2018/01/25 13:06:18 Running on Python 3.6.3 (default, Dec 17 2017, 12:56:31) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-18)].
2018/01/25 13:06:18 Loading a config file from /home/www/dfast/resources/dfc_config/dfast_web_config.py
2018/01/25 13:06:18 OS type is Linux.
2018/01/25 13:06:18 Adding /home/www/dfast_core/bin/Linux to PATH.
2018/01/25 13:06:18 DFAST pipeline started. (version 1.0.2)
2018/01/25 13:06:18 Results will be generated into '/home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation'.
2018/01/25 13:06:18 Loading a genomic fasta file from /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/input/genome.fna
2018/01/25 13:06:18 Genome source information: organism=, strain=
2018/01/25 13:06:18 The query genome is treated as a draft genome with 26 sequences.
2018/01/25 13:06:18 Sequences shorter than 200 will be eliminated.
2018/01/25 13:06:18 Sequences will be renamed as sequence01, sequence02...
2018/01/25 13:06:18 Locus_tag settings: locus_tag_prefix=LOCUS and step=10.
2018/01/25 13:06:18 Locus_tags are assigned separately to each feature type. e.g. CDS: LOCUS_000xx, rRNA: LOCUS_r000xx, tRNA: LOCUS_t000xx, tmRNA: LOCUS_tm000xx.
2018/01/25 13:06:18 Remove_Partial_Feature is enabled.
2018/01/25 13:06:18 Remove_Overlapping_Feature is enabled. Priority: ['assembly_gap', 'CRISPR', ('tmRNA', 'tRNA', 'rRNA'), 'CDS']
2018/01/25 13:06:18 Initializing structural annotation tools... 
2018/01/25 13:06:18 GAPannotator initialized. (Version 1.0)
2018/01/25 13:06:18 Setting GAPannotator options. {'len_cutoff': 5, 'linkage_evidence': 'paired-ends', 'gap_type': 'within scaffold'}
2018/01/25 13:06:18 Checking MetaGeneAnnotator... 
2018/01/25 13:06:18 MetaGeneAnnotator initialized. (Version 2008/08/19)
2018/01/25 13:06:18 Setting MetaGeneAnnotator options. {'cmd_options': '-s'}
2018/01/25 13:06:18 Checking Aragorn version... 
2018/01/25 13:06:18 Aragorn initialized. (Version 1.2.38)
2018/01/25 13:06:18 Setting Aragorn options. {'gcode': '-gcbact', 'cmd_options': '-l'}
2018/01/25 13:06:18 Checking Barrnap version... 
2018/01/25 13:06:18 Barrnap initialized. (Version 0.8)
2018/01/25 13:06:18 Checking CRT version... 
2018/01/25 13:06:18 CRT initialized. (Version 1.2)
2018/01/25 13:06:18 Setting CRT options. {'jar_file': '/home/www/dfast_core/bin/common/CRT1.2-CLI.jar', 'java_options': '', 'cmd_options': ''}
2018/01/25 13:06:18 Checking Java version... 
2018/01/25 13:06:18 Java initialized. (Version 1.8.0_151)
2018/01/25 13:06:18 Initializing annotation components... 
2018/01/25 13:06:18 DBsearch initialized.
2018/01/25 13:06:18 Setting DBsearch options. {'cpu': 1, 'skipAnnotatedFeatures': True, 'evalue_cutoff': 1e-06, 'qcov_cutoff': 75, 'scov_cutoff': 75, 'aligner': 'ghostx', 'aligner_options': {}, 'database': '/home/www/dfast_core/db/protein/DFAST-LAB'}
2018/01/25 13:06:18 Checking GHOSTX version... 
2018/01/25 13:06:18 GHOSTX initialized. (Version 1.3.6)
2018/01/25 13:06:18 Reference DB loaded. 64421 sequences. [dbname=DFAST-LAB, version=1.0.1, contributor=yt, modified=20171117]
2018/01/25 13:06:18 DBsearch initialized.
