Mercurial > repos > pimarin > bakta

comparison test-data/tmp/TEST_1.log @ 3:eea334d9988b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 73af464cc860250c3fa3dd433602283ab5a44f53-dirty
author pimarin
date Thu, 22 Dec 2022 15:01:43 +0000
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2:ca9e2125c5de 3:eea334d9988b
1 14:34:38.821 - INFO - UTILS - version=1.6.1
2 14:34:38.821 - INFO - UTILS - developer: Oliver Schwengers, github.com/oschwengers
3 14:34:38.821 - INFO - UTILS - command: /home/pierre/miniconda3/envs/__bakta@1.6.1/bin/bakta --threads 6 --db ./database_path --min-contig-length 1 --prefix TEST_1 --translation-table 11 --gram ? ../NC_002127.1.fna
4 14:34:38.821 - INFO - UTILS - local time: 2022-12-21 14:34:38
5 14:34:38.822 - INFO - UTILS - machine: type=x86_64, cores=8
6 14:34:38.822 - INFO - UTILS - system: type=Linux, release=5.15.0-56-generic
7 14:34:38.822 - INFO - UTILS - python: version=3.10.8, implementation=CPython
8 14:34:38.822 - INFO - CONFIG - threads=6
9 14:34:38.822 - INFO - CONFIG - verbose=False
10 14:34:38.822 - INFO - CONFIG - debug=False
11 14:34:38.822 - INFO - CONFIG - database: type=parameter, path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/database_path
12 14:34:38.823 - INFO - CONFIG - tmp-path=/tmp/tmpxm45i679
13 14:34:38.823 - INFO - CONFIG - genome-path=/home/pierre/tools-iuc/tools/bakta/test-data/NC_002127.1.fna
14 14:34:38.823 - INFO - CONFIG - min_contig_length=1
15 14:34:38.823 - INFO - CONFIG - prefix=TEST_1
16 14:34:38.823 - INFO - CONFIG - output-path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp
17 14:34:38.823 - INFO - CONFIG - genus=None
18 14:34:38.823 - INFO - CONFIG - species=None
19 14:34:38.823 - INFO - CONFIG - strain=None
20 14:34:38.823 - INFO - CONFIG - plasmid=None
21 14:34:38.823 - INFO - CONFIG - complete=False
22 14:34:38.823 - INFO - CONFIG - prodigal_tf=None
23 14:34:38.823 - INFO - CONFIG - translation_table=11
24 14:34:38.823 - INFO - CONFIG - gram=?
25 14:34:38.823 - INFO - CONFIG - compliant=False
26 14:34:38.823 - INFO - CONFIG - locus=None
27 14:34:38.823 - INFO - CONFIG - locus-tag=None
28 14:34:38.823 - INFO - CONFIG - keep_contig_headers=False
29 14:34:38.823 - INFO - CONFIG - replicon-table=None
30 14:34:38.823 - INFO - CONFIG - skip-tRNA=False
31 14:34:38.823 - INFO - CONFIG - skip-tmRNA=False
32 14:34:38.823 - INFO - CONFIG - skip-rRNA=False
33 14:34:38.823 - INFO - CONFIG - skip-ncRNA=False
34 14:34:38.823 - INFO - CONFIG - skip-ncRNA-region=False
35 14:34:38.823 - INFO - CONFIG - skip-CRISPR=False
36 14:34:38.823 - INFO - CONFIG - skip-CDS=False
37 14:34:38.823 - INFO - CONFIG - skip-pseudo=False
38 14:34:38.823 - INFO - CONFIG - skip-sORF=False
39 14:34:38.823 - INFO - CONFIG - skip-gap=False
40 14:34:38.823 - INFO - CONFIG - skip-ori=False
41 14:34:38.823 - INFO - CONFIG - skip-plot=False
42 14:34:38.823 - INFO - DB - detected: major=4, minor=0, date=2022-08-25
43 14:34:38.883 - INFO - UTILS - dependency: tool=tRNAscan-SE, version=v2.0.11
44 14:34:38.884 - INFO - UTILS - dependency: tool=aragorn, version=v1.2.41
45 14:34:38.887 - INFO - UTILS - dependency: tool=cmscan, version=v1.1.4
46 14:34:38.888 - INFO - UTILS - dependency: tool=pilercr, version=v1.6.0
47 14:34:38.889 - INFO - UTILS - dependency: tool=amrfinder, version=v3.11.2
48 14:34:38.914 - INFO - UTILS - dependency: tool=hmmsearch, version=v3.3.2
49 14:34:38.919 - INFO - UTILS - dependency: tool=diamond, version=v2.0.15
50 14:34:38.955 - INFO - UTILS - dependency: tool=blastn, version=v2.13.0
51 14:34:39.223 - INFO - UTILS - dependency: tool=circos, version=v1.6.1
52 14:34:39.227 - INFO - FASTA - imported: id=NC_002127.1, length=1330, description=Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence, genomic=True, dna=True
53 14:34:39.227 - INFO - MAIN - imported sequences=1
54 14:34:39.227 - INFO - UTILS - qc: revised sequence: id=contig_1, orig-id=NC_002127.1, type=plasmid, complete=True, topology=circular, name=unnamed1, description='[completeness=complete] [topology=circular] [gcode=11]', orig-description='Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence'
55 14:34:39.227 - INFO - FASTA - write genome sequences: path=/tmp/tmpxm45i679/contigs.fna, description=False, wrap=False
56 14:34:39.338 - INFO - T_RNA - predicted=0
57 14:34:39.340 - INFO - TM_RNA - predicted=0
58 14:34:39.346 - INFO - R_RNA - predicted=0
59 14:34:39.352 - INFO - NC_RNA - predicted=0
60 14:34:39.357 - INFO - NC_RNA_REGION - predicted=0
61 14:34:39.359 - INFO - CRISPR - predicted=0
62 14:34:39.359 - INFO - CDS - skip creation of prodigal training info object: meta=True, closed=False
