[Saturday September 13 17:46:25 2025] [Notice] Using the settings file A24/project_settings.conf.
[Saturday September 13 17:46:25 2025] [Notice] Assigning COG categories to CDS translations from reference genome sequence in A24/reference_genome.
[Saturday September 13 19:47:38 2025] [Notice] Creating CGView XML files.
[Saturday September 13 19:48:08 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 19:48:08 2025] [Notice] Creating CGView maps.
[Saturday September 13 19:48:28 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 19:58:28 2025] [Notice] Creating CGView XML files.
[Saturday September 13 19:59:00 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 19:59:00 2025] [Notice] Creating CGView maps.
[Saturday September 13 19:59:20 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 20:07:42 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:08:10 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 20:08:10 2025] [Notice] Creating CGView maps.
[Saturday September 13 20:08:35 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 20:29:12 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:29:18 2025] [Error] The following command failed: perl A24/cgview_xml_builder.pl -size medium -sequence 'A24/reference_genome/A24-292.gbk' -output 'A24/maps/cgview_xml/medium.xml' -orf_size 50 -starts 'ttg|ctg|att|atc|ata|atg|gtg' -stops 'taa|tag|tga' -linear F -orfs F -gc_content T -gc_skew T -legend T -details T -feature_labels F -gene_labels F -hit_labels F -orf_labels F -condensed F -draw_divider_rings F -parse_reading_frame F -show_queries F -use_opacity F -gene_decoration arc -cct 1 -scale_blast T -log 'A24/maps/cgview_xml/medium.log' -analysis A24/analysis/analysis_1.gff  -genes A24/features/A24-292.gbk_cds_cogs.gff A24/features/important_feature.gff  -custom 'backboneRadius=800' 'arrowheadLength=6' 'labelPlacementQuality=best' 'featureThickness=30' 'featureThicknessPlot=120' '_cct_blast_thickness=40' 'featureSlotSpacing=8'.

[Saturday September 13 20:29:18 2025] [Error] The following command failed: perl A24/cgview_xml_builder.pl -size medium -sequence 'A24/reference_genome/A24-292.gbk' -output 'A24/maps/cgview_xml/medium.xml' -orf_size 50 -starts 'ttg|ctg|att|atc|ata|atg|gtg' -stops 'taa|tag|tga' -linear F -orfs F -gc_content T -gc_skew T -legend T -details T -feature_labels F -gene_labels F -hit_labels F -orf_labels F -condensed F -draw_divider_rings F -parse_reading_frame F -show_queries F -use_opacity F -gene_decoration arc -cct 1 -scale_blast T -log 'A24/maps/cgview_xml/medium.log' -analysis A24/analysis/analysis_1.gff  -genes A24/features/A24-292.gbk_cds_cogs.gff A24/features/important_feature.gff  -custom 'backboneRadius=800' 'arrowheadLength=6' 'labelPlacementQuality=best' 'featureThickness=30' 'featureThicknessPlot=120' '_cct_blast_thickness=40' 'featureSlotSpacing=8'. at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 1694.
	main::_buildCgviewXml(HASH(0x61d82e4cd6c8), HASH(0x61d82e2c9210)) called at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 1060
	main::_xmlCreation(HASH(0x61d82e2c9210), Util::Configurator=HASH(0x61d82e4c3dc0), Util::LogManager=HASH(0x61d82e4ccd20)) called at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 96


[Saturday September 13 20:31:18 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:31:45 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 20:31:45 2025] [Notice] Creating CGView maps.
[Saturday September 13 20:32:00 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 20:34:24 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:34:29 2025] [Error] The following command failed: perl A24/cgview_xml_builder.pl -size medium -sequence 'A24/reference_genome/A24-292.gbk' -output 'A24/maps/cgview_xml/medium.xml' -orf_size 50 -starts 'ttg|ctg|att|atc|ata|atg|gtg' -stops 'taa|tag|tga' -linear F -orfs F -gc_content T -gc_skew T -legend T -details T -feature_labels F -gene_labels F -hit_labels F -orf_labels F -condensed F -draw_divider_rings F -parse_reading_frame F -show_queries F -use_opacity F -gene_decoration arc -cct 1 -scale_blast T -log 'A24/maps/cgview_xml/medium.log' -analysis A24/analysis/analysis_1.gff  -genes A24/features/A24-292.gbk_cds_cogs.gff A24/features/important_feature.gff  -custom 'backboneRadius=800' 'arrowheadLength=6' 'labelPlacementQuality=best' 'featureThickness=30' 'featureThicknessPlot=120' '_cct_blast_thickness=40' 'featureSlotSpacing=8'.

