-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathCP066974.1.10008.fasta.fixstart.log
259 lines (259 loc) · 25.6 KB
/
CP066974.1.10008.fasta.fixstart.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
10:09:44.572 - INFO - UTILS - version=1.9.4
10:09:44.573 - INFO - UTILS - developer: Oliver Schwengers, github.com/oschwengers
10:09:44.573 - INFO - UTILS - command: /data/djs217/anaconda3/envs/bakta_env/bin/bakta -v --genus Xanthomonas --complete --plasmid unnamed CP066974.1.10008.fasta.fixstart.fasta
10:09:44.573 - INFO - UTILS - local time: 2024-09-04 10:09:44
10:09:44.577 - INFO - UTILS - machine: type=x86_64, cores=32
10:09:44.577 - INFO - UTILS - system: type=Linux, release=5.15.0-118-generic
10:09:44.577 - INFO - UTILS - python: version=3.10.14, implementation=CPython
10:09:44.577 - INFO - CONFIG - threads=32
10:09:44.577 - INFO - CONFIG - verbose=True
10:09:44.577 - INFO - CONFIG - debug=False
10:09:44.578 - INFO - CONFIG - database: type=environment, path=/data/djs217/bakta/db
10:09:44.578 - INFO - CONFIG - tmp-path=/tmp/tmp7mdx085e
10:09:44.578 - INFO - CONFIG - genome-path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.fasta
10:09:44.578 - INFO - CONFIG - min_contig_length=1
10:09:44.578 - INFO - CONFIG - prefix=CP066974.1.10008.fasta.fixstart
10:09:44.578 - INFO - CONFIG - output-path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator
10:09:44.578 - INFO - CONFIG - force=False
10:09:44.578 - INFO - CONFIG - genus=Xanthomonas
10:09:44.578 - INFO - CONFIG - species=None
10:09:44.578 - INFO - CONFIG - strain=None
10:09:44.578 - INFO - CONFIG - plasmid=unnamed
10:09:44.578 - INFO - CONFIG - complete=True
10:09:44.578 - INFO - CONFIG - prodigal_tf=None
10:09:44.578 - INFO - CONFIG - translation_table=11
10:09:44.578 - INFO - CONFIG - gram=?
10:09:44.579 - INFO - CONFIG - compliant=False
10:09:44.579 - INFO - CONFIG - meta=False
10:09:44.579 - INFO - CONFIG - locus=None
10:09:44.579 - INFO - CONFIG - locus-tag=None
10:09:44.579 - INFO - CONFIG - keep_contig_headers=False
10:09:44.579 - INFO - CONFIG - replicon-table=None
10:09:44.579 - INFO - CONFIG - regions=None
10:09:44.579 - INFO - CONFIG - skip-tRNA=False
10:09:44.579 - INFO - CONFIG - skip-tmRNA=False
10:09:44.579 - INFO - CONFIG - skip-rRNA=False
10:09:44.579 - INFO - CONFIG - skip-ncRNA=False
10:09:44.579 - INFO - CONFIG - skip-ncRNA-region=False
10:09:44.579 - INFO - CONFIG - skip-CRISPR=False
10:09:44.579 - INFO - CONFIG - skip-CDS=False
10:09:44.579 - INFO - CONFIG - skip-pseudo=False
10:09:44.579 - INFO - CONFIG - skip-sORF=False
10:09:44.579 - INFO - CONFIG - skip-gap=False
10:09:44.579 - INFO - CONFIG - skip-ori=False
10:09:44.579 - INFO - CONFIG - skip-plot=False
10:09:44.579 - INFO - DB - detected: major=5, minor=1, type=full, date=2024-01-19
10:09:44.687 - INFO - UTILS - dependency: tool=tRNAscan-SE, version=v2.0.12, path=/data/djs217/anaconda3/envs/bakta_env/bin/tRNAscan-SE
10:09:44.690 - INFO - UTILS - dependency: tool=Aragorn, version=v1.2.41, path=/data/djs217/anaconda3/envs/bakta_env/bin/aragorn
10:09:44.699 - INFO - UTILS - dependency: tool=CMscan, version=v1.1.5, path=/data/djs217/anaconda3/envs/bakta_env/bin/cmscan
10:09:44.705 - INFO - UTILS - dependency: tool=PilerCR, version=v1.6.0, path=/data/djs217/anaconda3/envs/bakta_env/bin/pilercr
10:09:44.827 - INFO - UTILS - dependency: tool=Pyrodigal, version=v3.5.1, path=/data/djs217/anaconda3/envs/bakta_env/bin/python3.10
10:09:44.833 - INFO - UTILS - dependency: tool=AMRFinderPlus, version=v3.12.8, path=/data/djs217/anaconda3/envs/bakta_env/bin/amrfinder
10:09:44.929 - INFO - UTILS - dependency: tool=Pyhmmer, version=v0.10.14, path=/data/djs217/anaconda3/envs/bakta_env/bin/python3.10
10:09:44.938 - INFO - UTILS - dependency: tool=Diamond, version=v2.1.8, path=/data/djs217/anaconda3/envs/bakta_env/bin/diamond
10:09:45.069 - INFO - UTILS - dependency: tool=Blastn, version=v2.16.0, path=/data/djs217/anaconda3/envs/bakta_env/bin/blastn
