2022/05/24 08:32:04 Running on Python 3.8.2 (default, Apr 23 2020, 14:22:33) 
[GCC 8.3.0].
2022/05/24 08:32:04 Loading a config file from /dfast_core/example/dfc_config/dfast_web_config.py
2022/05/24 08:32:04 DFAST_DB_ROOT is specified [/dfast_core_db]
2022/05/24 08:32:04 OS type is Linux.
2022/05/24 08:32:04 Adding /dfast_core/bin/Linux to PATH.
2022/05/24 08:32:04 DFAST pipeline started. (version 1.2.16)
2022/05/24 08:32:04 Results will be generated into '/dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation'.
2022/05/24 08:32:04 Loading a genomic fasta file from /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/input/genome.fna
2022/05/24 08:32:04 Genome source information: organism=, strain=
2022/05/24 08:32:04 The query genome is treated as a draft genome with 18 sequences.
2022/05/24 08:32:04 Sequences shorter than 200 will be eliminated.
2022/05/24 08:32:04 Sequences will be renamed as sequence01, sequence02...
2022/05/24 08:32:04 Locus_tag settings: locus_tag_prefix=LOCUS and step=10.
2022/05/24 08:32:04 Locus_tags are assigned separately to each feature type. e.g. CDS: LOCUS_000xx, rRNA: LOCUS_r000xx, tRNA: LOCUS_t000xx, tmRNA: LOCUS_tm000xx.
2022/05/24 08:32:04 Remove_Partial_Feature is enabled.
2022/05/24 08:32:04 Remove_Overlapping_Feature is enabled. Priority: ['assembly_gap', 'CRISPR', ('tmRNA', 'tRNA', 'rRNA'), 'CDS']
2022/05/24 08:32:04 Initializing structural annotation tools... 
2022/05/24 08:32:04 GAPannotator initialized. (Version 1.0)
2022/05/24 08:32:04 Setting GAPannotator options. {'len_cutoff': 5, 'linkage_evidence': 'paired-ends', 'gap_type': 'within scaffold'}
2022/05/24 08:32:04 Checking MetaGeneAnnotator... 
2022/05/24 08:32:04 MetaGeneAnnotator initialized. (Version 2008/08/19)
2022/05/24 08:32:04 Setting MetaGeneAnnotator options. {'cmd_options': '-s', 'transl_table': 11}
2022/05/24 08:32:04 Checking Aragorn version... 
2022/05/24 08:32:04 Aragorn initialized. (Version 1.2.38)
2022/05/24 08:32:04 Setting Aragorn options. {'gcode': '-gcbact', 'cmd_options': '-l', 'transl_table': 11}
2022/05/24 08:32:04 Checking Barrnap version... 
2022/05/24 08:32:04 Barrnap initialized. (Version 0.8)
2022/05/24 08:32:04 Checking CRT version... 
2022/05/24 08:32:04 CRT initialized. (Version 1.2)
2022/05/24 08:32:04 Setting CRT options. {'jar_file': '/dfast_core/bin/common/CRT1.2-CLI.jar', 'java_options': '', 'cmd_options': ''}
2022/05/24 08:32:04 Checking Java version... 
2022/05/24 08:32:04 Java initialized. (Version 11.0.9.1)
2022/05/24 08:32:04 Initializing annotation components... 
2022/05/24 08:32:04 DBsearch initialized.
2022/05/24 08:32:04 Setting DBsearch options. {'cpu': 3, 'skipAnnotatedFeatures': True, 'evalue_cutoff': 1e-06, 'qcov_cutoff': 75, 'scov_cutoff': 75, 'pident_cutoff': 0, 'aligner': 'ghostx', 'aligner_options': {}, 'database': '/dfast_core_db/protein/DFAST-default.ref', 'db_name': ''}
2022/05/24 08:32:04 Checking GHOSTX version... 
2022/05/24 08:32:05 GHOSTX initialized. (Version 1.3.6)
2022/05/24 08:32:06 Reference DB loaded. 405077 sequences. [version=1.1.6.2, dbname=DFAST-default, contributor=yt,ddbj, modified=20210422]
2022/05/24 08:32:06 PseudoGeneDetection initialized.
2022/05/24 08:32:06 Setting PseudoGeneDetection options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2022/05/24 08:32:06 Checking lastdb version... 
2022/05/24 08:32:06 lastdb initialized. (Version 959)
2022/05/24 08:32:06 Setting lastdb options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2022/05/24 08:32:06 Checking lastal version... 
2022/05/24 08:32:06 lastal initialized. (Version 959)
2022/05/24 08:32:06 Setting lastal options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2022/05/24 08:32:06 Checking Blastp version... 
2022/05/24 08:32:06 Blastp initialized. (Version 2.6.0)
2022/05/24 08:32:07 Start structural annotation process using 3 CPUs
2022/05/24 08:32:09 9 assembly_gap features were detected by GAPannotator.
2022/05/24 08:32:10 2483 CDS features were detected by MetaGeneAnnotator.
2022/05/24 08:32:10 54 tRNA features were detected by Aragorn.
2022/05/24 08:32:10 0 rRNA features were detected by Barrnap.
2022/05/24 08:32:10 4 CRISPR (later will be replaced by repeat_region) features were detected by CRT.
2022/05/24 08:32:10 Removed 14 partial features.
2022/05/24 08:32:10 Removed 9 overlapping features.
2022/05/24 08:32:10 Start executing functional annotation components.
2022/05/24 08:32:10 DBsearch will be performed using 3 CPUs.
2022/05/24 08:32:39 DBsearch done 3/3.
2022/05/24 08:32:39 DBsearch done 1/3.
2022/05/24 08:32:40 DBsearch done 2/3.
2022/05/24 08:32:41 Last format DB will be performed using 1 CPUs.
2022/05/24 08:32:41 Last format DB done 1/1.
2022/05/24 08:32:41 Last alignment will be performed using 1 CPUs.
2022/05/24 08:32:43 Last alignment done 1/1.
2022/05/24 08:32:43 21 CDS features were marked as possible pseudo due to internal stop codons.
2022/05/24 08:32:43 32 CDS features were marked as possible pseudo due to frameshift.
2022/05/24 08:32:43 Assigning locus_tags to CDS, rRNA, tRNA, tmRNA
2022/05/24 08:32:44 Setting output verbosity level to 3.
2022/05/24 08:32:44 Writing a genome fasta file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/genome.fna
2022/05/24 08:32:44 Writing a CDS fasta file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/cds.fna
2022/05/24 08:32:44 Writing a protein fasta file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/protein.faa
2022/05/24 08:32:44 Writing an RNA fasta file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/rna.fna
2022/05/24 08:32:44 Writing a GFF file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/genome.gff
2022/05/24 08:32:44 Writing a GenBank format file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/genome.gbk
2022/05/24 08:32:44 Writing an EMBL format file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/genome.embl
2022/05/24 08:32:45 Writing a DDBJ annotation file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/ddbj/mss.ann
2022/05/24 08:32:45 Writing a DDBJ sequence file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/ddbj/mss.fasta
2022/05/24 08:32:46 'center_name' is not specified. 'my_center' is used tentatively.
2022/05/24 08:32:46 Writing a GenBank tbl file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/genbank/genbank.tbl
2022/05/24 08:32:46 Writing a GenBank fsa file to /dfast_volumes/jobs/282dfb3e-1de1-4ee9-8ee4-13dc9945087e/annotation/genbank/genbank.fsa
2022/05/24 08:32:46 DFAST pipeline completed!
2022/05/24 08:32:46 Total running time: 0h0m42s