAXMLHPC Tool Name raxml with rapid bootstrapping 16:31:33,453 DEBUG DefaultToolRegistryBuilder:266 - RAXMLHPC toolResourceId CIPRES_CLUSTER 16:31:33,453 DEBUG DefaultToolRegistryBuilder:268 - RAXMLHPC inputParameters 1 16:31:33,453 DEBUG DefaultToolRegistryBuilder:270 - RAXMLHPC outputParameters 0 16:31:33,454 DEBUG DefaultToolRegistryBuilder:271 - RAXMLHPC configfile pisexml/raxmlhpc.xml 16:31:33,454 DEBUG DefaultToolRegistryBuilder:275 - RAXMLHPC configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/raxmlhpc.xml 16:31:33,454 DEBUG DefaultToolRegistryBuilder:279 - RAXMLHPC commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,455 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: RID3PAUP to group: WEB 16:31:33,455 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool RID3PAUP 16:31:33,455 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,455 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool RID3PAUP 16:31:33,456 DEBUG DefaultToolRegistryBuilder:239 - RID3PAUP Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,456 DEBUG DefaultToolRegistryBuilder:264 - RID3PAUP Tool Name rid3paup 16:31:33,456 DEBUG DefaultToolRegistryBuilder:266 - RID3PAUP toolResourceId 8BALL 16:31:33,457 DEBUG DefaultToolRegistryBuilder:268 - RID3PAUP inputParameters 1 16:31:33,457 DEBUG DefaultToolRegistryBuilder:270 - RID3PAUP outputParameters 0 16:31:33,457 DEBUG DefaultToolRegistryBuilder:271 - RID3PAUP configfile pisexml/rid3paup.xml 16:31:33,458 DEBUG DefaultToolRegistryBuilder:275 - RID3PAUP configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/rid3paup.xml 16:31:33,458 DEBUG DefaultToolRegistryBuilder:279 - RID3PAUP commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,458 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: RID3RAXML to group: WEB 16:31:33,459 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool RID3RAXML 16:31:33,459 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,459 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool RID3RAXML 16:31:33,460 DEBUG DefaultToolRegistryBuilder:239 - RID3RAXML Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,460 DEBUG DefaultToolRegistryBuilder:264 - RID3RAXML Tool Name rid3raxml 16:31:33,460 DEBUG DefaultToolRegistryBuilder:266 - RID3RAXML toolResourceId 8BALL 16:31:33,460 DEBUG DefaultToolRegistryBuilder:268 - RID3RAXML inputParameters 1 16:31:33,461 DEBUG DefaultToolRegistryBuilder:270 - RID3RAXML outputParameters 0 16:31:33,461 DEBUG DefaultToolRegistryBuilder:271 - RID3RAXML configfile pisexml/rid3raxml.xml 16:31:33,461 DEBUG DefaultToolRegistryBuilder:275 - RID3RAXML configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/rid3raxml.xml 16:31:33,462 DEBUG DefaultToolRegistryBuilder:279 - RID3RAXML commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,462 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: ALIGN to group: WEB 16:31:33,462 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool ALIGN 16:31:33,463 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,464 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool ALIGN 16:31:33,464 DEBUG DefaultToolRegistryBuilder:239 - ALIGN Input parameter query1_ mapped to sourceDocumentType: UNKNOWN:SEQUENCE:FASTA 16:31:33,464 DEBUG DefaultToolRegistryBuilder:261 - ALIGN Output parameteroutfile sourceDocumentType: UNKNOWN:UNKNOWN:FASTOUT 16:31:33,465 DEBUG DefaultToolRegistryBuilder:264 - ALIGN Tool Name Compute the global alignment of two protein or DNA sequences 16:31:33,465 DEBUG DefaultToolRegistryBuilder:266 - ALIGN toolResourceId 8BALL 16:31:33,465 DEBUG DefaultToolRegistryBuilder:268 - ALIGN inputParameters 1 16:31:33,466 DEBUG DefaultToolRegistryBuilder:270 - ALIGN outputParameters 1 16:31:33,466 DEBUG DefaultToolRegistryBuilder:271 - ALIGN configfile pisexml/align.xml 16:31:33,466 DEBUG DefaultToolRegistryBuilder:275 - ALIGN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/align.xml 16:31:33,467 DEBUG DefaultToolRegistryBuilder:279 - ALIGN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,467 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: BL2SEQ to group: WEB 16:31:33,470 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool BL2SEQ 16:31:33,470 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,471 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool BL2SEQ 16:31:33,472 DEBUG DefaultToolRegistryBuilder:239 - BL2SEQ Input parameter first_sequence_ mapped to sourceDocumentType: UNKNOWN:SEQUENCE:FASTA 16:31:33,472 DEBUG DefaultToolRegistryBuilder:261 - BL2SEQ Output parameteroutfile sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,472 DEBUG DefaultToolRegistryBuilder:264 - BL2SEQ Tool Name Blast on 2 sequences (NCBI) 16:31:33,473 DEBUG DefaultToolRegistryBuilder:266 - BL2SEQ toolResourceId 8BALL 16:31:33,473 DEBUG DefaultToolRegistryBuilder:268 - BL2SEQ inputParameters 1 16:31:33,473 DEBUG DefaultToolRegistryBuilder:270 - BL2SEQ outputParameters 1 16:31:33,474 DEBUG DefaultToolRegistryBuilder:271 - BL2SEQ configfile pisexml/bl2seq.xml 16:31:33,474 DEBUG DefaultToolRegistryBuilder:275 - BL2SEQ configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/bl2seq.xml 16:31:33,474 DEBUG DefaultToolRegistryBuilder:279 - BL2SEQ commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,475 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: BLASTN to group: WEB 16:31:33,475 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool BLASTN 16:31:33,476 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,476 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool BLASTN 16:31:33,476 DEBUG DefaultToolRegistryBuilder:239 - BLASTN Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,477 DEBUG DefaultToolRegistryBuilder:261 - BLASTN Output parametertmp_outfile sourceDocumentType: NUCLEIC_ACID:BLAST_OUTPUT:BLAST_TEXT 16:31:33,477 DEBUG DefaultToolRegistryBuilder:264 - BLASTN Tool Name with gaps 16:31:33,478 DEBUG DefaultToolRegistryBuilder:266 - BLASTN toolResourceId 8BALL 16:31:33,478 DEBUG DefaultToolRegistryBuilder:268 - BLASTN inputParameters 1 16:31:33,478 DEBUG DefaultToolRegistryBuilder:270 - BLASTN outputParameters 1 16:31:33,479 DEBUG DefaultToolRegistryBuilder:271 - BLASTN configfile pisexml/blastn.xml 16:31:33,481 DEBUG DefaultToolRegistryBuilder:275 - BLASTN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/blastn.xml 16:31:33,497 DEBUG DefaultToolRegistryBuilder:279 - BLASTN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,497 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: BLASTP to group: WEB 16:31:33,498 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool BLASTP 16:31:33,498 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,498 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool BLASTP 16:31:33,498 DEBUG DefaultToolRegistryBuilder:239 - BLASTP Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,499 DEBUG DefaultToolRegistryBuilder:261 - BLASTP Output parametertmp_outfile sourceDocumentType: PROTEIN:BLAST_OUTPUT:BLAST_TEXT 16:31:33,499 DEBUG DefaultToolRegistryBuilder:264 - BLASTP Tool Name with gaps 16:31:33,499 DEBUG DefaultToolRegistryBuilder:266 - BLASTP toolResourceId 8BALL 16:31:33,499 DEBUG DefaultToolRegistryBuilder:268 - BLASTP inputParameters 1 16:31:33,500 DEBUG DefaultToolRegistryBuilder:270 - BLASTP outputParameters 1 16:31:33,500 DEBUG DefaultToolRegistryBuilder:271 - BLASTP configfile pisexml/blastp.xml 16:31:33,500 DEBUG DefaultToolRegistryBuilder:275 - BLASTP configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/blastp.xml 16:31:33,500 DEBUG DefaultToolRegistryBuilder:279 - BLASTP commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,501 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: BLASTX to group: WEB 16:31:33,501 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool BLASTX 16:31:33,501 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,501 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool BLASTX 16:31:33,501 DEBUG DefaultToolRegistryBuilder:239 - BLASTX Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:UNKNOWN 16:31:33,502 DEBUG DefaultToolRegistryBuilder:261 - BLASTX Output parametertmp_outfile sourceDocumentType: PROTEIN:BLAST_OUTPUT:BLAST_TEXT 16:31:33,502 DEBUG DefaultToolRegistryBuilder:264 - BLASTX Tool Name with gaps 16:31:33,502 DEBUG DefaultToolRegistryBuilder:266 - BLASTX toolResourceId 8BALL 16:31:33,502 DEBUG DefaultToolRegistryBuilder:268 - BLASTX inputParameters 1 16:31:33,502 DEBUG DefaultToolRegistryBuilder:270 - BLASTX outputParameters 1 16:31:33,503 DEBUG DefaultToolRegistryBuilder:271 - BLASTX configfile pisexml/blastx.xml 16:31:33,503 DEBUG DefaultToolRegistryBuilder:275 - BLASTX configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/blastx.xml 16:31:33,503 DEBUG DefaultToolRegistryBuilder:279 - BLASTX commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,503 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: BLIMPS to group: WEB 16:31:33,504 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool BLIMPS 16:31:33,504 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,504 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool BLIMPS 16:31:33,504 DEBUG DefaultToolRegistryBuilder:239 - BLIMPS Input parameter sequence_file_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,504 DEBUG DefaultToolRegistryBuilder:264 - BLIMPS Tool Name BLocks IMProved Searcher 16:31:33,505 DEBUG DefaultToolRegistryBuilder:266 - BLIMPS toolResourceId 8BALL 16:31:33,505 DEBUG DefaultToolRegistryBuilder:268 - BLIMPS inputParameters 1 16:31:33,505 DEBUG DefaultToolRegistryBuilder:270 - BLIMPS outputParameters 0 16:31:33,505 DEBUG DefaultToolRegistryBuilder:271 - BLIMPS configfile pisexml/blimps.xml 16:31:33,506 DEBUG DefaultToolRegistryBuilder:275 - BLIMPS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/blimps.xml 16:31:33,506 DEBUG DefaultToolRegistryBuilder:279 - BLIMPS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,506 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: BOXSHADE to group: WEB 16:31:33,506 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool BOXSHADE 16:31:33,506 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,507 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool BOXSHADE 16:31:33,507 DEBUG DefaultToolRegistryBuilder:239 - BOXSHADE Input parameter alignment_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,507 DEBUG DefaultToolRegistryBuilder:264 - BOXSHADE Tool Name Printouts from multiple-aligned protein or DNA sequences 16:31:33,507 DEBUG DefaultToolRegistryBuilder:266 - BOXSHADE toolResourceId 8BALL 16:31:33,507 DEBUG DefaultToolRegistryBuilder:268 - BOXSHADE inputParameters 1 16:31:33,508 DEBUG DefaultToolRegistryBuilder:270 - BOXSHADE outputParameters 0 16:31:33,508 DEBUG DefaultToolRegistryBuilder:271 - BOXSHADE configfile pisexml/boxshade.xml 16:31:33,512 DEBUG DefaultToolRegistryBuilder:275 - BOXSHADE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/boxshade.xml 16:31:33,512 DEBUG DefaultToolRegistryBuilder:279 - BOXSHADE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,513 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CLIQUE to group: WEB 16:31:33,513 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CLIQUE 16:31:33,514 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,514 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CLIQUE 16:31:33,514 DEBUG DefaultToolRegistryBuilder:239 - CLIQUE Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,515 DEBUG DefaultToolRegistryBuilder:264 - CLIQUE Tool Name Clique - Compatibility Program 16:31:33,515 DEBUG DefaultToolRegistryBuilder:266 - CLIQUE toolResourceId 8BALL 16:31:33,515 DEBUG DefaultToolRegistryBuilder:268 - CLIQUE inputParameters 1 16:31:33,515 DEBUG DefaultToolRegistryBuilder:270 - CLIQUE outputParameters 0 16:31:33,516 DEBUG DefaultToolRegistryBuilder:271 - CLIQUE configfile pisexml/clique.xml 16:31:33,516 DEBUG DefaultToolRegistryBuilder:275 - CLIQUE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/clique.xml 16:31:33,516 DEBUG DefaultToolRegistryBuilder:279 - CLIQUE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,517 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CLUSTALW_N to group: WEB 16:31:33,517 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CLUSTALW_N 16:31:33,517 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,518 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CLUSTALW_N 16:31:33,518 DEBUG DefaultToolRegistryBuilder:239 - CLUSTALW_N Input parameter infile_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,518 DEBUG DefaultToolRegistryBuilder:264 - CLUSTALW_N Tool Name Multiple Alignments 16:31:33,518 DEBUG DefaultToolRegistryBuilder:266 - CLUSTALW_N toolResourceId 8BALL 16:31:33,519 DEBUG DefaultToolRegistryBuilder:268 - CLUSTALW_N inputParameters 1 16:31:33,519 DEBUG DefaultToolRegistryBuilder:270 - CLUSTALW_N outputParameters 0 16:31:33,519 DEBUG DefaultToolRegistryBuilder:271 - CLUSTALW_N configfile pisexml/clustalw_n.xml 16:31:33,520 DEBUG DefaultToolRegistryBuilder:275 - CLUSTALW_N configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/clustalw_n.xml 16:31:33,520 