10:09:45.483 - INFO - UTILS - dependency: tool=Circos, version=v0.69.8, path=/data/djs217/anaconda3/envs/bakta_env/bin/circos
10:09:45.506 - INFO - FASTA - imported: id=CP066974.1, length=38763, description=Xanthomonas campestris pv. campestris strain 10008 plasmid unnamed2, genomic=True, dna=True
10:09:45.507 - INFO - MAIN - imported sequences=1
10:09:45.507 - INFO - UTILS - qc: revised sequence: id=contig_1, orig-id=CP066974.1, 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 10008 plasmid unnamed2'
10:09:45.507 - INFO - FASTA - write genome sequences: path=/tmp/tmp7mdx085e/contigs.fna, description=False, wrap=False
10:09:46.163 - INFO - T_RNA - predicted=0
10:09:46.208 - INFO - TM_RNA - predicted=0
10:09:46.330 - INFO - R_RNA - predicted=0
10:09:47.016 - INFO - NC_RNA - predicted=0
10:09:47.290 - INFO - NC_RNA_REGION - predicted=0
10:09:47.325 - INFO - CRISPR - predicted=0
10:09:47.325 - INFO - CDS - create prodigal training info object: meta=False, closed=False
10:09:47.403 - INFO - CDS - contig=contig_1, start=1, stop=1995, strand=+, frame=1, truncated=5-prime, start-type=Edge, RBS-motif=None
10:09:47.403 - INFO - CDS - contig=contig_1, start=1992, stop=2483, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.403 - INFO - CDS - contig=contig_1, start=2480, stop=3493, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.403 - INFO - CDS - contig=contig_1, start=3707, stop=4021, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.403 - INFO - CDS - contig=contig_1, start=4024, stop=4290, strand=+, frame=1, truncated=no, start-type=GTG, RBS-motif=None
10:09:47.404 - INFO - CDS - contig=contig_1, start=4357, stop=6927, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.404 - INFO - CDS - contig=contig_1, start=6946, stop=7725, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.404 - INFO - CDS - contig=contig_1, start=8083, stop=9561, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.404 - INFO - CDS - contig=contig_1, start=9568, stop=10278, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.404 - INFO - CDS - contig=contig_1, start=10305, stop=11297, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.404 - INFO - CDS - contig=contig_1, start=11313, stop=12665, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.405 - INFO - CDS - contig=contig_1, start=12736, stop=13044, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.405 - INFO - CDS - contig=contig_1, start=13055, stop=13294, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.405 - INFO - CDS - contig=contig_1, start=13367, stop=13615, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.405 - INFO - CDS - contig=contig_1, start=13617, stop=15803, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.405 - INFO - CDS - contig=contig_1, start=15808, stop=16077, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.405 - INFO - CDS - contig=contig_1, start=16074, stop=16322, strand=+, frame=3, truncated=no, start-type=GTG, RBS-motif=None
10:09:47.405 - INFO - CDS - contig=contig_1, start=16338, stop=16616, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.405 - INFO - CDS - contig=contig_1, start=16572, stop=16904, strand=-, frame=2, truncated=no, start-type=GTG, RBS-motif=None
10:09:47.406 - INFO - CDS - contig=contig_1, start=17165, stop=17464, strand=+, frame=2, truncated=no, start-type=TTG, RBS-motif=GGA/GAG/AGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=17893, stop=18192, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=18255, stop=18485, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=18488, stop=18823, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=18820, stop=18960, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=19059, stop=19265, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=19421, stop=19783, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=19805, stop=20128, strand=-, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.406 - INFO - CDS - contig=contig_1, start=20580, stop=21044, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.407 - INFO - CDS - contig=contig_1, start=21041, stop=21910, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.407 - INFO - CDS - contig=contig_1, start=21944, stop=22279, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.407 - INFO - CDS - contig=contig_1, start=22283, stop=22888, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.407 - INFO - CDS - contig=contig_1, start=22911, stop=23366, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.407 - INFO - CDS - contig=contig_1, start=23390, stop=23647, strand=-, frame=3, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.407 - INFO - CDS - contig=contig_1, start=24240, stop=24356, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.407 - INFO - CDS - contig=contig_1, start=24642, stop=24965, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.407 - INFO - CDS - contig=contig_1, start=25369, stop=25647, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.408 - INFO - CDS - contig=contig_1, start=25716, stop=25871, strand=-, frame=2, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.408 - INFO - CDS - contig=contig_1, start=26237, stop=26635, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.408 - INFO - CDS - contig=contig_1, start=26705, stop=26902, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.408 - INFO - CDS - contig=contig_1, start=26899, stop=27138, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.408 - INFO - CDS - contig=contig_1, start=27152, stop=27745, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.408 - INFO - CDS - contig=contig_1, start=27798, stop=28025, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.408 - INFO - CDS - contig=contig_1, start=28132, stop=28281, strand=-, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.408 - INFO - CDS - contig=contig_1, start=28302, stop=28589, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.408 - INFO - CDS - contig=contig_1, start=29409, stop=30230, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.409 - INFO - CDS - contig=contig_1, start=31652, stop=32353, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.409 - INFO - CDS - contig=contig_1, start=32359, stop=32523, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.409 - INFO - CDS - contig=contig_1, start=32480, stop=33118, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.409 - INFO - CDS - contig=contig_1, start=33115, stop=33450, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=AGGA
10:09:47.409 - INFO - CDS - contig=contig_1, start=33490, stop=33792, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.409 - INFO - CDS - contig=contig_1, start=33795, stop=34259, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.409 - INFO - CDS - contig=contig_1, start=34264, stop=34860, strand=+, frame=1, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.409 - INFO - CDS - contig=contig_1, start=34853, stop=35443, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
10:09:47.410 - INFO - CDS - contig=contig_1, start=35693, stop=35938, strand=-, frame=3, truncated=no, start-type=ATG, RBS-motif=None
10:09:47.410 - INFO - CDS - contig=contig_1, start=36066, stop=38696, strand=+, frame=3, truncated=no, start-type=ATG, RBS-motif=GGA/GAG/AGG
10:09:47.410 - INFO - CDS - truncated CDS: contig=contig_1, start=1, stop=1995, strand=+, frame=1, truncated=5-prime, start-type=Edge, RBS-motif=None, aa-hexdigest=dc430cbe12c46bf74404623f4f506431, aa=[MVACVVCIFL..ADDDMDYMLP]
10:09:47.410 - INFO - CDS - contig=contig_1, start=1992, stop=2483, strand=+, nt=[ATGAAGAAAT..CACCCCATGA]
10:09:47.410 - INFO - CDS - contig=contig_1, start=2480, stop=3493, strand=+, nt=[ATGAACGCCA..AGCCGAGTAG]
10:09:47.410 - INFO - CDS - contig=contig_1, start=3707, stop=4021, strand=+, nt=[ATGAAGCTCC..GGTGTTCTGA]
10:09:47.410 - INFO - CDS - contig=contig_1, start=4024, stop=4290, strand=+, nt=[GTGGACGAAC..CCGCGCATAG]
10:09:47.410 - INFO - CDS - contig=contig_1, start=4357, stop=6927, strand=+, nt=[ATGCAGCGAC..CGAAGCCTAA]
