2024/02/07 09:03:24 Running on Python 3.8.2 (default, Apr 23 2020, 14:22:33) 
[GCC 8.3.0].
2024/02/07 09:03:24 Loading a config file from /dfast_core/example/dfc_config/dfast_web_config.py
2024/02/07 09:03:24 DFAST_DB_ROOT is specified [/dfast_core_db]
2024/02/07 09:03:24 OS type is Linux.
2024/02/07 09:03:24 Adding /dfast_core/bin/Linux to PATH.
2024/02/07 09:03:24 DFAST pipeline started. (version 1.2.20)
2024/02/07 09:03:24 Results will be generated into '/dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation'.
2024/02/07 09:03:24 Loading a genomic fasta file from /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/input/genome.fna
2024/02/07 09:03:24 Genome source information: organism=, strain=
2024/02/07 09:03:24 The query genome is treated as a draft genome with 3 sequences.
2024/02/07 09:03:24 Sequences shorter than 200 will be eliminated.
2024/02/07 09:03:24 Sequences will be renamed as sequence1, sequence2...
2024/02/07 09:03:24 Locus_tag settings: locus_tag_prefix=LOCUS and step=10.
2024/02/07 09:03:24 Locus_tags are assigned separately to each feature type. e.g. CDS: LOCUS_000xx, rRNA: LOCUS_r000xx, tRNA: LOCUS_t000xx, tmRNA: LOCUS_tm000xx.
2024/02/07 09:03:24 Remove_Partial_Feature is enabled.
2024/02/07 09:03:24 Remove_Overlapping_Feature is enabled. Priority: ['assembly_gap', 'CRISPR', ('tmRNA', 'tRNA', 'rRNA'), 'CDS']
2024/02/07 09:03:24 Initializing structural annotation tools... 
2024/02/07 09:03:24 GAPannotator initialized. (Version 1.0)
2024/02/07 09:03:24 Setting GAPannotator options. {'len_cutoff': 5, 'linkage_evidence': 'paired-ends', 'gap_type': 'within scaffold'}
2024/02/07 09:03:24 Checking MetaGeneAnnotator... 
2024/02/07 09:03:24 MetaGeneAnnotator initialized. (Version 2008/08/19)
2024/02/07 09:03:24 Setting MetaGeneAnnotator options. {'cmd_options': '-s', 'transl_table': 11}
2024/02/07 09:03:24 Checking Aragorn version... 
2024/02/07 09:03:24 Aragorn initialized. (Version 1.2.38)
2024/02/07 09:03:24 Setting Aragorn options. {'gcode': '-gcbact', 'cmd_options': '-l', 'transl_table': 11}
2024/02/07 09:03:24 Checking Barrnap version... 
2024/02/07 09:03:24 Barrnap initialized. (Version 0.8)
2024/02/07 09:03:24 Checking CRT version... 
2024/02/07 09:03:24 CRT initialized. (Version 1.2)
2024/02/07 09:03:24 Setting CRT options. {'jar_file': '/dfast_core/bin/common/CRT1.2-CLI.jar', 'java_options': '', 'cmd_options': ''}
2024/02/07 09:03:24 Checking Java version... 
2024/02/07 09:03:24 Java initialized. (Version 11.0.9.1)
2024/02/07 09:03:24 Initializing annotation components... 
2024/02/07 09:03:24 DBsearch initialized.
2024/02/07 09:03:24 Setting DBsearch options. {'cpu': 3, 'skipAnnotatedFeatures': True, 'evalue_cutoff': 1e-06, 'qcov_cutoff': 75.0, 'scov_cutoff': 75.0, 'pident_cutoff': 0.0, 'aligner': 'ghostx', 'aligner_options': {}, 'database': '/dfast_core_db/protein/DFAST-default.ref', 'db_name': ''}
2024/02/07 09:03:24 Checking GHOSTX version... 
2024/02/07 09:03:24 GHOSTX initialized. (Version 1.3.6)
2024/02/07 09:03:26 Reference DB loaded. 381721 sequences. [version=1.2.0, dbname=DFAST-default, contributor=yt,ddbj, modified=20230404]
2024/02/07 09:03:26 PseudoGeneDetection initialized.
2024/02/07 09:03:26 Setting PseudoGeneDetection options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2024/02/07 09:03:26 Checking lastdb version... 
2024/02/07 09:03:26 lastdb initialized. (Version 959)
2024/02/07 09:03:26 Setting lastdb options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2024/02/07 09:03:26 Checking lastal version... 
2024/02/07 09:03:26 lastal initialized. (Version 959)
2024/02/07 09:03:26 Setting lastal options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2024/02/07 09:03:26 Checking Blastp version... 
2024/02/07 09:03:26 Blastp initialized. (Version 2.6.0)
2024/02/07 09:03:26 Start structural annotation process using 3 CPUs
2024/02/07 09:03:29 0 assembly_gap features were detected by GAPannotator.
2024/02/07 09:03:30 2352 CDS features were detected by MetaGeneAnnotator.
2024/02/07 09:03:30 57 tRNA features were detected by Aragorn.
2024/02/07 09:03:30 12 rRNA features were detected by Barrnap.
2024/02/07 09:03:30 1 CRISPR (later will be replaced by repeat_region) features were detected by CRT.
2024/02/07 09:03:31 Removed 8 overlapping features.
2024/02/07 09:03:31 Start executing functional annotation components.
2024/02/07 09:03:31 DBsearch will be performed using 3 CPUs.
2024/02/07 09:03:58 DBsearch done 2/3.
2024/02/07 09:04:02 DBsearch done 1/3.
2024/02/07 09:04:03 DBsearch done 3/3.
2024/02/07 09:04:04 Last format DB will be performed using 1 CPUs.
2024/02/07 09:04:04 Last format DB done 1/1.
2024/02/07 09:04:04 Last alignment will be performed using 1 CPUs.
2024/02/07 09:04:05 Last alignment done 1/1.
2024/02/07 09:04:06 19 CDS features were marked as possible pseudo due to internal stop codons.
2024/02/07 09:04:06 20 CDS features were marked as possible pseudo due to frameshift.
2024/02/07 09:04:06 Removed 0 partial features.
2024/02/07 09:04:06 Assigning locus_tags to CDS, rRNA, tRNA, tmRNA
2024/02/07 09:04:06 Setting output verbosity level to 3.
2024/02/07 09:04:06 Writing a genome fasta file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/genome.fna
2024/02/07 09:04:06 Writing a CDS fasta file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/cds.fna
2024/02/07 09:04:06 Writing a protein fasta file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/protein.faa
2024/02/07 09:04:06 Writing an RNA fasta file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/rna.fna
2024/02/07 09:04:06 Writing a GFF file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/genome.gff
2024/02/07 09:04:06 Writing a GenBank format file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/genome.gbk
2024/02/07 09:04:07 Writing an EMBL format file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/genome.embl
2024/02/07 09:04:07 Writing a DDBJ annotation file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/ddbj/mss.ann
2024/02/07 09:04:07 Writing a DDBJ sequence file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/ddbj/mss.fasta
2024/02/07 09:04:08 'center_name' is not specified. 'my_center' is used tentatively.
2024/02/07 09:04:08 Writing a GenBank tbl file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/genbank/genbank.tbl
2024/02/07 09:04:08 Writing a GenBank fsa file to /dfast_volumes/jobs/7d52e3dd-145e-44ac-b9fe-4d0d441098e9/annotation/genbank/genbank.fsa
2024/02/07 09:04:09 DFAST pipeline completed!
2024/02/07 09:04:09 Total running time: 0h0m45s