DEBUG DefaultToolRegistryBuilder:279 - CLUSTALW_N commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,520 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CLUSTALW_P to group: WEB 16:31:33,521 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CLUSTALW_P 16:31:33,521 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,521 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CLUSTALW_P 16:31:33,521 DEBUG DefaultToolRegistryBuilder:239 - CLUSTALW_P Input parameter infile_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,522 DEBUG DefaultToolRegistryBuilder:264 - CLUSTALW_P Tool Name Multiple Alignments 16:31:33,522 DEBUG DefaultToolRegistryBuilder:266 - CLUSTALW_P toolResourceId 8BALL 16:31:33,522 DEBUG DefaultToolRegistryBuilder:268 - CLUSTALW_P inputParameters 1 16:31:33,522 DEBUG DefaultToolRegistryBuilder:270 - CLUSTALW_P outputParameters 0 16:31:33,523 DEBUG DefaultToolRegistryBuilder:271 - CLUSTALW_P configfile pisexml/clustalw_p.xml 16:31:33,523 DEBUG DefaultToolRegistryBuilder:275 - CLUSTALW_P configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/clustalw_p.xml 16:31:33,523 DEBUG DefaultToolRegistryBuilder:279 - CLUSTALW_P commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,524 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CLUSTALW_DIST to group: WEB 16:31:33,524 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CLUSTALW_DIST 16:31:33,524 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,524 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CLUSTALW_DIST 16:31:33,525 DEBUG DefaultToolRegistryBuilder:239 - CLUSTALW_DIST Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,525 DEBUG DefaultToolRegistryBuilder:264 - CLUSTALW_DIST Tool Name Multiple Alignments 16:31:33,525 DEBUG DefaultToolRegistryBuilder:266 - CLUSTALW_DIST toolResourceId 8BALL 16:31:33,526 DEBUG DefaultToolRegistryBuilder:268 - CLUSTALW_DIST inputParameters 1 16:31:33,526 DEBUG DefaultToolRegistryBuilder:270 - CLUSTALW_DIST outputParameters 0 16:31:33,526 DEBUG DefaultToolRegistryBuilder:271 - CLUSTALW_DIST configfile pisexml/clustalw_dist.xml 16:31:33,526 DEBUG DefaultToolRegistryBuilder:275 - CLUSTALW_DIST configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/clustalw_dist.xml 16:31:33,527 DEBUG DefaultToolRegistryBuilder:279 - CLUSTALW_DIST commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,527 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CLUSTALW_PROFILE to group: WEB 16:31:33,527 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CLUSTALW_PROFILE 16:31:33,527 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,528 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CLUSTALW_PROFILE 16:31:33,528 DEBUG DefaultToolRegistryBuilder:239 - CLUSTALW_PROFILE Input parameter profile1_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,529 DEBUG DefaultToolRegistryBuilder:264 - CLUSTALW_PROFILE Tool Name Multiple Alignments 16:31:33,529 DEBUG DefaultToolRegistryBuilder:266 - CLUSTALW_PROFILE toolResourceId 8BALL 16:31:33,529 DEBUG DefaultToolRegistryBuilder:268 - CLUSTALW_PROFILE inputParameters 1 16:31:33,530 DEBUG DefaultToolRegistryBuilder:270 - CLUSTALW_PROFILE outputParameters 0 16:31:33,530 DEBUG DefaultToolRegistryBuilder:271 - CLUSTALW_PROFILE configfile pisexml/clustalw_profile.xml 16:31:33,530 DEBUG DefaultToolRegistryBuilder:275 - CLUSTALW_PROFILE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/clustalw_profile.xml 16:31:33,531 DEBUG DefaultToolRegistryBuilder:279 - CLUSTALW_PROFILE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,531 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CLUSTALW_TREE to group: WEB 16:31:33,531 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CLUSTALW_TREE 16:31:33,532 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,532 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CLUSTALW_TREE 16:31:33,532 DEBUG DefaultToolRegistryBuilder:239 - CLUSTALW_TREE Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,532 DEBUG DefaultToolRegistryBuilder:264 - CLUSTALW_TREE Tool Name Multiple Alignments 16:31:33,533 DEBUG DefaultToolRegistryBuilder:266 - CLUSTALW_TREE toolResourceId 8BALL 16:31:33,533 DEBUG DefaultToolRegistryBuilder:268 - CLUSTALW_TREE inputParameters 1 16:31:33,533 DEBUG DefaultToolRegistryBuilder:270 - CLUSTALW_TREE outputParameters 0 16:31:33,533 DEBUG DefaultToolRegistryBuilder:271 - CLUSTALW_TREE configfile pisexml/clustalw_tree.xml 16:31:33,534 DEBUG DefaultToolRegistryBuilder:275 - CLUSTALW_TREE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/clustalw_tree.xml 16:31:33,534 DEBUG DefaultToolRegistryBuilder:279 - CLUSTALW_TREE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,534 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: CONSENSE to group: WEB 16:31:33,538 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool CONSENSE 16:31:33,538 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,538 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool CONSENSE 16:31:33,539 DEBUG DefaultToolRegistryBuilder:239 - CONSENSE Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,539 DEBUG DefaultToolRegistryBuilder:264 - CONSENSE Tool Name consense - Consensus tree program 16:31:33,539 DEBUG DefaultToolRegistryBuilder:266 - CONSENSE toolResourceId 8BALL 16:31:33,540 DEBUG DefaultToolRegistryBuilder:268 - CONSENSE inputParameters 1 16:31:33,540 DEBUG DefaultToolRegistryBuilder:270 - CONSENSE outputParameters 0 16:31:33,540 DEBUG DefaultToolRegistryBuilder:271 - CONSENSE configfile pisexml/consense.xml 16:31:33,541 DEBUG DefaultToolRegistryBuilder:275 - CONSENSE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/consense.xml 16:31:33,541 DEBUG DefaultToolRegistryBuilder:279 - CONSENSE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,541 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DEGAPSEQ to group: WEB 16:31:33,541 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DEGAPSEQ 16:31:33,542 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,542 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DEGAPSEQ 16:31:33,542 DEBUG DefaultToolRegistryBuilder:239 - DEGAPSEQ Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,542 DEBUG DefaultToolRegistryBuilder:264 - DEGAPSEQ Tool Name Removes gap characters from sequences (EMBOSS) 16:31:33,543 DEBUG DefaultToolRegistryBuilder:266 - DEGAPSEQ toolResourceId 8BALL 16:31:33,543 DEBUG DefaultToolRegistryBuilder:268 - DEGAPSEQ inputParameters 1 16:31:33,543 DEBUG DefaultToolRegistryBuilder:270 - DEGAPSEQ outputParameters 0 16:31:33,544 DEBUG DefaultToolRegistryBuilder:271 - DEGAPSEQ configfile pisexml/degapseq.xml 16:31:33,544 DEBUG DefaultToolRegistryBuilder:275 - DEGAPSEQ configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/degapseq.xml 16:31:33,544 DEBUG DefaultToolRegistryBuilder:279 - DEGAPSEQ commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,545 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DNADIST to group: WEB 16:31:33,545 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DNADIST 16:31:33,545 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,545 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DNADIST 16:31:33,546 DEBUG DefaultToolRegistryBuilder:239 - DNADIST Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,546 DEBUG DefaultToolRegistryBuilder:264 - DNADIST Tool Name dnadist - Compute distance matrix from nucleotide sequences 16:31:33,547 DEBUG DefaultToolRegistryBuilder:266 - DNADIST toolResourceId 8BALL 16:31:33,547 DEBUG DefaultToolRegistryBuilder:268 - DNADIST inputParameters 1 16:31:33,547 DEBUG DefaultToolRegistryBuilder:270 - DNADIST outputParameters 0 16:31:33,548 DEBUG DefaultToolRegistryBuilder:271 - DNADIST configfile pisexml/dnadist.xml 16:31:33,548 DEBUG DefaultToolRegistryBuilder:275 - DNADIST configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/dnadist.xml 16:31:33,548 DEBUG DefaultToolRegistryBuilder:279 - DNADIST commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,550 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DNAPARS to group: WEB 16:31:33,550 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DNAPARS 16:31:33,550 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,550 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DNAPARS 16:31:33,551 DEBUG DefaultToolRegistryBuilder:239 - DNAPARS Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,551 DEBUG DefaultToolRegistryBuilder:264 - DNAPARS Tool Name dnapars - DNA Parsimony Program 16:31:33,551 DEBUG DefaultToolRegistryBuilder:266 - DNAPARS toolResourceId 8BALL 16:31:33,551 DEBUG DefaultToolRegistryBuilder:268 - DNAPARS inputParameters 1 16:31:33,552 DEBUG DefaultToolRegistryBuilder:270 - DNAPARS outputParameters 0 16:31:33,552 DEBUG DefaultToolRegistryBuilder:271 - DNAPARS configfile pisexml/dnapars.xml 16:31:33,552 DEBUG DefaultToolRegistryBuilder:275 - DNAPARS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/dnapars.xml 16:31:33,552 DEBUG DefaultToolRegistryBuilder:279 - DNAPARS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,553 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DOLLOP to group: WEB 16:31:33,553 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DOLLOP 16:31:33,553 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,553 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DOLLOP 16:31:33,554 DEBUG DefaultToolRegistryBuilder:239 - DOLLOP Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,554 DEBUG DefaultToolRegistryBuilder:264 - DOLLOP Tool Name dollop - Dollo and Polymorphism Parsimony Program 16:31:33,554 DEBUG DefaultToolRegistryBuilder:266 - DOLLOP toolResourceId 8BALL 16:31:33,554 DEBUG DefaultToolRegistryBuilder:268 - DOLLOP inputParameters 1 16:31:33,555 DEBUG DefaultToolRegistryBuilder:270 - DOLLOP outputParameters 0 16:31:33,555 DEBUG DefaultToolRegistryBuilder:271 - DOLLOP configfile pisexml/dollop.xml 16:31:33,555 DEBUG DefaultToolRegistryBuilder:275 - DOLLOP configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/dollop.xml 16:31:33,556 DEBUG DefaultToolRegistryBuilder:279 - DOLLOP commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,556 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DRAWGRAM to group: WEB 16:31:33,556 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DRAWGRAM 16:31:33,556 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,557 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DRAWGRAM 16:31:33,557 DEBUG DefaultToolRegistryBuilder:239 - DRAWGRAM Input parameter treefile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,557 DEBUG DefaultToolRegistryBuilder:264 - DRAWGRAM Tool Name drawgram - Plots a cladogram- or phenogram-like rooted tree 16:31:33,558 DEBUG DefaultToolRegistryBuilder:266 - DRAWGRAM toolResourceId 8BALL 16:31:33,558 DEBUG DefaultToolRegistryBuilder:268 - DRAWGRAM inputParameters 1 16:31:33,558 DEBUG DefaultToolRegistryBuilder:270 - DRAWGRAM outputParameters 0 16:31:33,558 DEBUG DefaultToolRegistryBuilder:271 - DRAWGRAM configfile pisexml/drawgram.xml 16:31:33,559 DEBUG DefaultToolRegistryBuilder:275 - DRAWGRAM configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/drawgram.xml 16:31:33,559 DEBUG DefaultToolRegistryBuilder:279 - DRAWGRAM commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,559 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DRAWTREE to group: WEB 16:31:33,560 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DRAWTREE 16:31:33,560 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,562 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DRAWTREE 16:31:33,563 DEBUG DefaultToolRegistryBuilder:239 - DRAWTREE Input parameter treefile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,563 DEBUG DefaultToolRegistryBuilder:264 - DRAWTREE Tool Name drawtree - Plots an unrooted tree diagram 16:31:33,563 DEBUG DefaultToolRegistryBuilder:266 - DRAWTREE toolResourceId 8BALL 16:31:33,564 DEBUG DefaultToolRegistryBuilder:268 - DRAWTREE inputParameters 1 16:31:33,564 DEBUG DefaultToolRegistryBuilder:270 - DRAWTREE outputParameters 0 16:31:33,564 DEBUG DefaultToolRegistryBuilder:271 - DRAWTREE configfile pisexml/drawtree.xml 16:31:33,564 DEBUG DefaultToolRegistryBuilder:275 - DRAWTREE configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/drawtree.xml 16:31:33,565 DEBUG DefaultToolRegistryBuilder:279 - DRAWTREE commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,565 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: DSSP to group: WEB 16:31:33,565 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool DSSP 16:31:33,565 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,566 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool DSSP 16:31:33,566 DEBUG DefaultToolRegistryBuilder:239 - DSSP Input parameter pdbfile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,566 DEBUG DefaultToolRegistryBuilder:264 - DSSP Tool Name Definition of secondary structure of proteins given a set of 3D coordinates 16:31:33,566 DEBUG DefaultToolRegistryBuilder:266 - DSSP toolResourceId 8BALL 16:31:33,567 DEBUG DefaultToolRegistryBuilder:268 - DSSP inputParameters 1 16:31:33,567 DEBUG DefaultToolRegistryBuilder:270 - DSSP outputParameters 0 16:31:33,567 DEBUG DefaultToolRegistryBuilder:271 - DSSP configfile pisexml/dssp.xml 16:31:33,567 DEBUG DefaultToolRegistryBuilder:275 - DSSP configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/dssp.xml 16:31:33,568 DEBUG DefaultToolRegistryBuilder:279 - DSSP commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,568 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FASTA_N to group: WEB 16:31:33,568 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FASTA_N 16:31:33,568 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,568 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FASTA_N 16:31:33,569 DEBUG DefaultToolRegistryBuilder:239 - FASTA_N Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,569 DEBUG DefaultToolRegistryBuilder:261 - FASTA_N Output parameteroutfile sourceDocumentType: NUCLEIC_ACID:FASTA_OUTPUT:FASTOUT 16:31:33,569 DEBUG DefaultToolRegistryBuilder:264 - FASTA_N Tool Name Sequence database search (version 3) 16:31:33,569 DEBUG DefaultToolRegistryBuilder:266 - FASTA_N toolResourceId 8BALL 16:31:33,570 DEBUG DefaultToolRegistryBuilder:268 - FASTA_N inputParameters 1 16:31:33,570 DEBUG DefaultToolRegistryBuilder:270 - FASTA_N outputParameters 1 16:31:33,570 DEBUG DefaultToolRegistryBuilder:271 - FASTA_N configfile pisexml/fasta_n.xml 16:31:33,570 DEBUG DefaultToolRegistryBuilder:275 - FASTA_N configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/fasta_n.xml 16:31:33,571 DEBUG DefaultToolRegistryBuilder:279 - FASTA_N commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,571 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FASTA_P to group: WEB 16:31:33,571 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FASTA_P 16:31:33,571 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,571 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FASTA_P 16:31:33,572 DEBUG DefaultToolRegistryBuilder:239 - FASTA_P Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,572 DEBUG DefaultToolRegistryBuilder:261 - FASTA_P Output parameteroutfile sourceDocumentType: PROTEIN:FASTA_OUTPUT:FASTOUT 16:31:33,572 DEBUG DefaultToolRegistryBuilder:264 - FASTA_P Tool Name Sequence database search (version 3) 16:31:33,572 DEBUG DefaultToolRegistryBuilder:266 - FASTA_P toolResourceId 8BALL 16:31:33,573 DEBUG DefaultToolRegistryBuilder:268 - FASTA_P inputParameters 1 16:31:33,573 DEBUG DefaultToolRegistryBuilder:270 - FASTA_P outputParameters 1 16:31:33,573 DEBUG DefaultToolRegistryBuilder:271 - FASTA_P configfile pisexml/fasta_p.xml 16:31:33,573 DEBUG DefaultToolRegistryBuilder:275 - FASTA_P configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/fasta_p.xml 16:31:33,574 DEBUG DefaultToolRegistryBuilder:279 - FASTA_P commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,574 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FASTX to group: WEB 16:31:33,574 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FASTX 16:31:33,574 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,574 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FASTX 16:31:33,575 DEBUG DefaultToolRegistryBuilder:239 - FASTX Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,587 DEBUG DefaultToolRegistryBuilder:261 - FASTX Output parameteroutfile sourceDocumentType: NUCLEIC_ACID:FASTA_OUTPUT:FASTOUT 16:31:33,587 DEBUG DefaultToolRegistryBuilder:264 - FASTX Tool Name Sequence database search (version 3) 16:31:33,587 DEBUG DefaultToolRegistryBuilder:266 - FASTX toolResourceId 8BALL 16:31:33,587 DEBUG DefaultToolRegistryBuilder:268 - FASTX inputParameters 1 16:31:33,588 DEBUG DefaultToolRegistryBuilder:270 - FASTX outputParameters 1 16:31:33,590 DEBUG DefaultToolRegistryBuilder:271 - FASTX configfile pisexml/fastx.xml 16:31:33,590 DEBUG DefaultToolRegistryBuilder:275 - FASTX configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/fastx.xml 16:31:33,590 DEBUG DefaultToolRegistryBuilder:279 - FASTX commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,590 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FASTY to group: WEB 16:31:33,591 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FASTY 16:31:33,591 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,591 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FASTY 16:31:33,592 DEBUG DefaultToolRegistryBuilder:239 - FASTY Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,592 DEBUG DefaultToolRegistryBuilder:261 - FASTY Output parameteroutfile sourceDocumentType: NUCLEIC_ACID:FASTA_OUTPUT:FASTOUT 16:31:33,592 DEBUG DefaultToolRegistryBuilder:264 - FASTY Tool Name Sequence database search (version 3) 16:31:33,592 DEBUG DefaultToolRegistryBuilder:266 - FASTY toolResourceId 8BALL 16:31:33,592 DEBUG DefaultToolRegistryBuilder:268 - FASTY inputParameters 1 16:31:33,592 DEBUG DefaultToolRegistryBuilder:270 - FASTY outputParameters 1 16:31:33,592 DEBUG DefaultToolRegistryBuilder:271 - FASTY configfile pisexml/fasty.xml 16:31:33,593 DEBUG DefaultToolRegistryBuilder:275 - FASTY configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/fasty.xml 16:31:33,593 DEBUG DefaultToolRegistryBuilder:279 - FASTY commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,593 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FINGERPRINTSCAN to group: WEB 16:31:33,593 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FINGERPRINTSCAN 16:31:33,593 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,593 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FINGERPRINTSCAN 16:31:33,594 DEBUG DefaultToolRegistryBuilder:239 - FINGERPRINTSCAN Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,594 DEBUG DefaultToolRegistryBuilder:264 - FINGERPRINTSCAN Tool Name Search against FingerPRINTScan with a protein query sequence to identify the closest matching PRINTS sequence motif fingerprints in a protein sequence. 16:31:33,594 DEBUG DefaultToolRegistryBuilder:266 - FINGERPRINTSCAN toolResourceId 8BALL 16:31:33,594 DEBUG DefaultToolRegistryBuilder:268 - FINGERPRINTSCAN inputParameters 1 16:31:33,594 DEBUG DefaultToolRegistryBuilder:270 - FINGERPRINTSCAN outputParameters 0 16:31:33,594 DEBUG DefaultToolRegistryBuilder:271 - FINGERPRINTSCAN configfile pisexml/fingerprintscan.xml 16:31:33,595 DEBUG DefaultToolRegistryBuilder:275 - FINGERPRINTSCAN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/fingerprintscan.xml 16:31:33,595 DEBUG DefaultToolRegistryBuilder:279 - FINGERPRINTSCAN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,595 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: FITCH to group: WEB 16:31:33,595 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool FITCH 16:31:33,596 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,596 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool FITCH 16:31:33,596 DEBUG DefaultToolRegistryBuilder:239 - FITCH Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,596 DEBUG DefaultToolRegistryBuilder:264 - FITCH Tool Name Fitch 16:31:33,597 DEBUG DefaultToolRegistryBuilder:266 - FITCH toolResourceId 8BALL 16:31:33,597 DEBUG DefaultToolRegistryBuilder:268 - FITCH inputParameters 1 16:31:33,597 DEBUG DefaultToolRegistryBuilder:270 - FITCH outputParameters 0 16:31:33,597 DEBUG DefaultToolRegistryBuilder:271 - FITCH configfile pisexml/fitch.xml 16:31:33,597 DEBUG DefaultToolRegistryBuilder:275 - FITCH configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/fitch.xml 16:31:33,598 DEBUG DefaultToolRegistryBuilder:279 - FITCH commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,598 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: HELIXTURNHELIX to group: WEB 16:31:33,598 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool HELIXTURNHELIX 16:31:33,598 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,598 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool HELIXTURNHELIX 16:31:33,598 DEBUG DefaultToolRegistryBuilder:239 - HELIXTURNHELIX Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,598 DEBUG DefaultToolRegistryBuilder:264 - HELIXTURNHELIX Tool Name Report nucleic acid binding motifs (EMBOSS) 16:31:33,599 DEBUG DefaultToolRegistryBuilder:266 - HELIXTURNHELIX toolResourceId 8BALL 16:31:33,599 DEBUG DefaultToolRegistryBuilder:268 - HELIXTURNHELIX inputParameters 1 16:31:33,599 DEBUG DefaultToolRegistryBuilder:270 - HELIXTURNHELIX outputParameters 0 16:31:33,599 DEBUG DefaultToolRegistryBuilder:271 - HELIXTURNHELIX configfile pisexml/helixturnhelix.xml 16:31:33,599 DEBUG DefaultToolRegistryBuilder:275 - HELIXTURNHELIX configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/helixturnhelix.xml 16:31:33,600 DEBUG DefaultToolRegistryBuilder:279 - HELIXTURNHELIX commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,600 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: HMMPFAM to group: WEB 16:31:33,600 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool HMMPFAM 16:31:33,600 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,600 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool HMMPFAM 16:31:33,601 DEBUG DefaultToolRegistryBuilder:239 - HMMPFAM Input parameter seqfile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,601 DEBUG DefaultToolRegistryBuilder:264 - HMMPFAM Tool Name hmmpfam - search sequences against an HMM database 16:31:33,601 DEBUG DefaultToolRegistryBuilder:266 - HMMPFAM toolResourceId 8BALL 16:31:33,601 DEBUG DefaultToolRegistryBuilder:268 - HMMPFAM inputParameters 1 16:31:33,601 DEBUG DefaultToolRegistryBuilder:270 - HMMPFAM outputParameters 0 16:31:33,602 DEBUG DefaultToolRegistryBuilder:271 - HMMPFAM configfile pisexml/hmmpfam.xml 16:31:33,602 DEBUG DefaultToolRegistryBuilder:275 - HMMPFAM configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/hmmpfam.xml 16:31:33,602 DEBUG DefaultToolRegistryBuilder:279 - HMMPFAM commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,602 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: KITSCH to group: WEB 16:31:33,603 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool KITSCH 16:31:33,603 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,603 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool KITSCH 16:31:33,603 DEBUG DefaultToolRegistryBuilder:239 - KITSCH Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,603 DEBUG DefaultToolRegistryBuilder:264 - KITSCH Tool Name kitsch - Fitch-Margoliash and Least Squares Methods with Evolutionary Clock 16:31:33,603 DEBUG DefaultToolRegistryBuilder:266 - KITSCH toolResourceId 8BALL 16:31:33,603 DEBUG DefaultToolRegistryBuilder:268 - KITSCH inputParameters 1 16:31:33,604 DEBUG DefaultToolRegistryBuilder:270 - KITSCH outputParameters 0 16:31:33,604 DEBUG DefaultToolRegistryBuilder:271 - KITSCH configfile pisexml/kitsch.xml 16:31:33,604 DEBUG DefaultToolRegistryBuilder:275 - KITSCH configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/kitsch.xml 16:31:33,605 DEBUG DefaultToolRegistryBuilder:279 - KITSCH commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,605 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: LALIGN to group: WEB 16:31:33,605 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool LALIGN 16:31:33,605 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,605 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool LALIGN 16:31:33,605 DEBUG DefaultToolRegistryBuilder:239 - LALIGN Input parameter query1_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,606 DEBUG DefaultToolRegistryBuilder:264 - LALIGN Tool Name Compute two protein or DNA sequences for local similarity and show the local sequence alignments 16:31:33,606 DEBUG DefaultToolRegistryBuilder:266 - LALIGN toolResourceId 8BALL 16:31:33,606 DEBUG DefaultToolRegistryBuilder:268 - LALIGN inputParameters 1 16:31:33,606 DEBUG DefaultToolRegistryBuilder:270 - LALIGN outputParameters 0 16:31:33,606 DEBUG DefaultToolRegistryBuilder:271 - LALIGN configfile pisexml/lalign.xml 16:31:33,607 DEBUG DefaultToolRegistryBuilder:275 - LALIGN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/lalign.xml 16:31:33,607 DEBUG DefaultToolRegistryBuilder:279 - LALIGN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,607 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MFOLD to group: WEB 16:31:33,607 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MFOLD 16:31:33,607 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,607 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MFOLD 16:31:33,608 DEBUG DefaultToolRegistryBuilder:239 - MFOLD Input parameter SEQ_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,608 DEBUG DefaultToolRegistryBuilder:264 - MFOLD Tool Name Prediction of RNA secondary structure 16:31:33,608 DEBUG DefaultToolRegistryBuilder:266 - MFOLD toolResourceId 8BALL 16:31:33,608 DEBUG DefaultToolRegistryBuilder:268 - MFOLD inputParameters 1 16:31:33,608 DEBUG DefaultToolRegistryBuilder:270 - MFOLD outputParameters 0 16:31:33,608 DEBUG DefaultToolRegistryBuilder:271 - MFOLD configfile pisexml/mfold.xml 16:31:33,609 DEBUG DefaultToolRegistryBuilder:275 - MFOLD configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/mfold.xml 16:31:33,609 DEBUG DefaultToolRegistryBuilder:279 - MFOLD commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,609 