10:09:47.410 - INFO - CDS - contig=contig_1, start=6946, stop=7725, strand=+, nt=[ATGACCATTC..CTTGAAGTGA]
10:09:47.410 - INFO - CDS - contig=contig_1, start=8083, stop=9561, strand=+, nt=[ATGGACCCGA..CGAGAGCTAA]
10:09:47.410 - INFO - CDS - contig=contig_1, start=9568, stop=10278, strand=+, nt=[ATGAGCAGCA..CACCCCCTAA]
10:09:47.410 - INFO - CDS - contig=contig_1, start=10305, stop=11297, strand=+, nt=[ATGCAAACCA..CCGTCGCTAA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=11313, stop=12665, strand=+, nt=[ATGCAGACCA..TGGCCCGTGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=12736, stop=13044, strand=+, nt=[ATGCCTGCAA..CCCGCTCTAG]
10:09:47.411 - INFO - CDS - contig=contig_1, start=13055, stop=13294, strand=+, nt=[ATGGCCCGCA..AGCTGCATGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=13367, stop=13615, strand=+, nt=[ATGAACGCAC..GGAGCGCTGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=13617, stop=15803, strand=+, nt=[ATGCGTCTAT..CAAGGTGTAA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=15808, stop=16077, strand=+, nt=[ATGCGTGCAT..TGACTCGTGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=16074, stop=16322, strand=+, nt=[GTGATACGCC..TGCTGTCTGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=16338, stop=16616, strand=+, nt=[ATGAAGGATG..AGAAGCCTAG]
10:09:47.411 - INFO - CDS - contig=contig_1, start=16572, stop=16904, strand=-, nt=[GTGACCGGCA..TGGCGTCTGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=17165, stop=17464, strand=+, nt=[TTGCTAAACG..GGGGGCGTGA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=17893, stop=18192, strand=+, nt=[ATGCATCACC..CGAAAACTAA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=18255, stop=18485, strand=+, nt=[ATGCACGACG..CAGGCACTAA]
10:09:47.411 - INFO - CDS - contig=contig_1, start=18488, stop=18823, strand=+, nt=[ATGCTGCTTG..GACCTCATGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=18820, stop=18960, strand=+, nt=[ATGAACTTCC..GCTCCTCTAG]
10:09:47.412 - INFO - CDS - contig=contig_1, start=19059, stop=19265, strand=+, nt=[ATGCCCGGAG..ACGCAGCTAG]
10:09:47.412 - INFO - CDS - contig=contig_1, start=19421, stop=19783, strand=+, nt=[ATGTACGAAA..AGACCAGTAA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=19805, stop=20128, strand=-, nt=[ATGAAGACAG..GATGCTCTAA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=20580, stop=21044, strand=+, nt=[ATGACATCAC..CGGCGCATGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=21041, stop=21910, strand=+, nt=[ATGAGCGACC..CACTCGTTGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=21944, stop=22279, strand=+, nt=[ATGACGCAGA..CAAGGACTGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=22283, stop=22888, strand=+, nt=[ATGCCGCATG..CTCCAAATAA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=22911, stop=23366, strand=+, nt=[ATGCCACTTA..CGAGGCATAA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=23390, stop=23647, strand=-, nt=[ATGGACCAGG..ACAGCGGTAG]
10:09:47.412 - INFO - CDS - contig=contig_1, start=24240, stop=24356, strand=+, nt=[ATGAAAAAAC..ACTCAACTAA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=24642, stop=24965, strand=+, nt=[ATGAGCCACA..GTTTGCCTGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=25369, stop=25647, strand=+, nt=[ATGCCTAAAT..ACCGGACTAG]
10:09:47.412 - INFO - CDS - contig=contig_1, start=25716, stop=25871, strand=-, nt=[ATGCAAGAGC..GGACGACTGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=26237, stop=26635, strand=+, nt=[ATGTTCACCG..CGAAGACTGA]
10:09:47.412 - INFO - CDS - contig=contig_1, start=26705, stop=26902, strand=+, nt=[ATGGACCAGG..TGCGGCATGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=26899, stop=27138, strand=+, nt=[ATGACCGCCG..CCAGCACTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=27152, stop=27745, strand=+, nt=[ATGCCTAAGC..CTACGCTTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=27798, stop=28025, strand=+, nt=[ATGAAACTGC..GTCCCGCTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=28132, stop=28281, strand=-, nt=[ATGCGCGCCG..TTTAACATGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=28302, stop=28589, strand=+, nt=[ATGCCGGGCT..AGGCGCCTAG]
