Tables created in the target database: Typical row count Created by 1 cgapAlias 153984 src/hg/hgCGAP/cgapAlias.sql 2 cgapBiocDesc 3730 src/hg/hgCGAP/cgapBiocDesc.sql 3 cgapBiocPathway 3730 src/hg/hgCGAP/cgapBiocPathway.sql 4 dupSpMrna 5993 src/hg/lib/dupSpMrna.sql 5 keggMapDesc 119 src/hg/protein/keggMapDesc.sql 6 keggPathway 4661 src/hg/protein/keggPathway.sql 7 kgAlias 101162 src/hg/lib/kgAlias.sql 8 kgProtAlias 41061 src/hg/lib/kgProtAlias.sql 9 kgXref 41061 src/hg/lib/kgXref.sql 10 knownGene 42260 src/hg/lib/knownGene.sql; 11 knownGeneLink 481 src/hg/lib/knownGeneLink.sql; 12 knownGeneMrna 41061 src/hg/lib/knownGeneMrna.sql 13 knownGenePep 41061 src/hg/lib/knownGenePep.sql 14 mrnaRefseq 231441 src/hg/protein/KGprocess.sh 15 spMrna 46559 src/hg/lib/spMrna.sql Tables created in the target database: Typical row count Populated by 1 cgapAlias 153984 hgCGAP 2 cgapBiocDesc 3730 hgCGAP 3 cgapBiocPathway 3730 hgCGAP 4 dupSpMrna 5993 spm7 result duplicate.tab 5 keggMapDesc 119 hgKegg result keggMapDesc.tab 6 keggPathway 4661 hgKegg result keggPathway.tab 7 kgAlias 101162 kgAliasM, kgAliasP, kgAliasRefseq, kgAliasKgXref 8 kgProtAlias 41061 kgProtAlias result kgProtAlias.tab 9 kgXref 41061 kgXref result kgXref.tab 10 knownGene 42260 spm7 result knownGene.tab + dnaGene dnaGene.tab 11 knownGeneLink 481 dnaGene result dnaLink.tab 12 knownGeneMrna 41061 rmKGPepMran result knownGeneMrna.tab 13 knownGenePep 41061 rmKGPepMrna result knownGenePep.tab 14 mrnaRefseq 231441 hgMrnaRefseq result mrnaRefseq.tab 15 spMrna 46559 kgResultBestMrna result best.lis =========================================================================== And in the Temp database: Created by 1 geneName 20880 src/hg/protein/Temp.sql 2 history 1 hgKgMrna 3 keggList 3978 src/hg/protein/Temp.sql 4 knownGene 0 src/hg/protein/Temp.sql 5 knownGene0 48040 src/hg/protein/Temp.sql 6 locus2Acc0 291320 src/hg/protein/Temp.sql 7 locus2Ref0 121896 src/hg/protein/Temp.sql 8 mrnaGene 70656 src/hg/protein/Temp.sql 9 pepSequence 0 src/hg/protein/Temp.sql 10 productName 43258 src/hg/protein/Temp.sql 11 refGene 70656 src/hg/protein/Temp.sql 12 refLink 138782 src/hg/protein/Temp.sql 13 refMrna 138782 src/hg/protein/Temp.sql 14 refPep 69337 src/hg/protein/Temp.sql 15 spMrna 69541 src/hg/protein/Temp.sql And in the Temp database: Populated by 1 geneName 20880 hgKgMrna 2 history 1 hgKgMrna 3 keggList 3978 getKeggList.pl result keggList.tab 4 knownGene 0 NOT LOADED 5 knownGene0 48040 spm6 result knownGene0.tab 6 locus2Acc0 291320 ftp.ncbi.nih.gov/refseq/LocusLink/loc2acc 7 locus2Ref0 121896 ftp.ncbi.nih.gov/refseq/LocusLink/loc2ref 8 mrnaGene 70656 a copy of refGene ? 9 pepSequence 0 NOT LOADED 10 productName 43258 hgKgMrna 11 refGene 70656 hgKgMrna 12 refLink 138782 hgKgMrna 13 refMrna 138782 hgKgMrna (knownGeneMrna?) 14 refPep 69337 hgKgMrna (knownGenePep?) 15 spMrna 69541 spm3 result proteinMrna.tab ======================================================================= Puzzles to be resolved: Why do I find geneName,refGene,refLink tables in current assemblies that have had the knownGenes process run on them ? I can not find anything in the build that would make them in that database. Why is kgXref working differently today than it did when Mm4 KG was built ? Today it can not find the geneSymbol and is instead putting the kgID in the geneSymbol column. This causes kgAliasM to find nothing. I can not reproduce the behavior that worked in the Mm4 KG build. ======================================================================= Databases in use: 1. knownGenes construction DB: kgDB 2. Temp construction DB: kgDBTemp 3. Target organism DB: hg16 4. swissProt DB: sp040115 5. proteins DB: proteins040115 Construction sequence produces the following files and tables: 1. mrna.fa via program gbGetSeqs from genbank updates 2. mrna.ra via program gbGetSeqs from genbank updates 3. all_mrna.psl via a 'select * from all_mrna' from target organism DB 4. mrna.lis via a grep of mrna.fa 5. loc2ref FTP from NCBI 6. loc2acc FTP from NCBI 7. mim2loc FTP from NCBI 8. Temp DB created, load loc2acc and loc2ref into Temp 9. mrnaRefseq created by reading from the loc2ref and loc2acc entries loaded into knownGenes construction DB 10. mrnaPep.fa created via kgGetPep reading mrna.lis and extracting from proteins and swissProt DBs 11. tight_mrna.psl created via pslReps reading all_mrna.psl 12. tables productName, geneName, refLink, refPep, refGene and refMrna created in Temp DB via hgKgMrna reading mrna.fa, mrna.ra, tight_mrna.psl, loc2ref, mrnaPep.fa and mim2loc 13. mrnaGene table created in Temp DB by loading refGene.tab from the hgKgMrna process (== a duplicate of refGene table ?)