Mercurial > repos > iuc > integron_finder

annotate test-data/test1_integron_log @ 3:bfd290fe1588 draft default tip

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