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Title :
-
JobID :
7fa58b39-d3be-4a56-93d0-942f280328e7
Job Status :
COMPLETE

[2022-12-22 13:30:27.793009] Job submitted.
[2022-12-22 13:30:27.847806] Job started.
[2022-12-22 13:31:27.198184] Job completed.


2022/12/22 04:30:29 Running on Python 3.8.2 (default, Apr 23 2020, 14:22:33) 
[GCC 8.3.0].
2022/12/22 04:30:29 Loading a config file from /dfast_core/example/dfc_config/dfast_web_config.py
2022/12/22 04:30:29 DFAST_DB_ROOT is specified [/dfast_core_db]
2022/12/22 04:30:29 OS type is Linux.
2022/12/22 04:30:29 Adding /dfast_core/bin/Linux to PATH.
2022/12/22 04:30:29 DFAST pipeline started. (version 1.2.18)
2022/12/22 04:30:29 Results will be generated into '/dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation'.
2022/12/22 04:30:29 Loading a genomic fasta file from /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/input/genome.fna
2022/12/22 04:30:29 Genome source information: organism=, strain=
2022/12/22 04:30:29 The query genome is treated as a draft genome with 354 sequences.
2022/12/22 04:30:29 Sequences shorter than 200 will be eliminated.
2022/12/22 04:30:29 Sequences will be renamed as sequence001, sequence002...
2022/12/22 04:30:29 Locus_tag settings: locus_tag_prefix=LOCUS and step=10.
2022/12/22 04:30:29 Locus_tags are assigned separately to each feature type. e.g. CDS: LOCUS_000xx, rRNA: LOCUS_r000xx, tRNA: LOCUS_t000xx, tmRNA: LOCUS_tm000xx.
2022/12/22 04:30:29 Remove_Partial_Feature is enabled.
2022/12/22 04:30:29 Remove_Overlapping_Feature is enabled. Priority: ['assembly_gap', 'CRISPR', ('tmRNA', 'tRNA', 'rRNA'), 'CDS']
2022/12/22 04:30:29 Initializing structural annotation tools... 
2022/12/22 04:30:29 GAPannotator initialized. (Version 1.0)
2022/12/22 04:30:29 Setting GAPannotator options. {'len_cutoff': 5, 'linkage_evidence': 'paired-ends', 'gap_type': 'within scaffold'}
2022/12/22 04:30:29 Checking MetaGeneAnnotator... 
2022/12/22 04:30:29 MetaGeneAnnotator initialized. (Version 2008/08/19)
2022/12/22 04:30:29 Setting MetaGeneAnnotator options. {'cmd_options': '-s', 'transl_table': 11}
2022/12/22 04:30:29 Checking Aragorn version... 
2022/12/22 04:30:29 Aragorn initialized. (Version 1.2.38)
2022/12/22 04:30:29 Setting Aragorn options. {'gcode': '-gcbact', 'cmd_options': '-l', 'transl_table': 11}
2022/12/22 04:30:29 Checking Barrnap version... 
2022/12/22 04:30:29 Barrnap initialized. (Version 0.8)
2022/12/22 04:30:29 Checking CRT version... 
2022/12/22 04:30:29 CRT initialized. (Version 1.2)
2022/12/22 04:30:29 Setting CRT options. {'jar_file': '/dfast_core/bin/common/CRT1.2-CLI.jar', 'java_options': '', 'cmd_options': ''}
2022/12/22 04:30:29 Checking Java version... 
2022/12/22 04:30:29 Java initialized. (Version 11.0.9.1)
2022/12/22 04:30:29 Initializing annotation components... 
2022/12/22 04:30:29 DBsearch initialized.
2022/12/22 04:30:29 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': ''}
2022/12/22 04:30:29 Checking GHOSTX version... 
2022/12/22 04:30:29 GHOSTX initialized. (Version 1.3.6)
2022/12/22 04:30:31 Reference DB loaded. 405077 sequences. [version=1.1.6.2, dbname=DFAST-default, contributor=yt,ddbj, modified=20210422]
2022/12/22 04:30:31 PseudoGeneDetection initialized.
