Mercurial > repos > thanhlv > integron_finder
comparison test-data/test1_integron_log @ 0:3a24265075bd draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/blob/master/tools/integron_finder commit 6b06711cfba45855d5a992ed1c73c472eaef644f
| author | thanhlv |
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| date | Mon, 13 Feb 2023 13:53:43 +0000 |
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| -1:000000000000 | 0:3a24265075bd |
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| 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/1/d/e/dataset_1dee618f-a951-40e4-8697-ae8f535f1e8b.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 | |
| 58 | |
| 59 ======================= | |
| 60 | |
| 61 [0m | |
| 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 : Adding proteins ... : | |
| 71 INFO : Writing out results for replicon ACBA.007.P01_13 | |
| 72 INFO : Merging integrons results. | |
| 73 |