2018/01/25 13:06:18 Setting DBsearch options. {'cpu': 1, 'skipAnnotatedFeatures': True, 'evalue_cutoff': 1e-06, 'qcov_cutoff': 75, 'scov_cutoff': 75, 'aligner': 'ghostx', 'aligner_options': {}, 'database': '/home/www/dfast_core/db/protein/DFAST-default.ref'}
2018/01/25 13:06:21 Reference DB loaded. 404804 sequences. [dbname=DFAST-default, version=1.1.1, contributor=yt, modified=20171117]
2018/01/25 13:06:21 PseudoGeneDetection initialized.
2018/01/25 13:06:21 Setting PseudoGeneDetection options. {'cpu': 1, 'skipAnnotatedFeatures': False, 'extension': 300, 'scov_cutoff': 85}
2018/01/25 13:06:21 Checking lastdb version... 
2018/01/25 13:06:21 lastdb initialized. (Version 852)
2018/01/25 13:06:21 Checking lastal version... 
2018/01/25 13:06:21 lastal initialized. (Version 852)
2018/01/25 13:06:21 Checking Blastp version... 
2018/01/25 13:06:21 Blastp initialized. (Version 2.6.0)
2018/01/25 13:06:21 Start structural annotation process using 3 CPUs
2018/01/25 13:06:24 140 assembly_gap features were detected by GAPannotator.
2018/01/25 13:06:24 2001 CDS features were detected by MetaGeneAnnotator.
2018/01/25 13:06:24 73 tRNA features were detected by Aragorn.
2018/01/25 13:06:25 3 rRNA features were detected by Barrnap.
2018/01/25 13:06:25 1 CRISPR (later will be replaced by repeat_region) features were detected by CRT.
2018/01/25 13:06:25 Removed 25 partial features.
2018/01/25 13:06:25 Removed 114 overlapping features.
2018/01/25 13:06:25 Start executing functional annotation components.
2018/01/25 13:06:25 DBsearch will be performed using 1 CPUs.
2018/01/25 13:06:48 DBsearch done 1/1.
2018/01/25 13:06:48 DBsearch will be performed using 1 CPUs.
2018/01/25 13:06:55 DBsearch done 1/1.
2018/01/25 13:06:58 Last format DB will be performed using 1 CPUs.
2018/01/25 13:06:58 Last format DB done 1/1.
2018/01/25 13:06:58 Last alignment will be performed using 1 CPUs.
2018/01/25 13:06:59 Last alignment done 1/1.
2018/01/25 13:06:59 62 CDS features were marked as possible pseudo due to internal stop codons.
2018/01/25 13:06:59 130 CDS features were marked as possible pseudo due to frameshift.
2018/01/25 13:06:59 Assigning locus_tags to CDS, rRNA, tRNA, tmRNA
2018/01/25 13:07:00 Setting output verbosity level to 3.
2018/01/25 13:07:00 Writing a genome fasta file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/genome.fna
2018/01/25 13:07:00 Writing a CDS fasta file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/cds.fna
2018/01/25 13:07:00 Writing a protein fasta file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/protein.faa
2018/01/25 13:07:00 Writing an RNA fasta file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/rna.faa
2018/01/25 13:07:00 Writing a GFF file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/genome.gff
2018/01/25 13:07:00 Writing a GenBank format file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/genome.gbk
2018/01/25 13:07:01 Writing an EMBL format file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/genome.embl
2018/01/25 13:07:01 Writing a DDBJ annotation file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/ddbj/mss.ann
2018/01/25 13:07:01 Writing a DDBJ sequence file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/ddbj/mss.fasta
2018/01/25 13:07:02 'center_name' is not specified. 'my_center' is used tentatively.
2018/01/25 13:07:02 Writing a GenBank tbl file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/genbank/genbank.tbl
2018/01/25 13:07:02 Writing a GenBank fsa file to /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/annotation/genbank/genbank.fsa
2018/01/25 13:07:02 DFAST pipeline completed!
2018/01/25 13:07:02 Total running time: 0h0m45s