Mercurial > repos > iuc > integron_finder

annotate test-data/test2_integron_log @ 3:bfd290fe1588 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder commit cbb56e087d23446b8159622e2e4b7a709c8529ad
author iuc
date Fri, 14 Jun 2024 21:19:29 +0000
parents 1ae00120dd24
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1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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2 **************************************************************************
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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3 ___ _ _____ _ _
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4 |_ _|_ __ | |_ ___ __ _ _ __ ___ _ __ | ___(_)_ __ __| | ___ _ __
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5 | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \ | |_ | | '_ \ / _` |/ _ \ '__|
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6 | || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
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7 |___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
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8 |___/
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10 **************************************************************************
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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12 integron_finder version 2.0.2
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13 Using:
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14 - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
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15 - numpy 1.19.4
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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16 - pandas 1.1.5
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17 - matplolib 3.3.3
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18 - biopython 1.78
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20 - Prodigal V2.6.3: February, 2016
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21 - INFERNAL 1.1.4 (Dec 2020)
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22 - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
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24 Authors:
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25 - Jean Cury, Bertrand Neron, Eduardo Rocha,
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27 Citation:
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29 Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
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30 IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
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31 Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
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33 If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
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35 Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
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36 PMID: 29112715
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39 =======================
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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41 integron_finder is free software: you can redistribute it and/or modify
1ae00120dd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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42 it under the terms of the GNU General Public License as published by
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43 the Free Software Foundation, either version 3 of the License, or
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44 (at your option) any later version.
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46 integron_finder is distributed in the hope that it will be useful,
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47 but WITHOUT ANY WARRANTY; without even the implied warranty of
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48 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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49 GNU General Public License for more details.
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51 You should have received a copy of the GNU General Public License
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52 along with this program (COPYING file).
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53 If not, see <http://www.gnu.org/licenses/>.
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55 =======================
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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
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59 =======================
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61 
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62 INFO : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
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64 INFO : Starting Default search ... :
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65 INFO : Default search done... :
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66 INFO : In replicon ACBA.007.P01_13, there are:
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67 INFO : - 1 complete integron(s) found with a total 3 attC site(s)
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68 INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
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69 INFO : - 0 In0 element(s) found with a total of 0 attC site
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70 INFO : Starting search with local_max...:
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71 INFO : Search with local_max done... :
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72 INFO : In replicon ACBA.007.P01_13, there are:
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73 INFO : - 1 complete integron(s) found with a total 4 attC site(s)
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74 INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
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75 INFO : - 0 In0 element(s) found with a total of 0 attC site
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76 INFO : Adding proteins ... :
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77 INFO : Writing out results for replicon ACBA.007.P01_13
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78 INFO : Merging integrons results.
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79