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| | ==Files Asked for in the Gene Database Testing Report== | | ==Files Asked for in the Gene Database Testing Report== |
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| − | For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[]] | + | For convenience, all of the files explicitly asked for in the sections below were compressed together in this file: [[File:Testingreport cw20151210.zip]] |
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| | ==Pre-requisites== | | ==Pre-requisites== |
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| | Postgres Database name: bpertussis_cw20151210_gmb3build5 | | Postgres Database name: bpertussis_cw20151210_gmb3build5 |
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| − | UniProt XML filename: [[]] | + | UniProt XML filename: [[File:Uniprot-proteome-UP000002676 cw20151210.zip]] |
| | * UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_12 | | * UniProt XML version (The version information was found at [http://uniprot.org/news the UniProt News Page]): 2015_12 |
| | * UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)] | | * UniProt XML download link: [http://www.uniprot.org/proteomes/UP000002676 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)] |
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| | ** Note: The import time was similar to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151203.gdb (2.59 minute). No interruptions occurred during this process. | | ** Note: The import time was similar to that when creating the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151203.gdb (2.59 minute). No interruptions occurred during this process. |
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| − | GO OBO-XML filename: [[]] | + | GO OBO-XML filename: [[File:Go daily-termdb cw20151210.zip]] |
| | * GO OBO-XML version (The version information was found in the file properties): Last Modified- December 10, 2015 (TIME?) | | * GO OBO-XML version (The version information was found in the file properties): Last Modified- December 10, 2015 (TIME?) |
| | * GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page] | | * GO OBO-XML download link: [http://geneontology.org/page/download-ontology#Legacy_Downloads Gene Ontology legacy download page] |
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| | ** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151203.gdb (7.08 minutes and 4.42 minutes respectively). No interruptions occurred during these processes. | | ** Note: The import and processing times were similar to those for the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151203.gdb (7.08 minutes and 4.42 minutes respectively). No interruptions occurred during these processes. |
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| − | GOA filename: [[]] | + | GOA filename: [[File:145.B pertussis ATCC BAA-589 cw20151210.zip]] |
| | * GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 08-Dec-2015 02:45 | | * GOA version (found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): Last Modified- 08-Dec-2015 02:45 |
| | * GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I] | | * GOA download link: [http://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/145.B_pertussis_ATCC_BAA-589.goa for ''Bordetella pertussis'' strain Tohama I] |
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| | ** Note: The import time was very similar to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151203.gdb (0.04 minutes). No interruptions occurred during this process. | | ** Note: The import time was very similar to that of the previous "Bordetella pertussis" gene database: bpertussis-std_cw20151203.gdb (0.04 minutes). No interruptions occurred during this process. |
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| − | Name of .gdb file: [[]] | + | Name of .gdb file: [[File:Bpertussis-std cw20151210.zip]] |
| | * Time taken to export: | | * Time taken to export: |
| | ** Start time: 1:19 AM | | ** Start time: 1:19 AM |
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| | ===TallyEngine=== | | ===TallyEngine=== |
| | * I ran the TallyEngine in GenMAPP Builder and specified the following files: | | * I ran the TallyEngine in GenMAPP Builder and specified the following files: |
Exception encountered, of type "Error"
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Backtrace:
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(82): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}