2022/12/22 04:30:31 Setting PseudoGeneDetection options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2022/12/22 04:30:31 Checking lastdb version... 
2022/12/22 04:30:31 lastdb initialized. (Version 959)
2022/12/22 04:30:31 Setting lastdb options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2022/12/22 04:30:31 Checking lastal version... 
2022/12/22 04:30:31 lastal initialized. (Version 959)
2022/12/22 04:30:31 Setting lastal options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85, 'transl_table': 11}
2022/12/22 04:30:31 Checking Blastp version... 
2022/12/22 04:30:32 Blastp initialized. (Version 2.6.0)
2022/12/22 04:30:32 Start structural annotation process using 3 CPUs
2022/12/22 04:30:34 4 assembly_gap features were detected by GAPannotator.
2022/12/22 04:30:35 2906 CDS features were detected by MetaGeneAnnotator.
2022/12/22 04:30:35 55 tRNA features were detected by Aragorn.
2022/12/22 04:30:35 4 rRNA features were detected by Barrnap.
2022/12/22 04:30:35 3 CRISPR (later will be replaced by repeat_region) features were detected by CRT.
2022/12/22 04:30:35 Removed 8 overlapping features.
2022/12/22 04:30:35 Start executing functional annotation components.
2022/12/22 04:30:35 DBsearch will be performed using 3 CPUs.
2022/12/22 04:31:04 DBsearch done 1/3.
2022/12/22 04:31:06 DBsearch done 3/3.
2022/12/22 04:31:08 DBsearch done 2/3.
2022/12/22 04:31:08 Last format DB will be performed using 1 CPUs.
2022/12/22 04:31:08 Last format DB done 1/1.
2022/12/22 04:31:08 Last alignment will be performed using 1 CPUs.
2022/12/22 04:31:12 Last alignment done 1/1.
2022/12/22 04:31:12 21 CDS features were marked as possible pseudo due to internal stop codons.
2022/12/22 04:31:12 26 CDS features were marked as possible pseudo due to frameshift.
2022/12/22 04:31:12 Partial CDS predicted at sequence002:[<0:1011](+) will be annotated as misc_feature
2022/12/22 04:31:12 Partial CDS predicted at sequence027:[292:>1089](-) will be annotated as misc_feature
2022/12/22 04:31:12 Partial CDS predicted at sequence028:[30:>1020](-) will be annotated as misc_feature
2022/12/22 04:31:12 Removed 246 partial features.
2022/12/22 04:31:12 Assigning locus_tags to CDS, rRNA, tRNA, tmRNA
2022/12/22 04:31:13 Setting output verbosity level to 3.
2022/12/22 04:31:13 Writing a genome fasta file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/genome.fna
2022/12/22 04:31:13 Writing a CDS fasta file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/cds.fna
2022/12/22 04:31:13 Writing a protein fasta file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/protein.faa
2022/12/22 04:31:13 Writing an RNA fasta file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/rna.fna
2022/12/22 04:31:13 Writing a GFF file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/genome.gff
2022/12/22 04:31:13 Writing a GenBank format file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/genome.gbk
2022/12/22 04:31:13 Writing an EMBL format file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/genome.embl
2022/12/22 04:31:14 Writing a DDBJ annotation file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/ddbj/mss.ann
2022/12/22 04:31:14 Writing a DDBJ sequence file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/ddbj/mss.fasta
2022/12/22 04:31:15 'center_name' is not specified. 'my_center' is used tentatively.
2022/12/22 04:31:15 Writing a GenBank tbl file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/genbank/genbank.tbl
2022/12/22 04:31:15 Writing a GenBank fsa file to /dfast_volumes/jobs/7fa58b39-d3be-4a56-93d0-942f280328e7/annotation/genbank/genbank.fsa
2022/12/22 04:31:16 DFAST pipeline completed!
2022/12/22 04:31:16 Total running time: 0h0m47s