10:09:47.413 - INFO - CDS - contig=contig_1, start=29409, stop=30230, strand=+, nt=[ATGCCAGCAG..GTTCAAATAG]
10:09:47.413 - INFO - CDS - contig=contig_1, start=31652, stop=32353, strand=+, nt=[ATGGAACTGC..TGCTGGCTAG]
10:09:47.413 - INFO - CDS - contig=contig_1, start=32359, stop=32523, strand=+, nt=[ATGCAAGTCG..GCGCAGGTAA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=32480, stop=33118, strand=+, nt=[ATGAAAACCG..CCAAGCATGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=33115, stop=33450, strand=+, nt=[ATGACCAGCG..GGCCGAGTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=33490, stop=33792, strand=+, nt=[ATGACGCATT..GCAGGTCTAA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=33795, stop=34259, strand=+, nt=[ATGGGTGCCC..GCGAGGTTAG]
10:09:47.413 - INFO - CDS - contig=contig_1, start=34264, stop=34860, strand=+, nt=[ATGTCTGTGA..TCATGAGTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=34853, stop=35443, strand=+, nt=[ATGAGTGACC..GCCACGCTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=35693, stop=35938, strand=-, nt=[ATGCGTCCGG..AACAGGCTGA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=36066, stop=38696, strand=+, nt=[ATGCAGCGGC..ACGGAGTTAA]
10:09:47.413 - INFO - CDS - contig=contig_1, start=1, stop=1995, strand=+, nt=[ATGGTCGCTT..GCTCCCATGA]
10:09:47.414 - INFO - CDS - predicted=55
10:09:47.652 - INFO - ORF - discarded=0
10:09:47.716 - INFO - UPS - looked-up=39
10:09:47.759 - INFO - IPS - looked-up=39
10:09:47.760 - INFO - ORF - write internal aa seqs: # seqs=16, path=/tmp/tmp7mdx085e/cds.psc.faa
10:11:24.155 - INFO - PSC - found: PSC=6, PSCC=2
10:11:24.204 - INFO - PSC - looked-up=47
10:11:24.245 - INFO - PSCC - looked-up=47
10:11:24.245 - INFO - ORF - write internal aa seqs: # seqs=55, path=/tmp/tmp7mdx085e/cds.expert.faa
10:11:25.041 - INFO - EXPERT-AMRFINDER - found=0
10:11:26.209 - INFO - EXPERT_AA_SEQ - found=0
10:11:26.209 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=copG
10:11:26.210 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbL
10:11:26.210 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbF
10:11:26.211 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbG
10:11:26.211 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=trbI
10:11:26.211 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=copG
10:11:26.211 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=parB
10:11:26.211 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=13367, stop=13615, strand=+
10:11:26.212 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=16338, stop=16616, strand=+
10:11:26.212 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=16572, stop=16904, strand=-
10:11:26.212 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=17165, stop=17464, strand=+
10:11:26.212 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=18255, stop=18485, strand=+
10:11:26.212 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=18488, stop=18823, strand=+
10:11:26.212 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=18820, stop=18960, strand=+
10:11:26.213 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=19059, stop=19265, strand=+
10:11:26.213 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=ptxR
10:11:26.213 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=20580, stop=21044, strand=+
10:11:26.213 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=21944, stop=22279, strand=+
10:11:26.213 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=22911, stop=23366, strand=+
10:11:26.213 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=23390, stop=23647, strand=-
10:11:26.214 - INFO - ANNOTATION - fix product: revise DUF. new=DUF6166 domain-containing protein, old=Family of unknown function (DUF6166)
10:11:26.214 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=dnaJ