63 14:34:39.379 - INFO - CDS - contig=contig_1, start=1, stop=141, strand=-, frame=2, truncated=3-prime, start-type=ATG, RBS-motif=AGGA/GGAG/GAGG
64 14:34:39.380 - INFO - CDS - contig=contig_1, start=413, stop=736, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG
65 14:34:39.380 - INFO - CDS - contig=contig_1, start=971, stop=1330, strand=-, frame=1, truncated=5-prime, start-type=Edge, RBS-motif=None
66 14:34:39.380 - INFO - CDS - edge CDS: contig=contig_1, start=971, stop=141, strand=-, frame=1, start-type=ATG, RBS-motif=AGGA/GGAG/GAGG, aa-hexdigest=1e7027cbe48346e06a83e802a9385584, aa=[MNKQQQTALN..SFALKKGIPI]
67 14:34:39.380 - INFO - CDS - contig=contig_1, start=413, stop=736, strand=+, nt=[ATGACAAAAC..GGCAGATTAG]
68 14:34:39.380 - INFO - CDS - contig=contig_1, start=971, stop=141, strand=-, nt=[ATGAACAAGC..TCCAATATAA]
69 14:34:39.384 - INFO - CDS - predicted=2
70 14:34:39.384 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/cds.spurious.faa
71 14:34:39.391 - INFO - ORF - discarded=0
72 14:34:39.392 - INFO - UPS - looked-up=0
73 14:34:39.392 - INFO - IPS - looked-up=0
74 14:34:39.392 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/cds.psc.faa
75 14:34:39.466 - INFO - PSC - found: PSC=0, PSCC=0
76 14:34:39.467 - INFO - PSC - looked-up=0
77 14:34:39.467 - INFO - PSCC - looked-up=0
78 14:34:39.467 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/cds.expert.faa
79 14:34:39.548 - INFO - EXPERT-AMRFINDER - found=0
80 14:34:39.624 - INFO - EXPERT_AA_SEQ - found=0
81 14:34:39.624 - INFO - ORF - write internal aa seqs: # seqs=1, path=/tmp/tmpxm45i679/cds.pseudo.candidates.faa
82 14:34:39.697 - INFO - CDS - found: pseudogene-candidates=0
83 14:34:39.698 - INFO - PSC - looked-up=0
84 14:34:39.698 - INFO - PSCC - looked-up=0
85 14:34:39.698 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/hypotheticals.faa
86 14:34:39.704 - INFO - CDS - predicted-pfams=0, CDS-w/-pfams=0
87 14:34:39.706 - INFO - S_ORF - predicted=22
88 14:34:39.706 - INFO - S_ORF - sORF filter: # valid=20, # discarded=2
89 14:34:39.706 - INFO - ORF - write internal aa seqs: # seqs=20, path=/tmp/tmpxm45i679/sorf.spurious.faa
90 14:34:39.712 - INFO - ORF - discarded=0
91 14:34:39.716 - INFO - UPS - looked-up=0
92 14:34:39.716 - INFO - IPS - looked-up=0
93 14:34:39.716 - INFO - ORF - write internal aa seqs: # seqs=20, path=/tmp/tmpxm45i679/sorf.faa
94 14:34:39.795 - INFO - S_ORF - found=0
95 14:34:39.796 - INFO - PSC - looked-up=0
96 14:34:39.833 - INFO - ORI - predicted=0
97 14:34:39.871 - INFO - ORI - predicted=0
98 14:34:39.872 - INFO - UTILS - generated sequence tag prefix: prefix=IHHALPPJCH, length=10, MD5=211A5993C1DD2EA7E96312462C14806B
99 14:34:39.872 - INFO - MAIN - selected features=2
100 14:34:39.872 - INFO - UTILS - generated sequence tag prefix: prefix=IHHALP, length=6, MD5=211A5993C1DD2EA7E96312462C14806B
101 14:34:39.872 - INFO - MAIN - locus tag prefix=IHHALP
102 14:34:39.872 - INFO - UTILS - genome-size=1330
103 14:34:39.872 - INFO - UTILS - GC=0.452
104 14:34:39.872 - INFO - UTILS - N=0.000
105 14:34:39.872 - INFO - UTILS - N50=1330
106 14:34:39.872 - INFO - UTILS - coding-ratio=0.620
107 14:34:39.872 - INFO - TSV - write tsv: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.tsv
108 14:34:39.872 - INFO - GFF - write GFF3: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.gff3
109 14:34:39.873 - INFO - INSDC - write GenBank: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.gbff
110 14:34:39.873 - INFO - INSDC - write EMBL: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.embl
111 14:34:39.874 - INFO - FASTA - write genome sequences: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.fna, description=True, wrap=True
112 14:34:39.874 - INFO - FASTA - write feature nucleotide sequences: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.ffn
113 14:34:39.874 - INFO - FASTA - write translated CDS/sORF: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.faa
114 14:34:39.874 - INFO - PLOT - split edge feature: contig=contig_1, start=971, stop=141, strand=-, edge=True
115 14:34:39.878 - INFO - PLOT - write circular genome plot: file-name=TEST_1, output-dir=/home/pierre/tools-iuc/tools/bakta/test-data/tmp
116 14:34:41.980 - INFO - TSV - write hypothetical tsv: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.hypotheticals.tsv
117 14:34:41.980 - INFO - FASTA - write translated CDS/sORF: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.hypotheticals.faa
118 14:34:41.981 - INFO - JSON - write JSON: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.json
119 14:34:41.982 - INFO - MAIN - removed tmp dir: /tmp/tmpxm45i679