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| There is a problem with all.joiner rules and the -database parameter. This is taken from an email from Ann in 2007:
| | This page is no longer maintained. |
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| Bob and I just ran into something sneaky with running joinerCheck or runJoiner.csh. There are some rules that can be tricky and we are not exactly sure why. What we do know is the kind of output you can be on the lookout for to know that you're dealing with a "tricky" rule. The output sort of makes it look like the rule has run (with no problems), but it really hasn't run at all.
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| Example of rules that aren't really running from joinerCheck:
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| [hgwdev:~/joiner> joinerCheck -keys -database=fr2 -identifier=blastHg18KGPep04Id all.joiner
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| Checking keys on database fr2
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| from runJoiner.csh:
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| [hgwdev:~/joiner> runJoiner.csh fr2 blastHg18KG
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| found identifiers:
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| blastHg18KGRef04Id
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| blastHg18KGPep04Id
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| Checking keys on database fr2
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| Checking keys on database fr2
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| If the rule had really run there would be some output saying something like X hits out of Y ok.
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| The way to force these rules to run is to leave off the "database" parameter (you can only do this when using the joinerCheck (runJoiner.csh can't handle that)). This will run the rule for all databases that are listed -- just pick yours out of the output.
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| [hgwdev:~/joiner> joinerCheck -keys -identifier=blastHg18KGPep04Id all.joiner Checking keys on database (null)
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| anoCar1.blastHg18KG.qName - hits 45332 of 45332 ok
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| equCab1.blastHg18KG.qName - hits 61628 of 61628 ok
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| ornAna1.blastHg18KG.qName - hits 35761 of 35761 ok
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| oryLat1.blastHg18KG.qName - hits 38111 of 38111 ok
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| bosTau2.blastHg18KG.qName - hits 56832 of 56832 ok
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| strPur1.blastHg18KG.qName - hits 30907 of 30907 ok
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| mm8.blastHg18KG.qName - hits 70754 of 70754 ok
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| fr2.blastHg18KG.qName - hits 40510 of 40510 ok
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| dm2.blastHg18KG.qName - hits 22239 of 22239 ok
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| felCat3.blastHg18KG.qName - hits 37715 of 37715 ok
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| canFam2.blastHg18KG.qName - hits 62741 of 62741 ok
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| danRer4.blastHg18KG.qName - hits 44692 of 44692 ok
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| xenTro2.blastHg18KG.qName - hits 40291 of 40291 ok
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| galGal3.blastHg18KG.qName - hits 35851 of 35851 ok
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| monDom4.blastHg18KG.qName - hits 63264 of 63264 ok
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| hg18.blastKGRef04.acc - hits 36727 of 36727 ok
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| hg18.knownGene.name - hits 0 of 56722
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| Error: 56722 of 56722 elements of hg18.knownGene.name are not in key blastKGPep04.name line 1995 of all.joiner
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| Example miss: UC001AAA.1
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| [[Category:Browser QA tracks]]
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