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MIX to group: WEB 16:31:33,609 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MIX 16:31:33,609 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,609 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MIX 16:31:33,610 DEBUG DefaultToolRegistryBuilder:239 - MIX Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,610 DEBUG DefaultToolRegistryBuilder:264 - MIX Tool Name mix - Mixed method parsimony 16:31:33,610 DEBUG DefaultToolRegistryBuilder:266 - MIX toolResourceId 8BALL 16:31:33,610 DEBUG DefaultToolRegistryBuilder:268 - MIX inputParameters 1 16:31:33,610 DEBUG DefaultToolRegistryBuilder:270 - MIX outputParameters 0 16:31:33,610 DEBUG DefaultToolRegistryBuilder:271 - MIX configfile pisexml/mix.xml 16:31:33,611 DEBUG DefaultToolRegistryBuilder:275 - MIX configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/mix.xml 16:31:33,611 DEBUG DefaultToolRegistryBuilder:279 - MIX commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,611 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MSA to group: WEB 16:31:33,611 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MSA 16:31:33,611 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,612 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MSA 16:31:33,612 DEBUG DefaultToolRegistryBuilder:239 - MSA Input parameter seqs_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,612 DEBUG DefaultToolRegistryBuilder:264 - MSA Tool Name multiple sequence alignment 16:31:33,612 DEBUG DefaultToolRegistryBuilder:266 - MSA toolResourceId 8BALL 16:31:33,613 DEBUG DefaultToolRegistryBuilder:268 - MSA inputParameters 1 16:31:33,613 DEBUG DefaultToolRegistryBuilder:270 - MSA outputParameters 0 16:31:33,613 DEBUG DefaultToolRegistryBuilder:271 - MSA configfile pisexml/msa.xml 16:31:33,613 DEBUG DefaultToolRegistryBuilder:275 - MSA configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/msa.xml 16:31:33,613 DEBUG DefaultToolRegistryBuilder:279 - MSA commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,614 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MVIEW_ALIG to group: WEB 16:31:33,614 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MVIEW_ALIG 16:31:33,614 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,614 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MVIEW_ALIG 16:31:33,614 DEBUG DefaultToolRegistryBuilder:239 - MVIEW_ALIG Input parameter alig_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,614 DEBUG DefaultToolRegistryBuilder:264 - MVIEW_ALIG Tool Name a multiple alignment viewer 16:31:33,615 DEBUG DefaultToolRegistryBuilder:266 - MVIEW_ALIG toolResourceId 8BALL 16:31:33,615 DEBUG DefaultToolRegistryBuilder:268 - MVIEW_ALIG inputParameters 1 16:31:33,615 DEBUG DefaultToolRegistryBuilder:270 - MVIEW_ALIG outputParameters 0 16:31:33,615 DEBUG DefaultToolRegistryBuilder:271 - MVIEW_ALIG configfile pisexml/mview_alig.xml 16:31:33,615 DEBUG DefaultToolRegistryBuilder:275 - MVIEW_ALIG configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/mview_alig.xml 16:31:33,615 DEBUG DefaultToolRegistryBuilder:279 - MVIEW_ALIG commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,616 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: MVIEW_BLAST to group: WEB 16:31:33,616 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool MVIEW_BLAST 16:31:33,616 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,616 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool MVIEW_BLAST 16:31:33,616 DEBUG DefaultToolRegistryBuilder:239 - MVIEW_BLAST Input parameter blast_output_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,616 DEBUG DefaultToolRegistryBuilder:264 - MVIEW_BLAST Tool Name view Blast results as a multiple alignment 16:31:33,617 DEBUG DefaultToolRegistryBuilder:266 - MVIEW_BLAST toolResourceId 8BALL 16:31:33,617 DEBUG DefaultToolRegistryBuilder:268 - MVIEW_BLAST inputParameters 1 16:31:33,617 DEBUG DefaultToolRegistryBuilder:270 - MVIEW_BLAST outputParameters 0 16:31:33,617 DEBUG DefaultToolRegistryBuilder:271 - MVIEW_BLAST configfile pisexml/mview_blast.xml 16:31:33,617 DEBUG DefaultToolRegistryBuilder:275 - MVIEW_BLAST configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/mview_blast.xml 16:31:33,617 DEBUG DefaultToolRegistryBuilder:279 - MVIEW_BLAST commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,617 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: NEIGHBOR to group: WEB 16:31:33,618 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool NEIGHBOR 16:31:33,618 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,618 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool NEIGHBOR 16:31:33,618 DEBUG DefaultToolRegistryBuilder:239 - NEIGHBOR Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,618 DEBUG DefaultToolRegistryBuilder:264 - NEIGHBOR Tool Name neighbor - Neighbor-Joining and UPGMA methods 16:31:33,618 DEBUG DefaultToolRegistryBuilder:266 - NEIGHBOR toolResourceId 8BALL 16:31:33,619 DEBUG DefaultToolRegistryBuilder:268 - NEIGHBOR inputParameters 1 16:31:33,619 DEBUG DefaultToolRegistryBuilder:270 - NEIGHBOR outputParameters 0 16:31:33,619 DEBUG DefaultToolRegistryBuilder:271 - NEIGHBOR configfile pisexml/neighbor.xml 16:31:33,619 DEBUG DefaultToolRegistryBuilder:275 - NEIGHBOR configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/neighbor.xml 16:31:33,619 DEBUG DefaultToolRegistryBuilder:279 - NEIGHBOR commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,619 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PARS to group: WEB 16:31:33,620 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PARS 16:31:33,620 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,620 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PARS 16:31:33,620 DEBUG DefaultToolRegistryBuilder:239 - PARS Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,620 DEBUG DefaultToolRegistryBuilder:264 - PARS Tool Name pars - Discrete character parsimony 16:31:33,620 DEBUG DefaultToolRegistryBuilder:266 - PARS toolResourceId 8BALL 16:31:33,620 DEBUG DefaultToolRegistryBuilder:268 - PARS inputParameters 1 16:31:33,621 DEBUG DefaultToolRegistryBuilder:270 - PARS outputParameters 0 16:31:33,621 DEBUG DefaultToolRegistryBuilder:271 - PARS configfile pisexml/pars.xml 16:31:33,621 DEBUG DefaultToolRegistryBuilder:275 - PARS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/pars.xml 16:31:33,621 DEBUG DefaultToolRegistryBuilder:279 - PARS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,621 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PEPINFO to group: WEB 16:31:33,621 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PEPINFO 16:31:33,622 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,622 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PEPINFO 16:31:33,622 DEBUG DefaultToolRegistryBuilder:239 - PEPINFO Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,622 DEBUG DefaultToolRegistryBuilder:264 - PEPINFO Tool Name Plots simple amino acid properties in parallel (EMBOSS) 16:31:33,622 DEBUG DefaultToolRegistryBuilder:266 - PEPINFO toolResourceId 8BALL 16:31:33,622 DEBUG DefaultToolRegistryBuilder:268 - PEPINFO inputParameters 1 16:31:33,623 DEBUG DefaultToolRegistryBuilder:270 - PEPINFO outputParameters 0 16:31:33,623 DEBUG DefaultToolRegistryBuilder:271 - PEPINFO configfile pisexml/pepinfo.xml 16:31:33,623 DEBUG DefaultToolRegistryBuilder:275 - PEPINFO configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/pepinfo.xml 16:31:33,623 DEBUG DefaultToolRegistryBuilder:279 - PEPINFO commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,623 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PEPSTATS to group: WEB 16:31:33,623 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PEPSTATS 16:31:33,624 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,624 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PEPSTATS 16:31:33,624 DEBUG DefaultToolRegistryBuilder:239 - PEPSTATS Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,624 DEBUG DefaultToolRegistryBuilder:264 - PEPSTATS Tool Name Protein statistics (EMBOSS) 16:31:33,624 DEBUG DefaultToolRegistryBuilder:266 - PEPSTATS toolResourceId 8BALL 16:31:33,624 DEBUG DefaultToolRegistryBuilder:268 - PEPSTATS inputParameters 1 16:31:33,625 DEBUG DefaultToolRegistryBuilder:270 - PEPSTATS outputParameters 0 16:31:33,625 DEBUG DefaultToolRegistryBuilder:271 - PEPSTATS configfile pisexml/pepstats.xml 16:31:33,625 DEBUG DefaultToolRegistryBuilder:275 - PEPSTATS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/pepstats.xml 16:31:33,625 DEBUG DefaultToolRegistryBuilder:279 - PEPSTATS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,625 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PEPWINDOW to group: WEB 16:31:33,626 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PEPWINDOW 16:31:33,627 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,627 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PEPWINDOW 16:31:33,627 DEBUG DefaultToolRegistryBuilder:239 - PEPWINDOW Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,627 DEBUG DefaultToolRegistryBuilder:264 - PEPWINDOW Tool Name Displays protein hydropathy (EMBOSS) 16:31:33,627 DEBUG DefaultToolRegistryBuilder:266 - PEPWINDOW toolResourceId 8BALL 16:31:33,627 DEBUG DefaultToolRegistryBuilder:268 - PEPWINDOW inputParameters 1 16:31:33,628 DEBUG DefaultToolRegistryBuilder:270 - PEPWINDOW outputParameters 0 16:31:33,628 DEBUG DefaultToolRegistryBuilder:271 - PEPWINDOW configfile pisexml/pepwindow.xml 16:31:33,628 DEBUG DefaultToolRegistryBuilder:275 - PEPWINDOW configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/pepwindow.xml 16:31:33,628 DEBUG DefaultToolRegistryBuilder:279 - PEPWINDOW commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,628 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PFSCAN to group: WEB 16:31:33,629 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PFSCAN 16:31:33,629 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,629 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PFSCAN 16:31:33,629 DEBUG DefaultToolRegistryBuilder:239 - PFSCAN Input parameter seqfile_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,629 DEBUG DefaultToolRegistryBuilder:264 - PFSCAN Tool Name Profile Tools 16:31:33,629 DEBUG DefaultToolRegistryBuilder:266 - PFSCAN toolResourceId 8BALL 16:31:33,630 DEBUG DefaultToolRegistryBuilder:268 - PFSCAN inputParameters 1 16:31:33,630 DEBUG DefaultToolRegistryBuilder:270 - PFSCAN outputParameters 0 16:31:33,630 DEBUG DefaultToolRegistryBuilder:271 - PFSCAN configfile pisexml/pfscan.xml 16:31:33,633 DEBUG DefaultToolRegistryBuilder:275 - PFSCAN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/pfscan.xml 16:31:33,633 DEBUG DefaultToolRegistryBuilder:279 - PFSCAN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,633 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PFSEARCH to group: WEB 16:31:33,633 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PFSEARCH 16:31:33,633 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,634 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PFSEARCH 16:31:33,634 DEBUG DefaultToolRegistryBuilder:239 - PFSEARCH Input parameter profile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,634 DEBUG DefaultToolRegistryBuilder:264 - PFSEARCH Tool Name Profile Tools 16:31:33,634 DEBUG DefaultToolRegistryBuilder:266 - PFSEARCH toolResourceId 8BALL 16:31:33,634 DEBUG DefaultToolRegistryBuilder:268 - PFSEARCH inputParameters 1 16:31:33,634 DEBUG DefaultToolRegistryBuilder:270 - PFSEARCH outputParameters 0 16:31:33,635 DEBUG DefaultToolRegistryBuilder:271 - PFSEARCH configfile pisexml/pfsearch.xml 16:31:33,635 DEBUG DefaultToolRegistryBuilder:275 - PFSEARCH configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/pfsearch.xml 16:31:33,635 DEBUG DefaultToolRegistryBuilder:279 - PFSEARCH commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,635 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PHYML to group: WEB 16:31:33,635 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PHYML 16:31:33,635 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,636 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PHYML 16:31:33,636 DEBUG DefaultToolRegistryBuilder:239 - PHYML Input parameter alignment_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,636 DEBUG DefaultToolRegistryBuilder:264 - PHYML Tool Name a program that computes maximum likelihood phylogenies from DNA or AA homologous sequences 16:31:33,636 DEBUG DefaultToolRegistryBuilder:266 - PHYML toolResourceId 8BALL 16:31:33,636 DEBUG DefaultToolRegistryBuilder:268 - PHYML inputParameters 1 16:31:33,636 DEBUG DefaultToolRegistryBuilder:270 - PHYML outputParameters 0 16:31:33,637 DEBUG DefaultToolRegistryBuilder:271 - PHYML configfile pisexml/phyml.xml 16:31:33,637 DEBUG DefaultToolRegistryBuilder:275 - PHYML configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/phyml.xml 16:31:33,637 DEBUG DefaultToolRegistryBuilder:279 - PHYML commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,637 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PPSEARCH to group: WEB 16:31:33,637 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PPSEARCH 16:31:33,637 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,638 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PPSEARCH 16:31:33,638 DEBUG DefaultToolRegistryBuilder:239 - PPSEARCH Input parameter inputfile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,638 DEBUG DefaultToolRegistryBuilder:264 - PPSEARCH Tool Name Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is. This tool requires a protein sequence as input, but DNA/RNA may be translated into a protein sequence using transeq and then queried. 