[Saturday September 13 11:14:25 2025] [Notice] A new project has been created in hu.
[Saturday September 13 11:18:58 2025] [Notice] Using the settings file hu/project_settings.conf.
[Saturday September 13 11:18:58 2025] [Notice] Creating CGView XML files.
[Saturday September 13 11:19:23 2025] [Notice] CGView XML files have been created in hu/maps/cgview_xml.
[Saturday September 13 11:19:23 2025] [Notice] Creating CGView maps.
[Saturday September 13 11:19:43 2025] [Notice] CGView maps have been created in hu/maps.
[Saturday September 13 11:21:47 2025] [Notice] Using the settings file hu/project_settings.conf.
[Saturday September 13 11:21:47 2025] [Notice] Assigning COG categories to CDS translations from reference genome sequence in hu/reference_genome.
[Saturday September 13 11:21:58 2025] [Error] The following command failed: /usr/bin/perl /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/assign_cogs/assign_cogs.pl -i 'hu/reference_genome/A21-7.gbk' -o 'hu/features/A21-7.gbk_cds_cogs.gff' -s 'cds' -myva '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/db/cogs/myva' -whog '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/db/cogs/whog' -get_orfs '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/get_orfs/get_orfs.pl' -get_cds '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/get_cds/get_cds.pl' -local_bl '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/local_blast_client/local_blast_client.pl' -blastall '/usr/bin/blastall' -c '11' -e '0.1' -starts 'ttg|ctg|att|atc|ata|atg|gtg' -stops 'taa|tag|tga' -m_orf '50' -m_score '0'.

[Saturday September 13 11:21:58 2025] [Error] The following command failed: /usr/bin/perl /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/assign_cogs/assign_cogs.pl -i 'hu/reference_genome/A21-7.gbk' -o 'hu/features/A21-7.gbk_cds_cogs.gff' -s 'cds' -myva '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/db/cogs/myva' -whog '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/db/cogs/whog' -get_orfs '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/get_orfs/get_orfs.pl' -get_cds '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/get_cds/get_cds.pl' -local_bl '/home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/lib/scripts/local_blast_client/local_blast_client.pl' -blastall '/usr/bin/blastall' -c '11' -e '0.1' -starts 'ttg|ctg|att|atc|ata|atg|gtg' -stops 'taa|tag|tga' -m_orf '50' -m_score '0'. at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 931.
	main::_assignCogs(HASH(0x62eae4562970), Util::LogManager=HASH(0x62eae44615e8)) called at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 805
	main::_sequenceAnalysis(HASH(0x62eae425dce8), Util::Configurator=HASH(0x62eae4458528), Util::LogManager=HASH(0x62eae44615e8)) called at /home/xiangyang/Desktop/web_tool/Achromobacter/CGview/cgview_comparison_tool/scripts/cgview_comparison_tool.pl line 103


[Saturday September 13 14:27:10 2025] [Notice] Using the settings file hu/project_settings.conf.
[Saturday September 13 14:27:10 2025] [Notice] Assigning COG categories to CDS translations from reference genome sequence in hu/reference_genome.
[Saturday September 13 16:37:14 2025] [Notice] COG categories have been written to hu/features.
[Saturday September 13 16:37:14 2025] [Notice] Creating CGView XML files.
[Saturday September 13 16:37:44 2025] [Notice] CGView XML files have been created in hu/maps/cgview_xml.
[Saturday September 13 16:37:44 2025] [Notice] Creating CGView maps.
[Saturday September 13 16:38:02 2025] [Notice] CGView maps have been created in hu/maps.
[Saturday September 13 18:22:28 2025] [Notice] Creating CGView XML files.
[Saturday September 13 18:23:00 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 18:23:00 2025] [Notice] Creating CGView maps.
[Saturday September 13 18:23:30 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 19:05:52 2025] [Notice] Creating CGView XML files.
[Saturday September 13 19:06:25 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 19:06:25 2025] [Notice] Creating CGView maps.
[Saturday September 13 19:06:53 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 19:38:32 2025] [Notice] Creating CGView XML files.
[Saturday September 13 19:39:07 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 19:39:07 2025] [Notice] Creating CGView maps.
[Saturday September 13 19:40:03 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 21:05:22 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:05:52 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 21:05:52 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:06:25 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 21:11:55 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:12:29 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 21:12:29 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:13:07 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 21:37:15 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:37:42 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 21:37:42 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:38:12 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 21:39:19 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:39:50 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 21:39:50 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:40:24 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 21:43:51 2025] [Notice] Creating CGView XML files.
[Saturday September 13 21:44:24 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 21:44:24 2025] [Notice] Creating CGView maps.
[Saturday September 13 21:44:55 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 22:46:53 2025] [Notice] Using the settings file A217/project_settings.conf.
[Saturday September 13 22:46:53 2025] [Notice] Copying DNA sequences in A217/comparison_genomes for BLAST searches.
[Saturday September 13 22:46:53 2025] [Notice] DNA sequences have been copied to A217/comparison_genomes/dna.
[Saturday September 13 22:46:53 2025] [Notice] Creating CGView XML files.
[Saturday September 13 22:47:22 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 22:47:22 2025] [Notice] Creating CGView maps.
[Saturday September 13 22:47:38 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 22:48:52 2025] [Notice] Using the settings file A217/project_settings.conf.
[Saturday September 13 22:48:52 2025] [Notice] Copying DNA sequences in A217/comparison_genomes for BLAST searches.
[Saturday September 13 22:48:52 2025] [Notice] DNA sequences have been copied to A217/comparison_genomes/dna.
