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JAUBND020000035.1.Xc221-2.fasta.fixstart.log
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08:08:34.185 - INFO - UTILS - version=1.9.4
08:08:34.185 - INFO - UTILS - developer: Oliver Schwengers, github.com/oschwengers
08:08:34.185 - INFO - UTILS - command: /data/djs217/anaconda3/envs/bakta_env/bin/bakta -v --genus Xanthomonas --complete --plasmid unnamed JAUBND020000035.1.Xc221-2.fasta.fixstart.fasta
08:08:34.185 - INFO - UTILS - local time: 2024-09-04 08:08:34
08:08:34.189 - INFO - UTILS - machine: type=x86_64, cores=32
08:08:34.189 - INFO - UTILS - system: type=Linux, release=5.15.0-118-generic
08:08:34.189 - INFO - UTILS - python: version=3.10.14, implementation=CPython
08:08:34.189 - INFO - CONFIG - threads=32
08:08:34.189 - INFO - CONFIG - verbose=True
08:08:34.189 - INFO - CONFIG - debug=False
08:08:34.189 - INFO - CONFIG - database: type=environment, path=/data/djs217/bakta/db
08:08:34.190 - INFO - CONFIG - tmp-path=/tmp/tmpacxb8yck
08:08:34.190 - INFO - CONFIG - genome-path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.fasta
08:08:34.190 - INFO - CONFIG - min_contig_length=1
08:08:34.190 - INFO - CONFIG - prefix=JAUBND020000035.1.Xc221-2.fasta.fixstart
08:08:34.190 - INFO - CONFIG - output-path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator
08:08:34.190 - INFO - CONFIG - force=False
08:08:34.190 - INFO - CONFIG - genus=Xanthomonas
08:08:34.190 - INFO - CONFIG - species=None
08:08:34.190 - INFO - CONFIG - strain=None
08:08:34.190 - INFO - CONFIG - plasmid=unnamed
08:08:34.190 - INFO - CONFIG - complete=True
08:08:34.190 - INFO - CONFIG - prodigal_tf=None
08:08:34.190 - INFO - CONFIG - translation_table=11
08:08:34.190 - INFO - CONFIG - gram=?
08:08:34.190 - INFO - CONFIG - compliant=False
08:08:34.190 - INFO - CONFIG - meta=False
08:08:34.190 - INFO - CONFIG - locus=None
08:08:34.190 - INFO - CONFIG - locus-tag=None
08:08:34.190 - INFO - CONFIG - keep_contig_headers=False
08:08:34.190 - INFO - CONFIG - replicon-table=None
08:08:34.190 - INFO - CONFIG - regions=None
08:08:34.190 - INFO - CONFIG - skip-tRNA=False
08:08:34.190 - INFO - CONFIG - skip-tmRNA=False
08:08:34.190 - INFO - CONFIG - skip-rRNA=False
08:08:34.190 - INFO - CONFIG - skip-ncRNA=False
08:08:34.190 - INFO - CONFIG - skip-ncRNA-region=False
08:08:34.190 - INFO - CONFIG - skip-CRISPR=False
08:08:34.190 - INFO - CONFIG - skip-CDS=False
08:08:34.190 - INFO - CONFIG - skip-pseudo=False
08:08:34.190 - INFO - CONFIG - skip-sORF=False
08:08:34.190 - INFO - CONFIG - skip-gap=False
08:08:34.190 - INFO - CONFIG - skip-ori=False
08:08:34.190 - INFO - CONFIG - skip-plot=False
08:08:34.191 - INFO - DB - detected: major=5, minor=1, type=full, date=2024-01-19
08:08:34.293 - INFO - UTILS - dependency: tool=tRNAscan-SE, version=v2.0.12, path=/data/djs217/anaconda3/envs/bakta_env/bin/tRNAscan-SE
08:08:34.297 - INFO - UTILS - dependency: tool=Aragorn, version=v1.2.41, path=/data/djs217/anaconda3/envs/bakta_env/bin/aragorn
08:08:34.306 - INFO - UTILS - dependency: tool=CMscan, version=v1.1.5, path=/data/djs217/anaconda3/envs/bakta_env/bin/cmscan
08:08:34.312 - INFO - UTILS - dependency: tool=PilerCR, version=v1.6.0, path=/data/djs217/anaconda3/envs/bakta_env/bin/pilercr
08:08:34.418 - INFO - UTILS - dependency: tool=Pyrodigal, version=v3.5.1, path=/data/djs217/anaconda3/envs/bakta_env/bin/python3.10
08:08:34.424 - INFO - UTILS - dependency: tool=AMRFinderPlus, version=v3.12.8, path=/data/djs217/anaconda3/envs/bakta_env/bin/amrfinder
08:08:34.523 - INFO - UTILS - dependency: tool=Pyhmmer, version=v0.10.14, path=/data/djs217/anaconda3/envs/bakta_env/bin/python3.10
08:08:34.532 - INFO - UTILS - dependency: tool=Diamond, version=v2.1.8, path=/data/djs217/anaconda3/envs/bakta_env/bin/diamond
08:08:34.664 - INFO - UTILS - dependency: tool=Blastn, version=v2.16.0, path=/data/djs217/anaconda3/envs/bakta_env/bin/blastn
08:08:35.063 - INFO - UTILS - dependency: tool=Circos, version=v0.69.8, path=/data/djs217/anaconda3/envs/bakta_env/bin/circos
08:08:35.084 - INFO - FASTA - imported: id=JAUBND020000035.1, length=39903, description=Xanthomonas campestris pv. campestris strain Xc221-2 plasmid p39, whole genome shotgun sequence, genomic=True, dna=True
08:08:35.084 - INFO - MAIN - imported sequences=1