16:31:33,638 DEBUG DefaultToolRegistryBuilder:266 - PPSEARCH toolResourceId 8BALL 16:31:33,638 DEBUG DefaultToolRegistryBuilder:268 - PPSEARCH inputParameters 1 16:31:33,638 DEBUG DefaultToolRegistryBuilder:270 - PPSEARCH outputParameters 0 16:31:33,638 DEBUG DefaultToolRegistryBuilder:271 - PPSEARCH configfile pisexml/ppsearch.xml 16:31:33,639 DEBUG DefaultToolRegistryBuilder:275 - PPSEARCH configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/ppsearch.xml 16:31:33,639 DEBUG DefaultToolRegistryBuilder:279 - PPSEARCH commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,639 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: EPRIMER3 to group: WEB 16:31:33,639 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool EPRIMER3 16:31:33,639 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,639 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool EPRIMER3 16:31:33,640 DEBUG DefaultToolRegistryBuilder:239 - EPRIMER3 Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,640 DEBUG DefaultToolRegistryBuilder:264 - EPRIMER3 Tool Name Picks PCR primers and hybridization oligos (EMBOSS) 16:31:33,640 DEBUG DefaultToolRegistryBuilder:266 - EPRIMER3 toolResourceId 8BALL 16:31:33,640 DEBUG DefaultToolRegistryBuilder:268 - EPRIMER3 inputParameters 1 16:31:33,640 DEBUG DefaultToolRegistryBuilder:270 - EPRIMER3 outputParameters 0 16:31:33,640 DEBUG DefaultToolRegistryBuilder:271 - EPRIMER3 configfile pisexml/eprimer3.xml 16:31:33,641 DEBUG DefaultToolRegistryBuilder:275 - EPRIMER3 configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/eprimer3.xml 16:31:33,641 DEBUG DefaultToolRegistryBuilder:279 - EPRIMER3 commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,641 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PROSEARCH to group: WEB 16:31:33,641 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PROSEARCH 16:31:33,641 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,641 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PROSEARCH 16:31:33,642 DEBUG DefaultToolRegistryBuilder:239 - PROSEARCH Input parameter protein_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,642 DEBUG DefaultToolRegistryBuilder:264 - PROSEARCH Tool Name search Prosite patterns in a sequence 16:31:33,642 DEBUG DefaultToolRegistryBuilder:266 - PROSEARCH toolResourceId 8BALL 16:31:33,642 DEBUG DefaultToolRegistryBuilder:268 - PROSEARCH inputParameters 1 16:31:33,642 DEBUG DefaultToolRegistryBuilder:270 - PROSEARCH outputParameters 0 16:31:33,642 DEBUG DefaultToolRegistryBuilder:271 - PROSEARCH configfile pisexml/prosearch.xml 16:31:33,643 DEBUG DefaultToolRegistryBuilder:275 - PROSEARCH configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/prosearch.xml 16:31:33,643 DEBUG DefaultToolRegistryBuilder:279 - PROSEARCH commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,643 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PROTDIST to group: WEB 16:31:33,643 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PROTDIST 16:31:33,643 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,643 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PROTDIST 16:31:33,644 DEBUG DefaultToolRegistryBuilder:239 - PROTDIST Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,644 DEBUG DefaultToolRegistryBuilder:264 - PROTDIST Tool Name protdist - Program to compute distance matrix from protein sequences 16:31:33,644 DEBUG DefaultToolRegistryBuilder:266 - PROTDIST toolResourceId 8BALL 16:31:33,644 DEBUG DefaultToolRegistryBuilder:268 - PROTDIST inputParameters 1 16:31:33,644 DEBUG DefaultToolRegistryBuilder:270 - PROTDIST outputParameters 0 16:31:33,644 DEBUG DefaultToolRegistryBuilder:271 - PROTDIST configfile pisexml/protdist.xml 16:31:33,645 DEBUG DefaultToolRegistryBuilder:275 - PROTDIST configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/protdist.xml 16:31:33,645 DEBUG DefaultToolRegistryBuilder:279 - PROTDIST commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,645 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PROTPARS to group: WEB 16:31:33,645 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PROTPARS 16:31:33,645 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,647 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PROTPARS 16:31:33,647 DEBUG DefaultToolRegistryBuilder:239 - PROTPARS Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,647 DEBUG DefaultToolRegistryBuilder:264 - PROTPARS Tool Name protpars - Protein Sequence Parcimony Method 16:31:33,647 DEBUG DefaultToolRegistryBuilder:266 - PROTPARS toolResourceId 8BALL 16:31:33,648 DEBUG DefaultToolRegistryBuilder:268 - PROTPARS inputParameters 1 16:31:33,648 DEBUG DefaultToolRegistryBuilder:270 - PROTPARS outputParameters 0 16:31:33,648 DEBUG DefaultToolRegistryBuilder:271 - PROTPARS configfile pisexml/protpars.xml 16:31:33,648 DEBUG DefaultToolRegistryBuilder:275 - PROTPARS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/protpars.xml 16:31:33,648 DEBUG DefaultToolRegistryBuilder:279 - PROTPARS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,648 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PROTEUS to group: WEB 16:31:33,648 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PROTEUS 16:31:33,649 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,649 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PROTEUS 16:31:33,649 DEBUG DefaultToolRegistryBuilder:239 - PROTEUS Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,649 DEBUG DefaultToolRegistryBuilder:264 - PROTEUS Tool Name PROTEUS - Structure Prediction Server 16:31:33,649 DEBUG DefaultToolRegistryBuilder:266 - PROTEUS toolResourceId 8BALL 16:31:33,649 DEBUG DefaultToolRegistryBuilder:268 - PROTEUS inputParameters 1 16:31:33,649 DEBUG DefaultToolRegistryBuilder:270 - PROTEUS outputParameters 0 16:31:33,650 DEBUG DefaultToolRegistryBuilder:271 - PROTEUS configfile pisexml/proteus.xml 16:31:33,650 DEBUG DefaultToolRegistryBuilder:275 - PROTEUS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/proteus.xml 16:31:33,650 DEBUG DefaultToolRegistryBuilder:279 - PROTEUS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,650 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PRSS to group: WEB 16:31:33,650 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PRSS 16:31:33,650 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,650 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PRSS 16:31:33,651 DEBUG DefaultToolRegistryBuilder:239 - PRSS Input parameter query1_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,651 DEBUG DefaultToolRegistryBuilder:264 - PRSS Tool Name Evaluate the signinficance of a protein or DNA similarity. 16:31:33,651 DEBUG DefaultToolRegistryBuilder:266 - PRSS toolResourceId 8BALL 16:31:33,651 DEBUG DefaultToolRegistryBuilder:268 - PRSS inputParameters 1 16:31:33,651 DEBUG DefaultToolRegistryBuilder:270 - PRSS outputParameters 0 16:31:33,651 DEBUG DefaultToolRegistryBuilder:271 - PRSS configfile pisexml/prss.xml 16:31:33,652 DEBUG DefaultToolRegistryBuilder:275 - PRSS configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/prss.xml 16:31:33,652 DEBUG DefaultToolRegistryBuilder:279 - PRSS commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,652 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: PSIBLAST to group: WEB 16:31:33,652 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool PSIBLAST 16:31:33,652 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,652 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool PSIBLAST 16:31:33,653 DEBUG DefaultToolRegistryBuilder:239 - PSIBLAST Input parameter query_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,653 DEBUG DefaultToolRegistryBuilder:261 - PSIBLAST Output parametertxt_output sourceDocumentType: PROTEIN:BLAST_OUTPUT:BLAST_TEXT 16:31:33,653 DEBUG DefaultToolRegistryBuilder:264 - PSIBLAST Tool Name psiblast - Position Specific Iterative Blast 16:31:33,653 DEBUG DefaultToolRegistryBuilder:266 - PSIBLAST toolResourceId 8BALL 16:31:33,653 DEBUG DefaultToolRegistryBuilder:268 - PSIBLAST inputParameters 1 16:31:33,653 DEBUG DefaultToolRegistryBuilder:270 - PSIBLAST outputParameters 1 16:31:33,654 DEBUG DefaultToolRegistryBuilder:271 - PSIBLAST configfile pisexml/psiblast.xml 16:31:33,654 DEBUG DefaultToolRegistryBuilder:275 - PSIBLAST configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/psiblast.xml 16:31:33,654 DEBUG DefaultToolRegistryBuilder:279 - PSIBLAST commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,654 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: RESTRICT to group: WEB 16:31:33,654 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool RESTRICT 16:31:33,654 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,655 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool RESTRICT 16:31:33,655 DEBUG DefaultToolRegistryBuilder:239 - RESTRICT Input parameter sequence_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,655 DEBUG DefaultToolRegistryBuilder:264 - RESTRICT Tool Name Find Restriction Enzyme Sites Using Rebase (EMBOSS) 16:31:33,655 DEBUG DefaultToolRegistryBuilder:266 - RESTRICT toolResourceId 8BALL 16:31:33,655 DEBUG DefaultToolRegistryBuilder:268 - RESTRICT inputParameters 1 16:31:33,655 DEBUG DefaultToolRegistryBuilder:270 - RESTRICT outputParameters 0 16:31:33,656 DEBUG DefaultToolRegistryBuilder:271 - RESTRICT configfile pisexml/restrict.xml 16:31:33,656 DEBUG DefaultToolRegistryBuilder:275 - RESTRICT configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/restrict.xml 16:31:33,656 DEBUG DefaultToolRegistryBuilder:279 - RESTRICT commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,656 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: REVSEQ to group: WEB 16:31:33,656 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool REVSEQ 16:31:33,657 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,657 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool REVSEQ 16:31:33,657 DEBUG DefaultToolRegistryBuilder:239 - REVSEQ Input parameter sequence_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,657 DEBUG DefaultToolRegistryBuilder:264 - REVSEQ Tool Name Reverse and complement a sequence (EMBOSS) 16:31:33,657 DEBUG DefaultToolRegistryBuilder:266 - REVSEQ toolResourceId 8BALL 16:31:33,657 DEBUG DefaultToolRegistryBuilder:268 - REVSEQ inputParameters 1 16:31:33,658 DEBUG DefaultToolRegistryBuilder:270 - REVSEQ outputParameters 0 16:31:33,658 DEBUG DefaultToolRegistryBuilder:271 - REVSEQ configfile pisexml/revseq.xml 16:31:33,658 DEBUG DefaultToolRegistryBuilder:275 - REVSEQ configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/revseq.xml 16:31:33,658 DEBUG DefaultToolRegistryBuilder:279 - REVSEQ commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,658 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: RPSBLAST to group: WEB 16:31:33,658 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool RPSBLAST 16:31:33,659 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,659 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool RPSBLAST 16:31:33,659 DEBUG DefaultToolRegistryBuilder:239 - RPSBLAST Input parameter query_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,659 DEBUG DefaultToolRegistryBuilder:264 - RPSBLAST Tool Name RPS Blast: Reversed Position Specific Blast 16:31:33,659 DEBUG DefaultToolRegistryBuilder:266 - RPSBLAST toolResourceId 8BALL 16:31:33,659 DEBUG DefaultToolRegistryBuilder:268 - RPSBLAST inputParameters 1 16:31:33,660 DEBUG DefaultToolRegistryBuilder:270 - RPSBLAST outputParameters 0 16:31:33,660 DEBUG DefaultToolRegistryBuilder:271 - RPSBLAST configfile pisexml/rpsblast.xml 16:31:33,660 DEBUG DefaultToolRegistryBuilder:275 - RPSBLAST configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/rpsblast.xml 16:31:33,660 DEBUG DefaultToolRegistryBuilder:279 - RPSBLAST commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,660 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: SEQBOOT to group: WEB 16:31:33,660 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool SEQBOOT 16:31:33,661 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,661 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool SEQBOOT 16:31:33,661 DEBUG DefaultToolRegistryBuilder:239 - SEQBOOT Input parameter infile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,661 DEBUG DefaultToolRegistryBuilder:264 - SEQBOOT Tool Name seqboot - Bootstrap, Jackknife, or Permutation Resampling 16:31:33,661 DEBUG DefaultToolRegistryBuilder:266 - SEQBOOT toolResourceId 8BALL 16:31:33,661 DEBUG