[Saturday September 13 22:48:52 2025] [Notice] Creating CGView XML files.
[Saturday September 13 22:49:24 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 22:49:24 2025] [Notice] Creating CGView maps.
[Saturday September 13 22:49:41 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 22:56:31 2025] [Notice] Using the settings file A217/project_settings.conf.
[Saturday September 13 22:56:31 2025] [Notice] Splitting the reference genome sequence in A217/reference_genome for BLAST searches.
[Saturday September 13 22:56:36 2025] [Notice] Reference genome sequence has been split and written to A217/reference_genome/split.
[Saturday September 13 22:56:36 2025] [Notice] Copying DNA sequences in A217/comparison_genomes for BLAST searches.
[Saturday September 13 22:56:36 2025] [Notice] DNA sequences have been copied to A217/comparison_genomes/dna.
[Saturday September 13 22:56:36 2025] [Notice] Creating BLAST databases using the files in A217/comparison_genomes/dna.
[Saturday September 13 22:56:36 2025] [Notice] The BLAST databases have been created in A217/blast/blast_db.
[Saturday September 13 22:56:36 2025] [Notice] Performing BLAST comparisons between sequences in A217/reference_genome/split and databases in A217/blast/blast_db.
[Saturday September 13 22:56:39 2025] [Notice] The BLAST results have been written to A217/blast/blast_results_local.
[Saturday September 13 22:56:39 2025] [Notice] Creating CGView XML files.
[Saturday September 13 22:56:39 2025] [Notice] The following BLAST results will be drawn, from outside to center:
[Saturday September 13 22:56:39 2025] [Notice] A21-7_DNA_vs_region_DNA.fna_dna_DNA_blastn
[Saturday September 13 22:57:10 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 22:57:10 2025] [Notice] Creating CGView maps.
[Saturday September 13 22:57:29 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 23:11:11 2025] [Notice] Using the settings file A217/project_settings.conf.
[Saturday September 13 23:11:11 2025] [Notice] Creating CGView XML files.
[Saturday September 13 23:11:41 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 23:11:41 2025] [Notice] Creating CGView maps.
[Saturday September 13 23:11:58 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 23:14:10 2025] [Notice] Using the settings file A217/project_settings.conf.
[Saturday September 13 23:14:10 2025] [Notice] Splitting the reference genome sequence in A217/reference_genome for BLAST searches.
[Saturday September 13 23:14:13 2025] [Notice] Reference genome sequence has been split and written to A217/reference_genome/split.
[Saturday September 13 23:14:13 2025] [Notice] Copying DNA sequences in A217/comparison_genomes for BLAST searches.
[Saturday September 13 23:14:13 2025] [Notice] DNA sequences have been copied to A217/comparison_genomes/dna.
[Saturday September 13 23:14:13 2025] [Notice] Creating BLAST databases using the files in A217/comparison_genomes/dna.
[Saturday September 13 23:14:14 2025] [Notice] The BLAST databases have been created in A217/blast/blast_db.
[Saturday September 13 23:14:14 2025] [Notice] Performing BLAST comparisons between sequences in A217/reference_genome/split and databases in A217/blast/blast_db.
[Saturday September 13 23:14:17 2025] [Notice] The BLAST results have been written to A217/blast/blast_results_local.
[Saturday September 13 23:14:17 2025] [Notice] Creating CGView XML files.
[Saturday September 13 23:14:17 2025] [Notice] The following BLAST results will be drawn, from outside to center:
[Saturday September 13 23:14:17 2025] [Notice] A21-7_DNA_vs_region_DNA.fna_dna_DNA_blastn
[Saturday September 13 23:14:46 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 23:14:46 2025] [Notice] Creating CGView maps.
[Saturday September 13 23:15:03 2025] [Notice] CGView maps have been created in A217/maps.
[Saturday September 13 23:32:05 2025] [Notice] Using the settings file A217/project_settings.conf.
[Saturday September 13 23:32:05 2025] [Notice] Splitting the reference genome sequence in A217/reference_genome for BLAST searches.
[Saturday September 13 23:32:09 2025] [Notice] Reference genome sequence has been split and written to A217/reference_genome/split.
[Saturday September 13 23:32:09 2025] [Notice] Copying DNA sequences in A217/comparison_genomes for BLAST searches.
[Saturday September 13 23:32:09 2025] [Notice] DNA sequences have been copied to A217/comparison_genomes/dna.
[Saturday September 13 23:32:09 2025] [Notice] Creating BLAST databases using the files in A217/comparison_genomes/dna.
[Saturday September 13 23:32:09 2025] [Notice] The BLAST databases have been created in A217/blast/blast_db.
[Saturday September 13 23:32:09 2025] [Notice] Performing BLAST comparisons between sequences in A217/reference_genome/split and databases in A217/blast/blast_db.
[Saturday September 13 23:32:13 2025] [Notice] The BLAST results have been written to A217/blast/blast_results_local.
[Saturday September 13 23:32:13 2025] [Notice] Creating CGView XML files.
[Saturday September 13 23:32:13 2025] [Notice] The following BLAST results will be drawn, from outside to center:
[Saturday September 13 23:32:13 2025] [Notice] A21-7_DNA_vs_region_DNA.fna_dna_DNA_blastn
[Saturday September 13 23:32:46 2025] [Notice] CGView XML files have been created in A217/maps/cgview_xml.
[Saturday September 13 23:32:46 2025] [Notice] Creating CGView maps.
[Saturday September 13 23:33:06 2025] [Notice] CGView maps have been created in A217/maps.