[Saturday September 13 20:34:29 2025] [Error] The following command failed: perl A24/cgview_xml_builder.pl -size medium -sequence 'A24/reference_genome/A24-292.gbk' -output 'A24/maps/cgview_xml/medium.xml' -orf_size 50 -starts 'ttg|ctg|att|atc|ata|atg|gtg' -stops 'taa|tag|tga' -linear F -orfs F -gc_content T -gc_skew T -legend T -details T -feature_labels F -gene_labels F -hit_labels F -orf_labels F -condensed F -draw_divider_rings F -parse_reading_frame F -show_queries F -use_opacity F -gene_decoration arc -cct 1 -scale_blast T -log 'A24/maps/cgview_xml/medium.log' -analysis A24/analysis/analysis_1.gff  -genes A24/features/A24-292.gbk_cds_cogs.gff A24/features/important_feature.gff  -custom 'backboneRadius=800' 'arrowheadLength=6' 'labelPlacementQuality=best' 'featureThickness=30' 'featureThicknessPlot=120' '_cct_blast_thickness=40' 'featureSlotSpacing=8'. at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 1694.
	main::_buildCgviewXml(HASH(0x630d4953e2d8), HASH(0x630d49345760)) called at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 1060
	main::_xmlCreation(HASH(0x630d49345760), Util::Configurator=HASH(0x630d4953eb60), Util::LogManager=HASH(0x630d49547c40)) called at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 96


[Saturday September 13 20:35:48 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:36:16 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 20:36:16 2025] [Notice] Creating CGView maps.
[Saturday September 13 20:36:34 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 20:48:58 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:49:27 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 20:49:27 2025] [Notice] Creating CGView maps.
[Saturday September 13 20:49:46 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 20:53:35 2025] [Notice] Creating CGView XML files.
[Saturday September 13 20:54:02 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 20:54:02 2025] [Notice] Creating CGView maps.
[Saturday September 13 20:54:18 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 21:02:04 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:02:33 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 21:02:33 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:02:52 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 21:29:47 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:30:18 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 21:30:18 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:30:32 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 21:32:16 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:32:46 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 21:32:46 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:33:01 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 21:46:33 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:47:11 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 21:47:11 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:47:29 2025] [Notice] CGView maps have been created in A24/maps.
[Saturday September 13 23:37:16 2025] [Notice] Using the settings file A24/project_settings.conf.
[Saturday September 13 23:37:16 2025] [Notice] Splitting the reference genome sequence in A24/reference_genome for BLAST searches.
[Saturday September 13 23:37:21 2025] [Notice] Reference genome sequence has been split and written to A24/reference_genome/split.
[Saturday September 13 23:37:21 2025] [Notice] Copying DNA sequences in A24/comparison_genomes for BLAST searches.
[Saturday September 13 23:37:21 2025] [Notice] DNA sequences have been copied to A24/comparison_genomes/dna.
[Saturday September 13 23:37:21 2025] [Notice] Creating BLAST databases using the files in A24/comparison_genomes/dna.
[Saturday September 13 23:37:21 2025] [Notice] The BLAST databases have been created in A24/blast/blast_db.
[Saturday September 13 23:37:21 2025] [Notice] Performing BLAST comparisons between sequences in A24/reference_genome/split and databases in A24/blast/blast_db.
[Saturday September 13 23:37:24 2025] [Notice] The BLAST results have been written to A24/blast/blast_results_local.
[Saturday September 13 23:37:24 2025] [Notice] Creating CGView XML files.
[Saturday September 13 23:37:24 2025] [Notice] The following BLAST results will be drawn, from outside to center:
[Saturday September 13 23:37:24 2025] [Notice] A24-292_DNA_vs_region_DNA.fna_dna_DNA_blastn
[Saturday September 13 23:38:01 2025] [Notice] CGView XML files have been created in A24/maps/cgview_xml.
[Saturday September 13 23:38:01 2025] [Notice] Creating CGView maps.
[Saturday September 13 23:38:26 2025] [Notice] CGView maps have been created in A24/maps.