DefaultToolRegistryBuilder:268 - SEQBOOT inputParameters 1 16:31:33,662 DEBUG DefaultToolRegistryBuilder:270 - SEQBOOT outputParameters 0 16:31:33,662 DEBUG DefaultToolRegistryBuilder:271 - SEQBOOT configfile pisexml/seqboot.xml 16:31:33,662 DEBUG DefaultToolRegistryBuilder:275 - SEQBOOT configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/seqboot.xml 16:31:33,662 DEBUG DefaultToolRegistryBuilder:279 - SEQBOOT commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,663 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: SIXPACK to group: WEB 16:31:33,663 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool SIXPACK 16:31:33,663 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,663 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool SIXPACK 16:31:33,664 DEBUG DefaultToolRegistryBuilder:239 - SIXPACK Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,664 DEBUG DefaultToolRegistryBuilder:264 - SIXPACK Tool Name Display a DNA sequence with 6-frame translation and ORFs (EMBOSS) 16:31:33,664 DEBUG DefaultToolRegistryBuilder:266 - SIXPACK toolResourceId 8BALL 16:31:33,664 DEBUG DefaultToolRegistryBuilder:268 - SIXPACK inputParameters 1 16:31:33,664 DEBUG DefaultToolRegistryBuilder:270 - SIXPACK outputParameters 0 16:31:33,664 DEBUG DefaultToolRegistryBuilder:271 - SIXPACK configfile pisexml/sixpack.xml 16:31:33,665 DEBUG DefaultToolRegistryBuilder:275 - SIXPACK configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/sixpack.xml 16:31:33,665 DEBUG DefaultToolRegistryBuilder:279 - SIXPACK commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,665 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: SPIDEY to group: WEB 16:31:33,665 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool SPIDEY 16:31:33,665 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,665 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool SPIDEY 16:31:33,666 DEBUG DefaultToolRegistryBuilder:239 - SPIDEY Input parameter infile_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,666 DEBUG DefaultToolRegistryBuilder:264 - SPIDEY Tool Name Aligns mRNA sequences to a genomic sequence 16:31:33,666 DEBUG DefaultToolRegistryBuilder:266 - SPIDEY toolResourceId 8BALL 16:31:33,666 DEBUG DefaultToolRegistryBuilder:268 - SPIDEY inputParameters 1 16:31:33,666 DEBUG DefaultToolRegistryBuilder:270 - SPIDEY outputParameters 0 16:31:33,666 DEBUG DefaultToolRegistryBuilder:271 - SPIDEY configfile pisexml/spidey.xml 16:31:33,667 DEBUG DefaultToolRegistryBuilder:275 - SPIDEY configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/spidey.xml 16:31:33,667 DEBUG DefaultToolRegistryBuilder:279 - SPIDEY commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,667 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: SSEARCH_N to group: WEB 16:31:33,667 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool SSEARCH_N 16:31:33,667 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,667 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool SSEARCH_N 16:31:33,667 DEBUG DefaultToolRegistryBuilder:239 - SSEARCH_N Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,668 DEBUG DefaultToolRegistryBuilder:261 - SSEARCH_N Output parameteroutfile sourceDocumentType: NUCLEIC_ACID:FASTA_OUTPUT:FASTOUT 16:31:33,668 DEBUG DefaultToolRegistryBuilder:264 - SSEARCH_N Tool Name Sequence database search (version 3) 16:31:33,668 DEBUG DefaultToolRegistryBuilder:266 - SSEARCH_N toolResourceId 8BALL 16:31:33,668 DEBUG DefaultToolRegistryBuilder:268 - SSEARCH_N inputParameters 1 16:31:33,668 DEBUG DefaultToolRegistryBuilder:270 - SSEARCH_N outputParameters 1 16:31:33,668 DEBUG DefaultToolRegistryBuilder:271 - SSEARCH_N configfile pisexml/ssearch_n.xml 16:31:33,669 DEBUG DefaultToolRegistryBuilder:275 - SSEARCH_N configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/ssearch_n.xml 16:31:33,669 DEBUG DefaultToolRegistryBuilder:279 - SSEARCH_N commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,669 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: SSEARCH_P to group: WEB 16:31:33,669 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool SSEARCH_P 16:31:33,669 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,669 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool SSEARCH_P 16:31:33,670 DEBUG DefaultToolRegistryBuilder:239 - SSEARCH_P Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,670 DEBUG DefaultToolRegistryBuilder:261 - SSEARCH_P Output parameteroutfile sourceDocumentType: PROTEIN:FASTA_OUTPUT:FASTOUT 16:31:33,670 DEBUG DefaultToolRegistryBuilder:264 - SSEARCH_P Tool Name Sequence database search (version 3) 16:31:33,670 DEBUG DefaultToolRegistryBuilder:266 - SSEARCH_P toolResourceId 8BALL 16:31:33,670 DEBUG DefaultToolRegistryBuilder:268 - SSEARCH_P inputParameters 1 16:31:33,670 DEBUG DefaultToolRegistryBuilder:270 - SSEARCH_P outputParameters 1 16:31:33,670 DEBUG DefaultToolRegistryBuilder:271 - SSEARCH_P configfile pisexml/ssearch_p.xml 16:31:33,671 DEBUG DefaultToolRegistryBuilder:275 - SSEARCH_P configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/ssearch_p.xml 16:31:33,671 DEBUG DefaultToolRegistryBuilder:279 - SSEARCH_P commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,671 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TACG to group: WEB 16:31:33,671 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TACG 16:31:33,671 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,671 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TACG 16:31:33,672 DEBUG DefaultToolRegistryBuilder:239 - TACG Input parameter sequence_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,672 DEBUG DefaultToolRegistryBuilder:264 - TACG Tool Name Restriction Enzyme analysis 16:31:33,672 DEBUG DefaultToolRegistryBuilder:266 - TACG toolResourceId 8BALL 16:31:33,672 DEBUG DefaultToolRegistryBuilder:268 - TACG inputParameters 1 16:31:33,672 DEBUG DefaultToolRegistryBuilder:270 - TACG outputParameters 0 16:31:33,672 DEBUG DefaultToolRegistryBuilder:271 - TACG configfile pisexml/tacg.xml 16:31:33,673 DEBUG DefaultToolRegistryBuilder:275 - TACG configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tacg.xml 16:31:33,673 DEBUG DefaultToolRegistryBuilder:279 - TACG commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,673 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TBLASTN to group: WEB 16:31:33,673 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TBLASTN 16:31:33,674 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,674 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TBLASTN 16:31:33,674 DEBUG DefaultToolRegistryBuilder:239 - TBLASTN Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,674 DEBUG DefaultToolRegistryBuilder:261 - TBLASTN Output parametertmp_outfile sourceDocumentType: PROTEIN:BLAST_OUTPUT:BLAST_TEXT 16:31:33,674 DEBUG DefaultToolRegistryBuilder:264 - TBLASTN Tool Name with gaps 16:31:33,674 DEBUG DefaultToolRegistryBuilder:266 - TBLASTN toolResourceId 8BALL 16:31:33,675 DEBUG DefaultToolRegistryBuilder:268 - TBLASTN inputParameters 1 16:31:33,675 DEBUG DefaultToolRegistryBuilder:270 - TBLASTN outputParameters 1 16:31:33,675 DEBUG DefaultToolRegistryBuilder:271 - TBLASTN configfile pisexml/tblastn.xml 16:31:33,675 DEBUG DefaultToolRegistryBuilder:275 - TBLASTN configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tblastn.xml 16:31:33,675 DEBUG DefaultToolRegistryBuilder:279 - TBLASTN commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,675 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TBLASTX to group: WEB 16:31:33,675 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TBLASTX 16:31:33,676 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,676 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TBLASTX 16:31:33,678 DEBUG DefaultToolRegistryBuilder:239 - TBLASTX Input parameter query_ mapped to sourceDocumentType: NUCLEIC_ACID:SEQUENCE:FASTA 16:31:33,678 DEBUG DefaultToolRegistryBuilder:261 - TBLASTX Output parametertmp_outfile sourceDocumentType: PROTEIN:BLAST_OUTPUT:BLAST_TEXT 16:31:33,678 DEBUG DefaultToolRegistryBuilder:264 - TBLASTX Tool Name with gaps 16:31:33,678 DEBUG DefaultToolRegistryBuilder:266 - TBLASTX toolResourceId 8BALL 16:31:33,678 DEBUG DefaultToolRegistryBuilder:268 - TBLASTX inputParameters 1 16:31:33,678 DEBUG DefaultToolRegistryBuilder:270 - TBLASTX outputParameters 1 16:31:33,679 DEBUG DefaultToolRegistryBuilder:271 - TBLASTX configfile pisexml/tblastx.xml 16:31:33,679 DEBUG DefaultToolRegistryBuilder:275 - TBLASTX configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tblastx.xml 16:31:33,679 DEBUG DefaultToolRegistryBuilder:279 - TBLASTX commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,679 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TFASTA to group: WEB 16:31:33,679 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TFASTA 16:31:33,679 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,680 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TFASTA 16:31:33,680 DEBUG DefaultToolRegistryBuilder:239 - TFASTA Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,680 DEBUG DefaultToolRegistryBuilder:261 - TFASTA Output parameteroutfile sourceDocumentType: PROTEIN:FASTA_OUTPUT:FASTOUT 16:31:33,680 DEBUG DefaultToolRegistryBuilder:264 - TFASTA Tool Name Sequence database search (version 3) 16:31:33,680 DEBUG DefaultToolRegistryBuilder:266 - TFASTA toolResourceId 8BALL 16:31:33,680 DEBUG DefaultToolRegistryBuilder:268 - TFASTA inputParameters 1 16:31:33,680 DEBUG DefaultToolRegistryBuilder:270 - TFASTA outputParameters 1 16:31:33,681 DEBUG DefaultToolRegistryBuilder:271 - TFASTA configfile pisexml/tfasta.xml 16:31:33,681 DEBUG DefaultToolRegistryBuilder:275 - TFASTA configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tfasta.xml 16:31:33,681 DEBUG DefaultToolRegistryBuilder:279 - TFASTA commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,681 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TFASTX to group: WEB 16:31:33,681 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TFASTX 16:31:33,681 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,682 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TFASTX 16:31:33,682 DEBUG DefaultToolRegistryBuilder:239 - TFASTX Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,682 DEBUG DefaultToolRegistryBuilder:261 - TFASTX Output parameteroutfile sourceDocumentType: PROTEIN:FASTA_OUTPUT:FASTOUT 16:31:33,682 DEBUG DefaultToolRegistryBuilder:264 - TFASTX Tool Name Sequence database search (version 3) 16:31:33,682 DEBUG DefaultToolRegistryBuilder:266 - TFASTX toolResourceId 8BALL 16:31:33,683 DEBUG DefaultToolRegistryBuilder:268 - TFASTX inputParameters 1 16:31:33,683 DEBUG DefaultToolRegistryBuilder:270 - TFASTX outputParameters 1 16:31:33,683 DEBUG DefaultToolRegistryBuilder:271 - TFASTX configfile pisexml/tfastx.xml 16:31:33,683 DEBUG DefaultToolRegistryBuilder:275 - TFASTX configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tfastx.xml 16:31:33,683 DEBUG DefaultToolRegistryBuilder:279 - TFASTX commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,683 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TFASTY to group: WEB 16:31:33,683 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TFASTY 16:31:33,684 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,684 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TFASTY 16:31:33,684 DEBUG DefaultToolRegistryBuilder:239 - TFASTY Input parameter query_ mapped to sourceDocumentType: PROTEIN:SEQUENCE:FASTA 16:31:33,684 DEBUG DefaultToolRegistryBuilder:261 - TFASTY Output parameteroutfile sourceDocumentType: PROTEIN:FASTA_OUTPUT:FASTOUT 16:31:33,684 DEBUG DefaultToolRegistryBuilder:264 - TFASTY Tool Name Sequence database search (version 3) 16:31:33,684 DEBUG DefaultToolRegistryBuilder:266 - TFASTY toolResourceId 8BALL 16:31:33,685 DEBUG DefaultToolRegistryBuilder:268 - TFASTY inputParameters 1 16:31:33,685 DEBUG DefaultToolRegistryBuilder:270 - TFASTY outputParameters 1 16:31:33,685 DEBUG DefaultToolRegistryBuilder:271 - TFASTY configfile pisexml/tfasty.xml 16:31:33,685 DEBUG DefaultToolRegistryBuilder:275 - TFASTY configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tfasty.xml 16:31:33,685 DEBUG DefaultToolRegistryBuilder:279 - TFASTY commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,686 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TMAP to group: WEB 16:31:33,686 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TMAP 16:31:33,686 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,686 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TMAP 16:31:33,686 DEBUG DefaultToolRegistryBuilder:239 - TMAP Input parameter sequences_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,686 DEBUG DefaultToolRegistryBuilder:264 - TMAP Tool Name Displays membrane spanning regions (EMBOSS) 16:31:33,687 DEBUG DefaultToolRegistryBuilder:266 - TMAP toolResourceId 8BALL 16:31:33,687 DEBUG DefaultToolRegistryBuilder:268 - TMAP inputParameters 1 16:31:33,687 DEBUG DefaultToolRegistryBuilder:270 - TMAP outputParameters 0 16:31:33,687 DEBUG DefaultToolRegistryBuilder:271 - TMAP configfile pisexml/tmap.xml 