08:08:35.085 - INFO - UTILS - qc: revised sequence: id=contig_1, orig-id=JAUBND020000035.1, type=plasmid, complete=True, topology=circular, name=unnamed, description='[organism=Xanthomonas] [gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed]', orig-description='Xanthomonas campestris pv. campestris strain Xc221-2 plasmid p39, whole genome shotgun sequence'
08:08:35.085 - INFO - FASTA - write genome sequences: path=/tmp/tmpacxb8yck/contigs.fna, description=False, wrap=False
08:08:35.736 - INFO - T_RNA - predicted=0
08:08:35.778 - INFO - TM_RNA - predicted=0
08:08:35.900 - INFO - R_RNA - predicted=0
08:08:36.576 - INFO - NC_RNA - contig=contig_1, start=3678, stop=3770, strand=+, gene=C4, product=C4 antisense RNA, length=93, truncated=None, score=69.6, evalue=2.3e-10, nt=[TTCTATGGTG..CACCACCTTT]
08:08:36.577 - INFO - NC_RNA - predicted=1
08:08:36.861 - INFO - NC_RNA_REGION - predicted=0
08:08:36.894 - INFO - CRISPR - predicted=0
08:08:36.894 - INFO - CDS - create prodigal training info object: meta=False, closed=False
08:08:36.972 - INFO - CDS - contig=contig_1, start=1, stop=1995, strand=+, frame=1, truncated=5-prime, start-type=Edge, RBS-motif=None
08:08:36.973 - INFO - CDS - contig=contig_1, start=1992, stop=2483, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.973 - INFO - CDS - contig=contig_1, start=2480, stop=3055, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.973 - INFO - CDS - contig=contig_1, start=3091, stop=3543, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.973 - INFO - CDS - contig=contig_1, start=4047, stop=4868, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.973 - INFO - CDS - contig=contig_1, start=4897, stop=5049, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.973 - INFO - CDS - contig=contig_1, start=5322, stop=5462, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.973 - INFO - CDS - contig=contig_1, start=5521, stop=5778, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.973 - INFO - CDS - contig=contig_1, start=5919, stop=6875, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.974 - INFO - CDS - contig=contig_1, start=6954, stop=7268, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.974 - INFO - CDS - contig=contig_1, start=7271, stop=7537, strand=+, frame=2, truncated=no, start-type=GTG, RBS-motif=None
08:08:36.974 - INFO - CDS - contig=contig_1, start=7604, stop=10174, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.974 - INFO - CDS - contig=contig_1, start=10194, stop=10973, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.974 - INFO - CDS - contig=contig_1, start=11120, stop=11323, strand=+, frame=2, truncated=no, start-type=TTG, RBS-motif=GGA/GAG/AGG
08:08:36.974 - INFO - CDS - contig=contig_1, start=11519, stop=12046, strand=-, frame=3, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.974 - INFO - CDS - contig=contig_1, start=13023, stop=13733, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.974 - INFO - CDS - contig=contig_1, start=13759, stop=14751, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=14767, stop=16110, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=16181, stop=16489, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=16500, stop=16739, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.975 - INFO - CDS - contig=contig_1, start=16816, stop=17064, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=17066, stop=19243, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=19392, stop=19631, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=19647, stop=20231, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=20228, stop=20515, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.975 - INFO - CDS - contig=contig_1, start=20930, stop=21274, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.976 - INFO - CDS - contig=contig_1, start=21505, stop=21786, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.976 - INFO - CDS - contig=contig_1, start=21738, stop=22037, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.976 - INFO - CDS - contig=contig_1, start=22100, stop=22330, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.976 - INFO - CDS - contig=contig_1, start=22425, stop=22613, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.976 - INFO - CDS - contig=contig_1, start=22635, stop=22766, strand=-, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.976 - INFO - CDS - contig=contig_1, start=22782, stop=23276, strand=+, frame=3, truncated=no, start-type=GTG, RBS-motif=None
