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view test-data/test_1/logfile_test1.log @ 1:eccc7495c3d9 draft

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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 69aab27f0210af0f0986d63575f9bfdb3f9d1f6a
author iuc
date Fri, 14 Oct 2022 11:54:49 +0000
parents 2b6e795b22a9
children
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Found: rep2_2_repR(pEF1)_DQ198088
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
Found: rep11a_1_repA(pB82)_AB178871
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
Found: rep14a_2_ORF1(pKQ10)_EFU01917
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
{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',
                                                 '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,
                                                                                                                                                                                                                                        'accession': 'AB178871',
                                                                                                                                                                                                                                        'contig_name': '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',
                                                                                                                                                                                                                                        'coverage': 100.0,
                                                                                                                                                                                                                                        'hit_id': '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',
                                                                                                                                                                                                                                        'identity': 99.89,
                                                                                                                                                                                                                                        'note': 'repA(pB82)',
                                                                                                                                                                                                                                        'plasmid': 'rep11a',
                                                                                                                                                                                                                                        'position_in_ref': '1..945',
                                                                                                                                                                                                                                        'positions_in_contig': '308..1252',
                                                                                                                                                                                                                                        'template_length': 945}},
                                                 '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,
                                                                                                                                                                                                                                                'accession': 'EFU01917',
                                                                                                                                                                                                                                                'contig_name': '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',
                                                                                                                                                                                                                                                'coverage': 100.0,
                                                                                                                                                                                                                                                'hit_id': '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',
                                                                                                                                                                                                                                                'identity': 99.5,
                                                                                                                                                                                                                                                'note': 'ORF1(pKQ10)',
                                                                                                                                                                                                                                                'plasmid': 'rep14a',
                                                                                                                                                                                                                                                'position_in_ref': '1..402',
                                                                                                                                                                                                                                                'positions_in_contig': '1703..2104',
                                                                                                                                                                                                                                                'template_length': 402}}}},
                   'run_info': {'date': '09.09.2022', 'time': '08:52:55'},
                   'user_input': {'file_format': 'fasta',
                                  'filename(s)': ['/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat'],
                                  'method': 'blast'}}}