10:11:26.214 - INFO - ANNOTATION - fix product: revise DUF. new=DUF6573 domain-containing protein, old=Family of unknown function (DUF6573)
10:11:26.214 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=26705, stop=26902, strand=+
10:11:26.214 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=26899, stop=27138, strand=+
10:11:26.215 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=28132, stop=28281, strand=-
10:11:26.215 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=28302, stop=28589, strand=+
10:11:26.215 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=32359, stop=32523, strand=+
10:11:26.215 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=parA
10:11:26.215 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=33115, stop=33450, strand=+
10:11:26.215 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=33490, stop=33792, strand=+
10:11:26.216 - INFO - ANNOTATION - marked as hypothetical: contig=contig_1, start=35693, stop=35938, strand=-
10:11:26.216 - INFO - ANNOTATION - fix gene: extract symbol from protein name. symbol=traG
10:11:26.216 - INFO - ORF - write internal aa seqs: # seqs=20, path=/tmp/tmp7mdx085e/cds.pseudo.candidates.faa
10:13:23.968 - INFO - CDS - found: pseudogene-candidates=2
10:13:26.028 - INFO - CDS - found: pseudogenes=0
10:13:26.029 - INFO - PSC - looked-up=0
10:13:26.030 - INFO - PSCC - looked-up=0
10:13:32.377 - INFO - CDS - predicted-pfams=0, CDS-w/-pfams=0
10:13:32.429 - INFO - S_ORF - predicted=394
10:13:32.640 - INFO - S_ORF - sORF filter: # valid=106, # discarded=288
10:13:32.844 - INFO - ORF - discarded=0
10:13:33.154 - INFO - UPS - looked-up=0
10:13:33.156 - INFO - IPS - looked-up=0
10:13:33.156 - INFO - ORF - write internal aa seqs: # seqs=106, path=/tmp/tmp7mdx085e/sorf.faa
10:13:33.451 - INFO - S_ORF - found=0
10:13:33.452 - INFO - PSC - looked-up=0
10:13:33.452 - INFO - PSCC - looked-up=0
10:13:34.865 - INFO - ORI - predicted=0
10:13:35.087 - INFO - ORI - predicted=0
10:13:35.088 - INFO - UTILS - generated sequence tag prefix: prefix=GDCKHFCFJE, length=10, MD5=0DC41FCF3E9EDB566557C1093BF9B245
10:13:35.088 - INFO - MAIN - selected features=55
10:13:35.088 - INFO - UTILS - generated sequence tag prefix: prefix=GDCKHF, length=6, MD5=0DC41FCF3E9EDB566557C1093BF9B245
10:13:35.088 - INFO - MAIN - locus tag prefix=GDCKHF
10:13:35.089 - INFO - UTILS - genome-size=38763
10:13:35.090 - INFO - UTILS - GC=0.627
10:13:35.091 - INFO - UTILS - N=0.000
10:13:35.091 - INFO - UTILS - N50=38763
10:13:35.091 - INFO - UTILS - coding-ratio=0.819
10:13:35.092 - INFO - TSV - write tsv: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.tsv
10:13:35.093 - INFO - GFF - write GFF3: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.gff3
10:13:35.098 - INFO - INSDC - write GenBank: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.gbff
10:13:35.109 - INFO - INSDC - write EMBL: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.embl
10:13:35.117 - INFO - FASTA - write genome sequences: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.fna, description=True, wrap=True
10:13:35.118 - INFO - FASTA - write feature nucleotide sequences: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.ffn
10:13:35.118 - INFO - FASTA - write translated CDS/sORF: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.faa
10:13:35.164 - INFO - PLOT - write circular genome plot: file-name=CP066974.1.10008.fasta.fixstart, output-dir=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator
10:13:42.069 - INFO - TSV - write hypothetical tsv: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.hypotheticals.tsv
10:13:42.070 - INFO - FASTA - write translated CDS/sORF: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.hypotheticals.faa
10:13:42.071 - INFO - JSON - write JSON: path=/data/djs217/PROJECTS/18_Xcc_serbia/Xanthomonas_campestris_Serbia/11_circlator/CP066974.1.10008.fasta.fixstart.json
10:13:42.085 - INFO - MAIN - removed tmp dir: /tmp/tmp7mdx085e