08:08:36.976 - INFO - CDS - contig=contig_1, start=23376, stop=23642, strand=-, frame=2, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.976 - INFO - CDS - contig=contig_1, start=23756, stop=24214, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.976 - INFO - CDS - contig=contig_1, start=24211, stop=24672, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.976 - INFO - CDS - contig=contig_1, start=25148, stop=25453, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.977 - INFO - CDS - contig=contig_1, start=25530, stop=25847, strand=+, frame=3, truncated=no, start-type=TTG, RBS-motif=None
08:08:36.977 - INFO - CDS - contig=contig_1, start=26726, stop=26842, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.977 - INFO - CDS - contig=contig_1, start=27562, stop=27831, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.977 - INFO - CDS - contig=contig_1, start=27893, stop=28048, strand=-, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.977 - INFO - CDS - contig=contig_1, start=28416, stop=28814, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.977 - INFO - CDS - contig=contig_1, start=28771, stop=28956, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.977 - INFO - CDS - contig=contig_1, start=28953, stop=29192, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.977 - INFO - CDS - contig=contig_1, start=29208, stop=29801, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.977 - INFO - CDS - contig=contig_1, start=29854, stop=30081, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.977 - INFO - CDS - contig=contig_1, start=30274, stop=30618, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.978 - INFO - CDS - contig=contig_1, start=30719, stop=31303, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.978 - INFO - CDS - contig=contig_1, start=31309, stop=31434, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.978 - INFO - CDS - contig=contig_1, start=31660, stop=32481, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=None
08:08:36.978 - INFO - CDS - contig=contig_1, start=32662, stop=33138, strand=+, frame=1, truncated=no, start-type=GTG, RBS-motif=GGA/GAG/AGG
08:08:36.978 - INFO - CDS - contig=contig_1, start=33255, stop=33560, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.978 - INFO - CDS - contig=contig_1, start=33684, stop=34322, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.978 - INFO - CDS - contig=contig_1, start=34319, stop=34660, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.978 - INFO - CDS - contig=contig_1, start=34933, stop=35397, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
08:08:36.978 - INFO - CDS - contig=contig_1, start=35402, stop=35998, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.978 - INFO - CDS - contig=contig_1, start=35991, stop=36581, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
08:08:36.979 - INFO - CDS - contig=contig_1, start=36825, stop=39836, strand=+, frame=3, truncated=no, start-type=TTG, RBS-motif=None
08:08:36.979 - INFO - CDS - contig=contig_1, start=39841, stop=39903, strand=+, frame=1, truncated=3-prime, start-type=ATG, RBS-motif=GGAG/GAGG
08:08:36.979 - INFO - CDS - edge CDS: contig=contig_1, start=39841, stop=1995, strand=+, frame=1, start-type=ATG, RBS-motif=GGAG/GAGG, aa-hexdigest=3765a7ebe2f4e8aa6511eb067d373657, aa=[MAPQSKQREK..ADDDMDYMLP]
08:08:36.979 - INFO - CDS - contig=contig_1, start=1992, stop=2483, strand=+, nt=[ATGAAGAAAT..CACCCCATGA]
08:08:36.979 - INFO - CDS - contig=contig_1, start=2480, stop=3055, strand=+, nt=[ATGAACGCAT..TCCACTTTGA]
08:08:36.979 - INFO - CDS - contig=contig_1, start=3091, stop=3543, strand=+, nt=[ATGCGCCCCT..GACGGTTTGA]
08:08:36.979 - INFO - CDS - contig=contig_1, start=4047, stop=4868, strand=+, nt=[ATGTCAGCAG..CGAAACGTAG]
08:08:36.979 - INFO - CDS - contig=contig_1, start=4897, stop=5049, strand=+, nt=[ATGCCGCAAA..GGAGAAATAA]
08:08:36.979 - INFO - CDS - contig=contig_1, start=5322, stop=5462, strand=+, nt=[ATGACCCTGG..CCAGTGCTAG]
08:08:36.979 - INFO - CDS - contig=contig_1, start=5521, stop=5778, strand=+, nt=[ATGCCAGGCC..CGTACCGTAG]
08:08:36.979 - INFO - CDS - contig=contig_1, start=5919, stop=6875, strand=+, nt=[ATGATGAAAT..AGCCGAATGA]
