Mercurial > repos > iuc > plasmidfinder

comparison test-data/test_1/logfile_test1.log @ 0:2b6e795b22a9 draft

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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
author iuc
date Mon, 19 Sep 2022 08:47:42 +0000
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-1:000000000000 0:2b6e795b22a9
1 Found: rep2_2_repR(pEF1)_DQ198088
2 Saving: contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228
3 Found: rep11a_1_repA(pB82)_AB178871
4 Saving: contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
5 Found: rep14a_2_ORF1(pKQ10)_EFU01917
6 Saving: contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
7 {'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',
8 'Rep3': {'contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180': {'HSP_length': 945,
9 'accession': 'AB178871',
10 'contig_name': 'contig00003 '
11 'len=3227 '
12 'cov=2.2 '
13 'corr=0 '
14 'origname=NODE_3_length_3227_cov_2.232903_pilon '
15 'sw=shovill-spades/1.1.0 '
16 'date=20220302',
17 'coverage': 100.0,
18 'hit_id': 'contig00003 '
19 'len=3227 '
20 'cov=2.2 '
21 'corr=0 '
22 'origname=NODE_3_length_3227_cov_2.232903_pilon '
23 'sw=shovill-spades/1.1.0 '
24 'date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180',
25 'identity': 99.89,
26 'note': 'repA(pB82)',
27 'plasmid': 'rep11a',
28 'position_in_ref': '1..945',
29 'positions_in_contig': '308..1252',
30 'template_length': 945}},
31 'Rep_trans': {'contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488': {'HSP_length': 402,
32 'accession': 'EFU01917',
33 'contig_name': 'contig00008 '
34 'len=2292 '
35 'cov=2.6 '
36 'corr=0 '
37 'origname=NODE_11_length_2292_cov_2.631409_pilon '
38 'sw=shovill-spades/1.1.0 '
39 'date=20220302',
40 'coverage': 100.0,
41 'hit_id': 'contig00008 '
42 'len=2292 '
43 'cov=2.6 '
44 'corr=0 '
45 'origname=NODE_11_length_2292_cov_2.631409_pilon '
46 'sw=shovill-spades/1.1.0 '
47 'date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488',
48 'identity': 99.5,
49 'note': 'ORF1(pKQ10)',
50 'plasmid': 'rep14a',
51 'position_in_ref': '1..402',
52 'positions_in_contig': '1703..2104',
53 'template_length': 402}}}},
54 'run_info': {'date': '09.09.2022', 'time': '08:52:55'},
55 'user_input': {'file_format': 'fasta',
56 'filename(s)': ['/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat'],
57 'method': 'blast'}}}