16:31:33,687 DEBUG DefaultToolRegistryBuilder:275 - TMAP configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/tmap.xml 16:31:33,687 DEBUG DefaultToolRegistryBuilder:279 - TMAP commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,688 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: UNROOT to group: WEB 16:31:33,688 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool UNROOT 16:31:33,688 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,688 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool UNROOT 16:31:33,688 DEBUG DefaultToolRegistryBuilder:239 - UNROOT Input parameter treefile_ mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,688 DEBUG DefaultToolRegistryBuilder:264 - UNROOT Tool Name unroot: use of RETREE to unroot a tree 16:31:33,688 DEBUG DefaultToolRegistryBuilder:266 - UNROOT toolResourceId 8BALL 16:31:33,689 DEBUG DefaultToolRegistryBuilder:268 - UNROOT inputParameters 1 16:31:33,689 DEBUG DefaultToolRegistryBuilder:270 - UNROOT outputParameters 0 16:31:33,689 DEBUG DefaultToolRegistryBuilder:271 - UNROOT configfile pisexml/unroot.xml 16:31:33,689 DEBUG DefaultToolRegistryBuilder:275 - UNROOT configFileUrl jar:file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/pisexml/unroot.xml 16:31:33,689 DEBUG DefaultToolRegistryBuilder:279 - UNROOT commandRendererClassName org.ngbw.pise.commandrenderer.PiseCommandRenderer 16:31:33,690 DEBUG DefaultToolRegistryBuilder:114 - Dispatching ToolGroup SIRIUSWB 16:31:33,690 DEBUG DefaultToolRegistryBuilder:183 - Processing 2 Tools 16:31:33,690 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: TMALIGN to group: SIRIUSWB 16:31:33,690 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool TMALIGN 16:31:33,690 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,690 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool TMALIGN 16:31:33,691 DEBUG DefaultToolRegistryBuilder:239 - TMALIGN Input parameter null mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,691 DEBUG DefaultToolRegistryBuilder:264 - TMALIGN Tool Name TMalign_32: structure alignment program 16:31:33,691 DEBUG DefaultToolRegistryBuilder:266 - TMALIGN toolResourceId SNOOKER 16:31:33,691 DEBUG DefaultToolRegistryBuilder:268 - TMALIGN inputParameters 1 16:31:33,691 DEBUG DefaultToolRegistryBuilder:270 - TMALIGN outputParameters 0 16:31:33,691 DEBUG DefaultToolRegistryBuilder:271 - TMALIGN configfile null 16:31:33,692 DEBUG DefaultToolRegistryBuilder:279 - TMALIGN commandRendererClassName null 16:31:33,692 DEBUG DefaultToolRegistryBuilder:193 - Assign Tool: POVRAY to group: SIRIUSWB 16:31:33,692 DEBUG DefaultToolRegistryBuilder:194 - Dispatching Tool POVRAY 16:31:33,692 DEBUG DefaultToolRegistryBuilder:202 - Handling node Tool 16:31:33,693 DEBUG DefaultToolRegistryBuilder:210 - Configuring tool POVRAY 16:31:33,693 DEBUG DefaultToolRegistryBuilder:239 - POVRAY Input parameter null mapped to sourceDocumentType: UNKNOWN:UNKNOWN:UNKNOWN 16:31:33,693 DEBUG DefaultToolRegistryBuilder:264 - POVRAY Tool Name Povray: Open Source Raytracer 16:31:33,693 DEBUG DefaultToolRegistryBuilder:266 - POVRAY toolResourceId SNOOKER 16:31:33,693 DEBUG DefaultToolRegistryBuilder:268 - POVRAY inputParameters 1 16:31:33,693 DEBUG DefaultToolRegistryBuilder:270 - POVRAY outputParameters 0 16:31:33,693 DEBUG DefaultToolRegistryBuilder:271 - POVRAY configfile null 16:31:33,694 DEBUG DefaultToolRegistryBuilder:279 - POVRAY commandRendererClassName null 16:31:33,694 DEBUG DefaultToolRegistryBuilder:56 - extraTools is tool/.*-reg\.xml 16:31:33,694 DEBUG Resource:101 - getMatchingResources for tool/.*-reg\.xml 16:31:33,694 DEBUG Resource:70 - listResources tool/, .*-reg\.xml 16:31:33,694 DEBUG Resource:77 - Looking for extra tools, found directory tool/ at file:/Users/markmiller/.m2/repository/org/ngbw/sdk/1.3-SNAPSHOT/sdk-1.3-SNAPSHOT.jar!/tool/ 16:31:33,695 DEBUG DefaultToolRegistryBuilder:70 - Found 0 extra tools. 16:31:33,719 DEBUG DefaultConversionRegistryBuilder:50 - Processing 9 SourceDocumentReaders 16:31:33,720 DEBUG DefaultConversionRegistryBuilder:160 - Processing 7 SourceDocumentTypes 16:31:33,720 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:MSF : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,720 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:MSF : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,720 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:HTML : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,720 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:HTML : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,721 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for COMPOUND:STRUCTURE:MMCIF : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,721 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:STRUCTURE:MMCIF : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,721 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:STRUCTURE:MMCIF : org.ngbw.sdk.api.conversion.MockSourceDocumentReader 16:31:33,723 DEBUG DefaultConversionRegistryBuilder:160 - Processing 7 SourceDocumentTypes 16:31:33,725 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for TAXON:PHYLOGENETIC_TREE:NEWICK : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,725 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:PHYLOGENETIC_TREE:NEWICK : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,725 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:PHYLOGENETIC_TREE:NEWICK : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,727 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for CONTINUOUS_CHARACTER:MATRIX:PHYLIP : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,727 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for DISCRETE_CHARACTER:MATRIX:PHYLIP : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,727 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for APPLICATION_DATA:SERIALIZED_BINARY:SIRIUSWB : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,727 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for UNKNOWN:UNKNOWN:UNKNOWN : org.ngbw.sdk.conversion.UnknownSourceDocumentReader 16:31:33,728 DEBUG DefaultConversionRegistryBuilder:160 - Processing 7 SourceDocumentTypes 16:31:33,732 DEBUG FlatfileParser:275 - Map RecordType.COMPOUND_STRUCTURE to DataFormat.PDB 16:31:33,733 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.PDB regex: ^HEADER\s+.*(\w{4})\s+$ isCollection: false separator: null dateFormat: null 16:31:33,733 DEBUG FlatfileParser:265 - Adding RecordField: TYPE DataFormat.PDB regex: ^EXPDTA\s+(\w.*\w)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,734 DEBUG FlatfileParser:265 - Adding RecordField: RESOLUTION DataFormat.PDB regex: ^REMARK\s+.+RESOLUTION\.\s+([\d.*\d?]+)\s+ANGSTROMS\.\s+$ isCollection: false separator: null dateFormat: null 16:31:33,734 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.PDB regex: TITLE\s+\d?\s(.*\S)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,735 DEBUG FlatfileParser:265 - Adding RecordField: AUTHOR DataFormat.PDB regex: ^AUTHOR\s+\d?\s(.*\S;?)\s+$ isCollection: true separator: \s*,\s* dateFormat: null 16:31:33,735 DEBUG FlatfileParser:265 - Adding RecordField: MOLECULE DataFormat.PDB regex: ^COMPND\s+\d?\sMOLECULE:\s+(.*\S;?)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,735 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.PDB regex: ^SOURCE\s+\d?\sORGANISM_SCIENTIFIC:\s(\S.*[^\s;]);?\s+$ isCollection: true separator: null dateFormat: null 16:31:33,736 DEBUG FlatfileParser:265 - Adding RecordField: DEPOSITION_DATE DataFormat.PDB regex: ^HEADER\s+.*(\d{2}-\w{3}-\d{2})\s.*$ isCollection: false separator: null dateFormat: dd-MMM-yy 16:31:33,736 DEBUG FlatfileParser:265 - Adding RecordField: MODIFICATION_DATE DataFormat.PDB regex: ^REVDAT\s+\d?\s+(\d{2}-\w{3}-\d{2})\s.*$ isCollection: true separator: null dateFormat: dd-MMM-yy 16:31:33,736 DEBUG FlatfileParser:275 - Map RecordType.NUCLEIC_ACID_STRUCTURE to DataFormat.PDB 16:31:33,737 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.PDB regex: ^HEADER\s+.*(\w{4})\s+$ isCollection: false separator: null dateFormat: null 16:31:33,737 DEBUG FlatfileParser:265 - Adding RecordField: TYPE DataFormat.PDB regex: ^EXPDTA\s+(\w.*\w)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,737 DEBUG FlatfileParser:265 - Adding RecordField: RESOLUTION DataFormat.PDB regex: ^REMARK\s+.+RESOLUTION\.\s+([\d.*\d?]+)\s+ANGSTROMS\.\s+$ isCollection: false separator: null dateFormat: null 16:31:33,737 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.PDB regex: TITLE\s+\d?\s(.*\S)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,738 DEBUG FlatfileParser:265 - Adding RecordField: AUTHOR DataFormat.PDB regex: ^AUTHOR\s+\d?\s(.*\S;?)\s+$ isCollection: true separator: \s*,\s* dateFormat: null 16:31:33,738 DEBUG FlatfileParser:265 - Adding RecordField: MOLECULE DataFormat.PDB regex: ^COMPND\s+\d?\sMOLECULE:\s+(.*\S;?)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,738 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.PDB regex: ^SOURCE\s+\d?\sORGANISM_SCIENTIFIC:\s(\S.*[^\s;]);?\s+$ isCollection: true separator: null dateFormat: null 16:31:33,739 DEBUG FlatfileParser:265 - Adding RecordField: DEPOSITION_DATE DataFormat.PDB regex: ^HEADER\s+.*(\d{2}-\w{3}-\d{2})\s.*$ isCollection: false separator: null dateFormat: dd-MMM-yy 16:31:33,739 DEBUG FlatfileParser:265 - Adding RecordField: MODIFICATION_DATE DataFormat.PDB regex: ^REVDAT\s+\d?\s+(\d{2}-\w{3}-\d{2})\s.*$ isCollection: true separator: null dateFormat: dd-MMM-yy 16:31:33,740 DEBUG FlatfileParser:275 - Map RecordType.PROTEIN_STRUCTURE to DataFormat.PDB 16:31:33,740 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.PDB regex: ^HEADER\s+.*(\w{4})\s+$ isCollection: false separator: null dateFormat: null 16:31:33,740 DEBUG FlatfileParser:265 - Adding RecordField: TYPE DataFormat.PDB regex: ^EXPDTA\s+(\w.*\w)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,741 DEBUG FlatfileParser:265 - Adding RecordField: RESOLUTION DataFormat.PDB regex: ^REMARK\s+.+RESOLUTION\.\s+([\d.*\d?]+)\s+ANGSTROMS\.\s+$ isCollection: false separator: null dateFormat: null 16:31:33,741 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.PDB regex: TITLE\s+\d?\s(.*\S)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,741 DEBUG FlatfileParser:265 - Adding RecordField: AUTHOR DataFormat.PDB regex: ^AUTHOR\s+\d?\s(.*\S;?)\s+$ isCollection: true separator: \s*,\s* dateFormat: null 16:31:33,742 DEBUG FlatfileParser:265 - Adding RecordField: MOLECULE DataFormat.PDB regex: ^COMPND\s+\d?\sMOLECULE:\s+(.*\S;?)\s+$ isCollection: false separator: null dateFormat: null 16:31:33,742 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.PDB regex: ^SOURCE\s+\d?\sORGANISM_SCIENTIFIC:\s(\S.*[^\s;]);?\s+$ isCollection: true separator: null dateFormat: null 16:31:33,742 DEBUG FlatfileParser:265 - Adding RecordField: DEPOSITION_DATE DataFormat.PDB regex: ^HEADER\s+.*(\d{2}-\w{3}-\d{2})\s.*$ isCollection: false separator: null dateFormat: dd-MMM-yy 16:31:33,743 DEBUG FlatfileParser:265 - Adding RecordField: MODIFICATION_DATE DataFormat.PDB regex: ^REVDAT\s+\d?\s+(\d{2}-\w{3}-\d{2})\s.*$ isCollection: true separator: null dateFormat: dd-MMM-yy 16:31:33,743 DEBUG FlatfileParser:275 - Map RecordType.PROTEIN_SEQUENCE to DataFormat.UNIPROT 16:31:33,743 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.UNIPROT regex: ^AC\s+(\w+);.*$ isCollection: false separator: null dateFormat: null 16:31:33,743 DEBUG FlatfileParser:265 - Adding RecordField: ALTERNATIVE_ID DataFormat.UNIPROT regex: ^ID\s+([\w_]+).*$ isCollection: false separator: null dateFormat: null 16:31:33,744 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.UNIPROT regex: ^DE\s+(.*?)\.?$ isCollection: false separator: null dateFormat: null 16:31:33,744 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.UNIPROT regex: ^OS\s+([^()]+).*$ isCollection: false separator: null dateFormat: null 16:31:33,744 DEBUG FlatfileParser:265 - Adding RecordField: VERSION DataFormat.UNIPROT regex: ^DT.*entry version (\d*).*$ isCollection: false separator: null dateFormat: null 16:31:33,745 DEBUG FlatfileParser:275 - Map RecordType.PROTEIN_SEQUENCE to DataFormat.GENPEPT 16:31:33,745 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.GENPEPT regex: ^ACCESSION\s+(\S*) isCollection: false separator: null dateFormat: null 16:31:33,745 DEBUG FlatfileParser:265 - Adding RecordField: ALTERNATIVE_ID DataFormat.GENPEPT regex: ^VERSION\s+.*GI:(\d+) isCollection: false separator: null dateFormat: null 16:31:33,745 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.GENPEPT regex: ^DEFINITION\s+(.*[^\.]+)\.? isCollection: false separator: null dateFormat: null 16:31:33,746 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.GENPEPT regex: ^\s+ORGANISM\s+(.*) isCollection: false separator: null dateFormat: null 16:31:33,746 DEBUG FlatfileParser:265 - Adding RecordField: VERSION DataFormat.GENPEPT regex: ^VERSION\s+(\S+)\s+GI:.