08:08:36.979 - INFO - CDS - contig=contig_1, start=6954, stop=7268, strand=+, nt=[ATGAAGCTCC..GGTGTTCTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=7271, stop=7537, strand=+, nt=[GTGGACGAAC..CCGCGCATAG]
08:08:36.980 - INFO - CDS - contig=contig_1, start=7604, stop=10174, strand=+, nt=[ATGCAGCGAC..CCAAGCCTAA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=10194, stop=10973, strand=+, nt=[ATGAAAATTC..TATCAAGTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=11120, stop=11323, strand=+, nt=[TTGCCGGAAA..TATCAAGTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=11519, stop=12046, strand=-, nt=[ATGACGGTGA..TATTGCTTAG]
08:08:36.980 - INFO - CDS - contig=contig_1, start=13023, stop=13733, strand=+, nt=[ATGAGCAGCA..CGCCCCCTAA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=13759, stop=14751, strand=+, nt=[ATGCAAACCA..CCGTCGCTAA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=14767, stop=16110, strand=+, nt=[ATGCAGACCA..TGGTCCGTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=16181, stop=16489, strand=+, nt=[ATGCCTGCAA..CCCGCTCTAG]
08:08:36.980 - INFO - CDS - contig=contig_1, start=16500, stop=16739, strand=+, nt=[ATGGCCCGTC..GGCCGCATGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=16816, stop=17064, strand=+, nt=[ATGAACACAC..GGAGCGCTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=17066, stop=19243, strand=+, nt=[ATGCGTCTAT..CAAAGCGTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=19392, stop=19631, strand=+, nt=[ATGAAGCTCC..TGCTGTCTGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=19647, stop=20231, strand=+, nt=[ATGACCAACA..CGTCCAATGA]
08:08:36.980 - INFO - CDS - contig=contig_1, start=20228, stop=20515, strand=+, nt=[ATGATCACCC..AAAATCGTAG]
08:08:36.981 - INFO - CDS - contig=contig_1, start=20930, stop=21274, strand=+, nt=[ATGAAAGACA..AACGGCGTAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=21505, stop=21786, strand=+, nt=[ATGTGTCCAG..AGTTGGCTAG]
08:08:36.981 - INFO - CDS - contig=contig_1, start=21738, stop=22037, strand=+, nt=[ATGCATCACC..CGAAAACTAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=22100, stop=22330, strand=+, nt=[ATGCACGACG..CAGGCACTAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=22425, stop=22613, strand=+, nt=[ATGAATCTAT..TAGAGCGTAG]
08:08:36.981 - INFO - CDS - contig=contig_1, start=22635, stop=22766, strand=-, nt=[ATGTGGTTGC..GGCTGGATGA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=22782, stop=23276, strand=+, nt=[GTGAGCGTGA..TGCCCTGTAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=23376, stop=23642, strand=-, nt=[ATGGCTGCCC..AGTTGACTGA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=23756, stop=24214, strand=+, nt=[ATGACATCGC..ATCCCCATGA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=24211, stop=24672, strand=+, nt=[ATGACCACTG..AGTGAGCTAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=25148, stop=25453, strand=+, nt=[ATGAAGAAGA..GGGATACTGA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=25530, stop=25847, strand=+, nt=[TTGTCAGAGG..CGACCAATAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=26726, stop=26842, strand=+, nt=[ATGAAAAAAC..ACTCAACTAA]
08:08:36.981 - INFO - CDS - contig=contig_1, start=27562, stop=27831, strand=+, nt=[ATGGCCAAGA..GCCGGAGTAA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=27893, stop=28048, strand=-, nt=[ATGCAAGAAC..GCGGCACTGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=28416, stop=28814, strand=+, nt=[ATGTTTACAG..CGAAGACTGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=28771, stop=28956, strand=+, nt=[ATGCCGAGCC..AGCCGCATGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=28953, stop=29192, strand=+, nt=[ATGACTGCCG..CAACCACTGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=29208, stop=29801, strand=+, nt=[ATGCGCAAGC..CTACGCTTGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=29854, stop=30081, strand=+, nt=[ATGAAATTGC..GTCCCGCTAA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=30274, stop=30618, strand=+, nt=[ATGGAAACGC..AGGCGCGTAG]
08:08:36.982 - INFO - CDS - contig=contig_1, start=30719, stop=31303, strand=+, nt=[ATGCTGATCC..CGAGCCATAG]
08:08:36.982 - INFO - CDS - contig=contig_1, start=31309, stop=31434, strand=+, nt=[ATGAATCATG..AGCGATATGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=31660, stop=32481, strand=+, nt=[ATGTCAGCAG..GTTCGAGTAG]
