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comparison test-data/test2_integron_log @ 0:1ae00120dd24 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
author iuc
date Thu, 22 Sep 2022 13:51:14 +0000
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-1:000000000000 0:1ae00120dd24
1
2 **************************************************************************
3 ___ _ _____ _ _
4 |_ _|_ __ | |_ ___ __ _ _ __ ___ _ __ | ___(_)_ __ __| | ___ _ __
5 | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \ | |_ | | '_ \ / _` |/ _ \ '__|
6 | || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
7 |___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
8 |___/
9
10 **************************************************************************
11
12 integron_finder version 2.0.2
13 Using:
14 - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
15 - numpy 1.19.4
16 - pandas 1.1.5
17 - matplolib 3.3.3
18 - biopython 1.78
19
20 - Prodigal V2.6.3: February, 2016
21 - INFERNAL 1.1.4 (Dec 2020)
22 - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
23
24 Authors:
25 - Jean Cury, Bertrand Neron, Eduardo Rocha,
26
27 Citation:
28
29 Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
30 IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
31 Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
32
33 If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
34
35 Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
36 PMID: 29112715
37
38
39 =======================
40
41 integron_finder is free software: you can redistribute it and/or modify
42 it under the terms of the GNU General Public License as published by
43 the Free Software Foundation, either version 3 of the License, or
44 (at your option) any later version.
45
46 integron_finder is distributed in the hope that it will be useful,
47 but WITHOUT ANY WARRANTY; without even the implied warranty of
48 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
49 GNU General Public License for more details.
50
51 You should have received a copy of the GNU General Public License
52 along with this program (COPYING file).
53 If not, see <http://www.gnu.org/licenses/>.
54
55 =======================
56
57 command used: integron_finder /tmp/tmpz_euzvww/files/e/9/9/dataset_e996a731-6537-452b-87d7-09654e6d628a.dat --cpu 1 --keep-tmp --local-max -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
58
59 =======================
60
61 
62 INFO : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
63
64 INFO : Starting Default search ... :
65 INFO : Default search done... :
66 INFO : In replicon ACBA.007.P01_13, there are:
67 INFO : - 1 complete integron(s) found with a total 3 attC site(s)
68 INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
69 INFO : - 0 In0 element(s) found with a total of 0 attC site
70 INFO : Starting search with local_max...:
71 INFO : Search with local_max done... :
72 INFO : In replicon ACBA.007.P01_13, there are:
73 INFO : - 1 complete integron(s) found with a total 4 attC site(s)
74 INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
75 INFO : - 0 In0 element(s) found with a total of 0 attC site
76 INFO : Adding proteins ... :
77 INFO : Writing out results for replicon ACBA.007.P01_13
78 INFO : Merging integrons results.
79