* isCollection: false separator: null dateFormat: null 16:31:33,746 DEBUG FlatfileParser:275 - Map RecordType.NUCLEIC_ACID_SEQUENCE to DataFormat.GENBANK 16:31:33,747 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.GENBANK regex: ^ACCESSION\s+(\S*) isCollection: false separator: null dateFormat: null 16:31:33,747 DEBUG FlatfileParser:265 - Adding RecordField: ALTERNATIVE_ID DataFormat.GENBANK regex: ^VERSION\s+.*GI:(\d+) isCollection: false separator: null dateFormat: null 16:31:33,748 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.GENBANK regex: ^DEFINITION\s+(.*[^\.]+)\.? isCollection: false separator: null dateFormat: null 16:31:33,748 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.GENBANK regex: ^\s+ORGANISM\s+(.*) isCollection: false separator: null dateFormat: null 16:31:33,749 DEBUG FlatfileParser:265 - Adding RecordField: VERSION DataFormat.GENBANK regex: ^VERSION\s+(\S+)\s+GI:.* isCollection: false separator: null dateFormat: null 16:31:33,749 DEBUG FlatfileParser:275 - Map RecordType.NUCLEIC_ACID_SEQUENCE to DataFormat.EMBL 16:31:33,749 DEBUG FlatfileParser:265 - Adding RecordField: PRIMARY_ID DataFormat.EMBL regex: ^AC\s+(\w+);.*$ isCollection: false separator: null dateFormat: null 16:31:33,749 DEBUG FlatfileParser:265 - Adding RecordField: ALTERNATIVE_ID DataFormat.EMBL regex: ^ID\s+([\w_]+).*$ isCollection: false separator: null dateFormat: null 16:31:33,750 DEBUG FlatfileParser:265 - Adding RecordField: NAME DataFormat.EMBL regex: ^DE\s+(.*?)\.?$ isCollection: false separator: null dateFormat: null 16:31:33,752 DEBUG FlatfileParser:265 - Adding RecordField: ORGANISM DataFormat.EMBL regex: ^OS\s+([^()]+).*$ isCollection: false separator: null dateFormat: null 16:31:33,752 DEBUG FlatfileParser:265 - Adding RecordField: VERSION DataFormat.EMBL regex: ^DT.*entry version (\d*).*$ isCollection: false separator: null dateFormat: null 16:31:33,753 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for COMPOUND:STRUCTURE:PDB : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,754 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:STRUCTURE:PDB : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,756 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:STRUCTURE:PDB : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,757 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE:UNIPROT : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,758 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE:GENPEPT : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,758 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE:GENBANK : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,759 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE:EMBL : org.ngbw.sdk.conversion.FlatfileReader 16:31:33,761 DEBUG DefaultConversionRegistryBuilder:160 - Processing 2 SourceDocumentTypes 16:31:33,761 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE:FASTA : org.ngbw.sdk.conversion.FastaReader 16:31:33,762 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE:FASTA : org.ngbw.sdk.conversion.FastaReader 16:31:33,766 DEBUG DefaultConversionRegistryBuilder:160 - Processing 2 SourceDocumentTypes 16:31:33,766 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE:PDB_FINDER : org.ngbw.sdk.conversion.PdbFinderParser 16:31:33,766 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE:PDB_FINDER : org.ngbw.sdk.conversion.PdbFinderParser 16:31:33,767 DEBUG DefaultConversionRegistryBuilder:160 - Processing 10 SourceDocumentTypes 16:31:33,767 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:CLUSTAL : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,767 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:CLUSTAL : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,768 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:NEEDLE : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,768 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:NEEDLE : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,768 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:PHYLIP : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,768 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:PHYLIP : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,768 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:NEXUS : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,769 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:NEXUS : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,769 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:SEQUENCE_ALIGNMENT:FASTA : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,769 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:SEQUENCE_ALIGNMENT:FASTA : org.ngbw.sdk.conversion.SequenceAlignmentReader 16:31:33,770 DEBUG DefaultConversionRegistryBuilder:160 - Processing 2 SourceDocumentTypes 16:31:33,770 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:BLAST_OUTPUT:BLAST_TEXT : org.ngbw.sdk.conversion.BlastTEXTReader 16:31:33,771 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:BLAST_OUTPUT:BLAST_TEXT : org.ngbw.sdk.conversion.BlastTEXTReader 16:31:33,774 DEBUG DefaultConversionRegistryBuilder:160 - Processing 2 SourceDocumentTypes 16:31:33,774 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:BLAST_OUTPUT:BLAST_XML : org.ngbw.sdk.conversion.BlastXMLReader 16:31:33,774 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:BLAST_OUTPUT:BLAST_XML : org.ngbw.sdk.conversion.BlastXMLReader 16:31:33,776 DEBUG DefaultConversionRegistryBuilder:160 - Processing 2 SourceDocumentTypes 16:31:33,776 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for PROTEIN:FASTA_OUTPUT:FASTOUT : org.ngbw.sdk.conversion.FastaOutputReader 16:31:33,776 INFO DefaultConversionRegistry:183 - Registered SourceDocumentReader for NUCLEIC_ACID:FASTA_OUTPUT:FASTOUT : org.ngbw.sdk.conversion.FastaOutputReader 16:31:33,776 DEBUG DefaultConversionRegistryBuilder:59 - Processing 1 SourceDocumentConverters 16:31:33,779 INFO DefaultConversionRegistry:167 - Conversion: PROTEIN:SEQUENCE:UNIPROT to PROTEIN:SEQUENCE:FASTA converterClass org.ngbw.sdk.conversion.SequenceFormatConverter 16:31:33,779 INFO DefaultConversionRegistry:167 - Conversion: NUCLEIC_ACID:SEQUENCE:GENBANK to NUCLEIC_ACID:SEQUENCE:FASTA converterClass org.ngbw.sdk.conversion.SequenceFormatConverter 16:31:33,780 INFO DefaultConversionRegistry:167 - Conversion: PROTEIN:SEQUENCE:GENPEPT to PROTEIN:SEQUENCE:FASTA converterClass org.ngbw.sdk.conversion.SequenceFormatConverter 16:31:33,780 INFO DefaultConversionRegistry:167 - Conversion: NUCLEIC_ACID:SEQUENCE:EMBL to NUCLEIC_ACID:SEQUENCE:FASTA converterClass org.ngbw.sdk.conversion.SequenceFormatConverter 16:31:33,780 INFO DefaultConversionRegistry:167 - Conversion: NUCLEIC_ACID:SEQUENCE:PDB_FINDER to NUCLEIC_ACID:SEQUENCE:FASTA converterClass org.ngbw.sdk.conversion.SequenceFormatConverter 16:31:33,781 INFO DefaultConversionRegistry:167 - Conversion: PROTEIN:SEQUENCE:PDB_FINDER to PROTEIN:SEQUENCE:FASTA converterClass org.ngbw.sdk.conversion.SequenceFormatConverter 16:31:33,781 DEBUG DefaultConversionRegistryBuilder:68 - Processing 5 RecordFilters 16:31:33,782 DEBUG DefaultConversionRegistryBuilder:116 - Processing 1 DataFormat nodes for RecordFilter org.ngbw.sdk.conversion.BlastTEXTRecordFilter 16:31:33,782 INFO DefaultConversionRegistry:193 - Registered RecordFilter for BLAST_TEXT : org.ngbw.sdk.conversion.BlastTEXTRecordFilter 16:31:33,783 DEBUG DefaultConversionRegistryBuilder:116 - Processing 1 DataFormat nodes for RecordFilter org.ngbw.sdk.conversion.FastaOutputRecordFilter 16:31:33,784 INFO DefaultConversionRegistry:193 - Registered RecordFilter for FASTOUT : org.ngbw.sdk.conversion.FastaOutputRecordFilter 16:31:33,786 INFO FlatfileRecordFilter:133 - Registered DataFormat.FASTA startRegex: '^>.*' endRegex: 'null' 16:31:33,786 INFO FlatfileRecordFilter:133 - Registered DataFormat.GENBANK startRegex: '^LOCUS\s+' endRegex: '^\s*//\s*$' 16:31:33,786 INFO FlatfileRecordFilter:133 - Registered DataFormat.GENPEPT startRegex: '^LOCUS\s+' endRegex: '^\s*//\s*$' 16:31:33,787 INFO FlatfileRecordFilter:133 - Registered DataFormat.UNIPROT startRegex: '^ID\s+' endRegex: '^\s*//\s*$' 16:31:33,787 INFO FlatfileRecordFilter:133 - Registered DataFormat.EMBL startRegex: '^ID\s+' endRegex: '^\s*//\s*$' 16:31:33,787 INFO FlatfileRecordFilter:133 - Registered DataFormat.PDB startRegex: '^HEADER\s+' endRegex: '^END\s*$' 16:31:33,787 DEBUG DefaultConversionRegistryBuilder:116 - Processing 6 DataFormat nodes for RecordFilter org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,787 INFO DefaultConversionRegistry:193 - Registered RecordFilter for FASTA : org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,788 INFO DefaultConversionRegistry:193 - Registered RecordFilter for GENBANK : org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,788 INFO DefaultConversionRegistry:193 - Registered RecordFilter for GENPEPT : org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,788 INFO DefaultConversionRegistry:193 - Registered RecordFilter for UNIPROT : org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,788 INFO DefaultConversionRegistry:193 - Registered RecordFilter for EMBL : org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,788 INFO DefaultConversionRegistry:193 - Registered RecordFilter for PDB : org.ngbw.sdk.conversion.FlatfileRecordFilter 16:31:33,788 DEBUG DefaultConversionRegistryBuilder:116 - Processing 1 DataFormat nodes for RecordFilter org.ngbw.sdk.conversion.PdbFinderParser 16:31:33,789 INFO DefaultConversionRegistry:193 - Registered RecordFilter for PDB_FINDER : org.ngbw.sdk.conversion.PdbFinderParser 16:31:33,790 INFO XMLFileRecordFilter:51 - Registered DataFormat.UNIPROT_XML recordNode: 'entry' 16:31:33,791 INFO XMLFileRecordFilter:51 - Registered DataFormat.EMBL_XML recordNode: 'entry' 16:31:33,791 DEBUG DefaultConversionRegistryBuilder:116 - Processing 2 DataFormat nodes for RecordFilter org.ngbw.sdk.conversion.XMLFileRecordFilter 16:31:33,791 INFO DefaultConversionRegistry:193 - Registered RecordFilter for UNIPROT_XML : org.ngbw.sdk.conversion.XMLFileRecordFilter 16:31:33,791 INFO DefaultConversionRegistry:193 - Registered RecordFilter for EMBL_XML : org.ngbw.sdk.conversion.XMLFileRecordFilter 16:31:33,791 DEBUG DefaultConversionRegistryBuilder:77 - Processing 1 SequenceParsers 16:31:33,794 INFO DefaultSequenceParser:106 - Registered DataFormat.GENBANK regex: '\nORIGIN[^\n]*(.*)//' 16:31:33,794 INFO DefaultSequenceParser:106 - Registered DataFormat.GENPEPT regex: '\nORIGIN[^\n]*(.*)//' 16:31:33,795 INFO DefaultSequenceParser:106 - Registered DataFormat.FASTA regex: '>[^\n]+(.*)' 16:31:33,795 INFO DefaultSequenceParser:106 - Registered DataFormat.UNIPROT regex: '\nSQ.*;\n(.*)\n//' 16:31:33,795 INFO DefaultSequenceParser:106 - Registered DataFormat.EMBL regex: '\nSQ.*;\n(.*)\n//' 16:31:33,795 INFO DefaultSequenceParser:120 - Registered EntityType.NUCLEIC_ACID regex: '^([ATGCURYKMSWBDHVNXatgcurykmswbdhvnx-]+)$' 16:31:33,796 INFO DefaultSequenceParser:120 - Registered EntityType.PROTEIN regex: '^([A-Za-z\-\*]+)$' 16:31:33,796 DEBUG DefaultConversionRegistryBuilder:95 - Processing 5 Pattern nodes for SequenceParser org.ngbw.sdk.conversion.DefaultSequenceParser 16:31:33,796 INFO DefaultConversionRegistry:301 - Registered SequenceParser for FASTA : org.ngbw.sdk.conversion.DefaultSequenceParser 16:31:33,796 INFO DefaultConversionRegistry:301 - Registered SequenceParser for GENBANK : org.ngbw.sdk.conversion.DefaultSequenceParser 16:31:33,796 INFO DefaultConversionRegistry:301 - Registered SequenceParser for GENPEPT : org.ngbw.sdk.conversion.DefaultSequenceParser 16:31:33,797 INFO DefaultConversionRegistry:301 - Registered SequenceParser for UNIPROT : org.ngbw.sdk.conversion.DefaultSequenceParser 16:31:33,797 INFO DefaultConversionRegistry:301 - Registered SequenceParser for EMBL : org.ngbw.sdk.conversion.DefaultSequenceParser 16:31:33,799 INFO ServiceFactory:49 - ServiceFactory ready 16:31:33,801 DEBUG ConnectionSource:93 - Loading driver com.mysql.jdbc.Driver 16:31:33,807 DEBUG C3P0ConnectionSource:76 - url: jdbc:mysql://mysql.sdsc.edu:3312/ngbwtest 16:31:33,807 DEBUG C3P0ConnectionSource:77 - user: ngbw 16:31:33,808 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.debugUnreturnedConnectionStackTraces = true 16:31:33,808 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.acquireIncrement = 1 16:31:33,808 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.maxPoolSize = 5 16:31:33,808 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.minPoolSize = 1 16:31:33,808 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.maxStatements = 0 16:31:33,809 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.idleConnectionTestPeriod = 30 16:31:33,809 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.unreturnedConnectionTimeout = 120 16:31:33,809 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.maxIdleTime = 18000 16:31:33,809 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.initialPoolSize = 1 16:31:33,809 DEBUG C3P0ConnectionSource:94 - Setting property c3p0.maxIdleTimeExcessConnections = 300 Exception in thread "main" java.lang.ExceptionInInitializerError Caused by: java.lang.RuntimeException: Invalid property key: