[Sunday June 19 14:18:52 2011] [Notice] Using the settings file ./sample_projects/sample_project_5/project_settings_a.conf.
[Sunday June 19 14:18:52 2011] [Notice] Splitting the reference genome sequence in ./sample_projects/sample_project_5/reference_genome for BLAST searches.
[Sunday June 19 14:18:53 2011] [Notice] Reference genome sequence has been split and written to ./sample_projects/sample_project_5/reference_genome/split.
[Sunday June 19 14:18:53 2011] [Notice] Extracting ORF translations from reference genome sequence in ./sample_projects/sample_project_5/reference_genome for BLAST searches.
[Sunday June 19 14:18:54 2011] [Notice] Reference genome ORF translations have been written to ./sample_projects/sample_project_5/reference_genome/orfs.
[Sunday June 19 14:18:54 2011] [Notice] Splitting the comparison genome sequences in ./sample_projects/sample_project_5/comparison_genomes for BLAST searches.
[Sunday June 19 14:18:59 2011] [Notice] Comparison genome sequences have been split and written to ./sample_projects/sample_project_5/comparison_genomes/split.
[Sunday June 19 14:18:59 2011] [Notice] Extracting ORF translations from comparison genome sequences in ./sample_projects/sample_project_5/comparison_genomes for BLAST searches.
[Sunday June 19 14:20:37 2011] [Notice] Comparison genome ORF translations have been written to ./sample_projects/sample_project_5/comparison_genomes/orfs.
[Sunday June 19 14:20:37 2011] [Notice] Creating BLAST databases using the files in ./sample_projects/sample_project_5/comparison_genomes/split.
[Sunday June 19 14:20:37 2011] [Notice] The BLAST databases have been created in ./sample_projects/sample_project_5/blast/blast_db.
[Sunday June 19 14:20:37 2011] [Notice] Performing BLAST comparisons between sequences in ./sample_projects/sample_project_5/reference_genome/split and databases in ./sample_projects/sample_project_5/blast/blast_db.
[Sunday June 19 14:20:38 2011] [Notice] The BLAST results have been written to ./sample_projects/sample_project_5/blast/blast_results_local.
[Sunday June 19 14:20:38 2011] [Notice] Creating BLAST databases using the files in ./sample_projects/sample_project_5/comparison_genomes/orfs.
[Sunday June 19 14:20:40 2011] [Notice] The BLAST databases have been created in ./sample_projects/sample_project_5/blast/blast_db.
[Sunday June 19 14:20:40 2011] [Notice] Performing BLAST comparisons between sequences in ./sample_projects/sample_project_5/reference_genome/orfs and databases in ./sample_projects/sample_project_5/blast/blast_db.
[Sunday June 19 14:22:19 2011] [Notice] The BLAST results have been written to ./sample_projects/sample_project_5/blast/blast_results_local.
[Sunday June 19 14:22:19 2011] [Notice] Assigning COG categories to CDS translations from reference genome sequence in ./sample_projects/sample_project_5/reference_genome.
[Sunday June 19 14:23:51 2011] [Notice] COG categories have been written to ./sample_projects/sample_project_5/features.
[Sunday June 19 14:23:51 2011] [Notice] Creating CGView XML files.
[Sunday June 19 14:23:51 2011] [Notice] The following BLAST results will be drawn, from outside to center:
[Sunday June 19 14:23:51 2011] [Notice] NC_001823_DNA_vs_Arabidopsis_mito.gbk_split_DNA_blastn
[Sunday June 19 14:23:51 2011] [Notice] NC_001823_DNA_vs_E_coli.gbk_split_DNA_blastn
[Sunday June 19 14:23:51 2011] [Notice] NC_001823_DNA_vs_Human_mito.gbk_split_DNA_blastn
[Sunday June 19 14:23:51 2011] [Notice] NC_001823_ORFS_vs_Arabidopsis_mito.gbk_orfs_ORFS_blastp
[Sunday June 19 14:23:51 2011] [Notice] NC_001823_ORFS_vs_E_coli.gbk_orfs_ORFS_blastp
[Sunday June 19 14:23:51 2011] [Notice] NC_001823_ORFS_vs_Human_mito.gbk_orfs_ORFS_blastp
[Sunday June 19 14:23:55 2011] [Notice] CGView XML files have been created in ./sample_projects/sample_project_5/maps/cgview_xml.
[Sunday June 19 14:23:55 2011] [Notice] Creating CGView maps.
[Sunday June 19 14:24:27 2011] [Notice] CGView maps have been created in ./sample_projects/sample_project_5/maps.
[Sunday June 19 14:24:27 2011] [Notice] Using the settings file ./sample_projects/sample_project_5/project_settings_b.conf.
[Sunday June 19 14:24:27 2011] [Notice] Assigning COG categories to CDS translations from reference genome sequence in ./sample_projects/sample_project_5/reference_genome.
[Sunday June 19 14:24:27 2011] [Notice] Skipping COG assignment for './sample_projects/sample_project_5/reference_genome/NC_001823.gbk' using 'cds' since output already detected.
[Sunday June 19 14:24:27 2011] [Notice] COG categories have been written to ./sample_projects/sample_project_5/features.
[Sunday June 19 14:24:27 2011] [Notice] Creating CGView XML files.
[Sunday June 19 14:24:31 2011] [Notice] CGView XML files have been created in ./sample_projects/sample_project_5/maps/cgview_xml.
[Sunday June 19 14:24:31 2011] [Notice] Creating CGView maps.
[Sunday June 19 14:24:43 2011] [Notice] CGView maps have been created in ./sample_projects/sample_project_5/maps.
[Sunday June 19 14:24:43 2011] [Notice] Using the settings file ./sample_projects/sample_project_5/project_settings_c.conf.
[Sunday June 19 14:24:43 2011] [Notice] Assigning COG categories to ORF translations from reference genome sequence in ./sample_projects/sample_project_5/reference_genome.
[Sunday June 19 14:24:43 2011] [Notice] COG categories have been written to ./sample_projects/sample_project_5/features.
[Sunday June 19 14:24:43 2011] [Notice] Creating CGView XML files.
[Sunday June 19 14:24:46 2011] [Notice] CGView XML files have been created in ./sample_projects/sample_project_5/maps/cgview_xml.
[Sunday June 19 14:24:46 2011] [Notice] Creating CGView maps.
[Sunday June 19 14:25:15 2011] [Notice] CGView maps have been created in ./sample_projects/sample_project_5/maps.