08:08:36.982 - INFO - CDS - contig=contig_1, start=32662, stop=33138, strand=+, nt=[GTGGGGAAGT..TTCATCATGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=33255, stop=33560, strand=+, nt=[ATGGCCGACG..CGCCAGCTAA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=33684, stop=34322, strand=+, nt=[ATGAAAACCA..CCACGTATGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=34319, stop=34660, strand=+, nt=[ATGACCACTG..CGACGAATAG]
08:08:36.982 - INFO - CDS - contig=contig_1, start=34933, stop=35397, strand=+, nt=[ATGGGTGCCC..GCGAGGTTAG]
08:08:36.982 - INFO - CDS - contig=contig_1, start=35402, stop=35998, strand=+, nt=[ATGTCTGTGA..TCATGAGTGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=35991, stop=36581, strand=+, nt=[ATGAGTGACC..GCCACGCTGA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=36825, stop=39836, strand=+, nt=[TTGTCATTTG..ACGGAGTTAA]
08:08:36.982 - INFO - CDS - contig=contig_1, start=39841, stop=1995, strand=+, nt=[ATGGCACCAC..GCTCCCATGA]
08:08:36.983 - INFO - CDS - predicted=57
08:08:37.220 - INFO - ORF - discarded=0
08:08:37.413 - INFO - UPS - looked-up=41
08:08:37.510 - INFO - IPS - looked-up=41
08:08:37.510 - INFO - ORF - write internal aa seqs: # seqs=16, path=/tmp/tmpacxb8yck/cds.psc.faa
08:10:13.385 - INFO - PSC - found: PSC=5, PSCC=2
08:10:13.432 - INFO - PSC - looked-up=48
08:10:13.476 - INFO - PSCC - looked-up=48
08:10:13.476 - INFO - ORF - write internal aa seqs: # seqs=57, path=/tmp/tmpacxb8yck/cds.expert.faa
08:10:14.231 - INFO - EXPERT-AMRFINDER - found=0
08:10:15.507 - INFO - EXPERT_AA_SEQ - found=0
08:10:15.508 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=copG
08:10:15.509 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=tnpR
08:10:15.509 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=3091, stop=3543, strand=+
08:10:15.509 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=4897, stop=5049, strand=+
08:10:15.509 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=5322, stop=5462, strand=+
08:10:15.510 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=tadA
08:10:15.510 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbC
08:10:15.510 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=11120, stop=11323, strand=+
08:10:15.510 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=11519, stop=12046, strand=-
08:10:15.510 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbF
08:10:15.511 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbG
08:10:15.511 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbI
08:10:15.511 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=copG
08:10:15.511 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=parB
08:10:15.512 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=16816, stop=17064, strand=+
08:10:15.512 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.512 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=19392, stop=19631, strand=+
08:10:15.512 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.512 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=20228, stop=20515, strand=+
08:10:15.512 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=20930, stop=21274, strand=+
08:10:15.513 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=21505, stop=21786, strand=+
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=22100, stop=22330, strand=+
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=22425, stop=22613, strand=+
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=22635, stop=22766, strand=-
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=22782, stop=23276, strand=+
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=23376, stop=23642, strand=-
08:10:15.513 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=23756, stop=24214, strand=+
08:10:15.514 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=25530, stop=25847, strand=+
08:10:15.514 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.514 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=26726, stop=26842, strand=+
08:10:15.514 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.514 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=27562, stop=27831, strand=+
08:10:15.514 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=dnaJ
08:10:15.515 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=28771, stop=28956, strand=+
08:10:15.515 - INFO - ANNOTATION - remove product: mark proteins with suspect products as hypothetical. old=Genome assembly B1459, plasmid I
08:10:15.515 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=28953, stop=29192, strand=+
08:10:15.515 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=30274, stop=30618, strand=+
08:10:15.515 - INFO - ANNOTATION - fix product: revise DUF. new=DUF6012 domain-containing protein, old=DUF6012 family protein
08:10:15.515 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=31309, stop=31434, strand=+
08:10:15.516 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=32662, stop=33138, strand=+
08:10:15.516 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=kfrA
08:10:15.516 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=parA
08:10:15.516 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=34319, stop=34660, strand=+
08:10:15.517 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=traG
08:10:15.517 - INFO - ORF - write internal aa seqs: # seqs=25, path=/tmp/tmpacxb8yck/cds.pseudo.candidates.faa
08:12:05.998 - INFO - CDS - found: pseudogene-candidates=3
08:12:07.298 - INFO - CDS - pseudogene observation: contig=contig_1, start=23756, stop=24214, strand=+, effect=stop, cause=mutation, position=23714
08:12:07.298 - INFO - CDS - pseudogene: contig=contig_1, start=23756, stop=24214, strand=+, insertions=[], deletions=[], mutations=[23714], effect=Internal stop codon at 23714
08:12:07.299 - INFO - CDS - found: pseudogenes=1
08:12:07.300 - INFO - PSC - looked-up=1
08:12:07.302 - INFO - PSCC - looked-up=0
08:12:07.303 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=23756, stop=24214, strand=+
08:12:13.351 - INFO - CDS - predicted-pfams=0, CDS-w/-pfams=0
08:12:13.406 - INFO - S_ORF - predicted=368
08:12:13.579 - INFO - S_ORF - sORF filter: # valid=132, # discarded=236
08:12:13.782 - INFO - ORF - discarded=0
08:12:14.136 - INFO - UPS - looked-up=0
08:12:14.137 - INFO - IPS - looked-up=0
08:12:14.138 - INFO - ORF - write internal aa seqs: # seqs=132, path=/tmp/tmpacxb8yck/sorf.faa
08:12:14.390 - INFO - S_ORF - found=0
08:12:14.391 - INFO - PSC - looked-up=0
08:12:14.392 - INFO - PSCC - looked-up=0
08:12:15.791 - INFO - ORI - predicted=0
08:12:15.993 - INFO - ORI - predicted=0
08:12:15.994 - INFO - UTILS - generated sequence tag prefix: prefix=MNAIIPIAMB, length=10, MD5=67A2292A6B04540D113296A0CF8DAD1B
08:12:15.995 - INFO - MAIN - selected features=58
08:12:15.995 - INFO - UTILS - generated sequence tag prefix: prefix=MNAIIP, length=6, MD5=67A2292A6B04540D113296A0CF8DAD1B
08:12:15.995 - INFO - MAIN - locus tag prefix=MNAIIP
08:12:15.996 - INFO - UTILS - genome-size=39903
08:12:15.997 - INFO - UTILS - GC=0.621
08:12:15.998 - INFO - UTILS - N=0.000
08:12:15.998 - INFO - UTILS - N50=39903
08:12:15.998 - INFO - UTILS - coding-ratio=0.804
08:12:15.999 - INFO - TSV - write tsv: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.tsv
08:12:16.000 - INFO - GFF - write GFF3: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.gff3
08:12:16.005 - INFO - INSDC - write GenBank: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.gbff
08:12:16.016 - INFO - INSDC - write EMBL: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.embl
08:12:16.025 - INFO - FASTA - write genome sequences: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.fna, description=True, wrap=True
08:12:16.026 - INFO - FASTA - write feature nucleotide sequences: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.ffn
08:12:16.026 - INFO - FASTA - write translated CDS/sORF: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.faa
08:12:16.026 - INFO - PLOT - split edge feature: contig=contig_1, start=39841, stop=1995, strand=+, edge=True
08:12:16.069 - INFO - PLOT - write circular genome plot: file-name=JAUBND020000035.1.Xc221-2.fasta.fixstart, output-dir=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator
08:12:22.662 - INFO - TSV - write hypothetical tsv: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.hypotheticals.tsv
08:12:22.663 - INFO - FASTA - write translated CDS/sORF: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.hypotheticals.faa
08:12:22.664 - INFO - JSON - write JSON: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/JAUBND020000035.1.Xc221-2.fasta.fixstart.json
08:12:22.679 - INFO - MAIN - removed tmp dir: /tmp/tmpacxb8yck