[Sunday June 19 09:34:33 2011] [Notice] Using the settings file ./sample_projects/sample_project_1/project_settings_a.conf.
[Sunday June 19 09:34:33 2011] [Notice] Assigning COG categories to CDS translations from reference genome sequence in ./sample_projects/sample_project_1/reference_genome.
[Sunday June 19 09:34:42 2011] [Notice] COG categories have been written to ./sample_projects/sample_project_1/features.
[Sunday June 19 09:34:42 2011] [Notice] Creating CGView XML files.
[Sunday June 19 09:34:43 2011] [Notice] CGView XML files have been created in ./sample_projects/sample_project_1/maps/cgview_xml.
[Sunday June 19 09:34:43 2011] [Notice] Creating CGView maps.
[Sunday June 19 09:34:50 2011] [Notice] CGView maps have been created in ./sample_projects/sample_project_1/maps.
[Sunday June 19 09:34:50 2011] [Notice] Using the settings file ./sample_projects/sample_project_1/project_settings_b.conf.
[Sunday June 19 09:34:50 2011] [Notice] Extracting ORF translations from reference genome sequence in ./sample_projects/sample_project_1/reference_genome for BLAST searches.
[Sunday June 19 09:34:50 2011] [Notice] Reference genome ORF translations have been written to ./sample_projects/sample_project_1/reference_genome/orfs.
[Sunday June 19 09:34:50 2011] [Notice] Copying protein sequences in ./sample_projects/sample_project_1/comparison_genomes for BLAST searches.
[Sunday June 19 09:34:50 2011] [Notice] Protein sequences have been copied to ./sample_projects/sample_project_1/comparison_genomes/proteins.
[Sunday June 19 09:34:50 2011] [Notice] Creating BLAST databases using the files in ./sample_projects/sample_project_1/comparison_genomes/proteins.
[Sunday June 19 09:34:50 2011] [Notice] The BLAST databases have been created in ./sample_projects/sample_project_1/blast/blast_db.
[Sunday June 19 09:34:50 2011] [Notice] Performing BLAST comparisons between sequences in ./sample_projects/sample_project_1/reference_genome/orfs and databases in ./sample_projects/sample_project_1/blast/blast_db.
[Sunday June 19 09:34:50 2011] [Notice] The BLAST results have been written to ./sample_projects/sample_project_1/blast/blast_results_local.
[Sunday June 19 09:34:50 2011] [Notice] Assigning COG categories to ORF translations from reference genome sequence in ./sample_projects/sample_project_1/reference_genome.
[Sunday June 19 09:34:50 2011] [Notice] COG categories have been written to ./sample_projects/sample_project_1/features.
[Sunday June 19 09:34:50 2011] [Notice] Creating CGView XML files.
[Sunday June 19 09:34:50 2011] [Notice] CGView XML files have been created in ./sample_projects/sample_project_1/maps/cgview_xml.
[Sunday June 19 09:34:50 2011] [Notice] Creating CGView maps.
[Sunday June 19 09:34:56 2011] [Notice] CGView maps have been created in ./sample_projects/sample_project_1/maps.
[Sunday June 19 09:34:56 2011] [Notice] Using the settings file ./sample_projects/sample_project_1/project_settings_c.conf.
[Sunday June 19 09:34:56 2011] [Notice] Splitting the reference genome sequence in ./sample_projects/sample_project_1/reference_genome for BLAST searches.
[Sunday June 19 09:34:57 2011] [Notice] Reference genome sequence has been split and written to ./sample_projects/sample_project_1/reference_genome/split.
[Sunday June 19 09:34:57 2011] [Notice] Splitting the comparison genome sequences in ./sample_projects/sample_project_1/comparison_genomes for BLAST searches.
[Sunday June 19 09:34:57 2011] [Notice] Comparison genome sequences have been split and written to ./sample_projects/sample_project_1/comparison_genomes/split.
[Sunday June 19 09:34:57 2011] [Notice] Creating BLAST databases using the files in ./sample_projects/sample_project_1/comparison_genomes/split.
[Sunday June 19 09:34:57 2011] [Notice] The BLAST databases have been created in ./sample_projects/sample_project_1/blast/blast_db.
[Sunday June 19 09:34:57 2011] [Notice] Performing BLAST comparisons between sequences in ./sample_projects/sample_project_1/reference_genome/split and databases in ./sample_projects/sample_project_1/blast/blast_db.
[Sunday June 19 09:34:58 2011] [Notice] The BLAST results have been written to ./sample_projects/sample_project_1/blast/blast_results_local.
[Sunday June 19 09:34:58 2011] [Notice] Assigning COG categories to CDS translations from reference genome sequence in ./sample_projects/sample_project_1/reference_genome.
[Sunday June 19 09:34:58 2011] [Notice] Skipping COG assignment for './sample_projects/sample_project_1/reference_genome/NC_007719.gbk' using 'cds' since output already detected.
[Sunday June 19 09:34:58 2011] [Notice] COG categories have been written to ./sample_projects/sample_project_1/features.
[Sunday June 19 09:34:58 2011] [Notice] Creating CGView XML files.
[Sunday June 19 09:34:58 2011] [Notice] The following BLAST results will be drawn, from outside to center:
[Sunday June 19 09:34:58 2011] [Notice] NC_007719_DNA_vs_NC_007717.gbk_split_DNA_blastn
[Sunday June 19 09:34:58 2011] [Notice] NC_007719_DNA_vs_NC_007718.gbk_split_DNA_blastn
[Sunday June 19 09:34:58 2011] [Notice] NC_007719_DNA_vs_NC_007720.gbk_split_DNA_blastn
[Sunday June 19 09:34:58 2011] [Notice] CGView XML files have been created in ./sample_projects/sample_project_1/maps/cgview_xml.
[Sunday June 19 09:34:58 2011] [Notice] Creating CGView maps.
[Sunday June 19 09:35:04 2011] [Notice] CGView maps have been created in ./sample_projects/sample_project_1/maps.
