=====Checking all inverse links==== [Checking inverses under class CCO] [Checking inverses under class Evidence] [Checking inverses under class People] [Checking inverses under class Proteins] [Checking inverses under class Reactions] [Checking inverses under class All-Genes] [Checking inverses under class Transcription-Units] [Checking inverses under class Compounds] [Checking inverses under class Enzymatic-Reactions] [Checking inverses under class Regulation] ===== Checking and removing any values from PATHWAY-LINKS that point to nonexistent frames ==== Removing link from pwy DAPLYSINESYN-PWY to nonexistent pwys (PEPTIDOGLYCANSYN-PWY) Removing link from pwy PWY-5188 to nonexistent pwys (P381-PWY) ===== Checking modified protein links to eliminate nonexistent frames ==== ===== Cross-referencing compounds and reactions ==== ==== Calculating sub and super pathways ==== ===== Finding missing sub pathway links ==== ==== Checking for missing sub pathway links ==== Warning:PWY-4001 is completely contained within ASPASN-PWY but is not listed in the SUB-PATHWAYS slot Warning:ASPARTATESYN-PWY is completely contained within ASPARAGINE-BIOSYNTHESIS but is not listed in the SUB-PATHWAYS slot Warning:ASPARTATESYN-PWY is completely contained within GLUTDEG-PWY but is not listed in the SUB-PATHWAYS slot Warning:HOMOCYSDEGR-PWY is completely contained within PWY-801 but is not listed in the SUB-PATHWAYS slot Warning:PWY1F-467 is completely contained within PWY-1121 but is not listed in the SUB-PATHWAYS slot Warning:PANTO-PWY is completely contained within PWY-4221 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5123 is completely contained within POLYISOPRENSYN-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-5122 is completely contained within PWY-5123 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5123 is completely contained within PWY-5121 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5120 is completely contained within PWY-5121 but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within 1CMET2-PWY but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within PWY-2201 but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within PWY-3841 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5034 is completely contained within PWY-5047 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-662 is completely contained within P1-PWY but is not listed in the SUB-PATHWAYS slot Warning:ARGDEG-III-PWY is completely contained within POLYAMINSYN3-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY0-823 is completely contained within POLYAMSYN-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-1141 is completely contained within CAROTENOID-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-4001 is completely contained within ASPARAGINE-DEG1-PWY but is not listed in the SUB-PATHWAYS slot Warning:GLUTDEG-PWY is completely contained within GLUTAMINEFUM-PWY but is not listed in the SUB-PATHWAYS slot Warning:GLUTSYN-PWY is completely contained within GLUTAMINEFUM-PWY but is not listed in the SUB-PATHWAYS slot Warning:GLUGLNSYN-PWY is completely contained within PWY-3282 but is not listed in the SUB-PATHWAYS slot Warning:PWY-4341 is completely contained within PWY-3282 but is not listed in the SUB-PATHWAYS slot Warning:GLNSYN-PWY is completely contained within PWY-3282 but is not listed in the SUB-PATHWAYS slot Warning:GLNSYN-PWY is completely contained within PWY-381 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5340 is completely contained within SO4ASSIM-PWY but is not listed in the SUB-PATHWAYS slot Warning:P21-PWY is completely contained within NONOXIPENT-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-1881 is completely contained within ANARESPDON-PWY but is not listed in the SUB-PATHWAYS slot ==Done checking all the links== ==== Checking pathways for duplicate reactions in REACTION-LIST slot ==== == Done checking pathways for duplicate reactions == ==== Verifying replicon components and positions ==== == Done verifying replicon components == ===== Validating Gene Ontology (GO) Terms ===== == Done validating GO terms == ===== Changing compound name strings to frame IDs in a variety of slots ===== [Checking class Enzymatic-Reactions] [Checking class Reactions] == Done changing compound name strings to compound frame IDs == ===== Checking pathway predecessors/reactions/subs ==== Removing nonexistent pwy from super-pathway: GLYCOLYSIS-E-D Adjusting predecessor list of super-pathway GLYCOLYSIS-E-D Removing nonexistent pwy from super-pathway: GLUCONSUPER-PWY ===== Removing newlines from names ==== ===== Clearing computed slot values ==== == Done running all the Misc automatic checks == ===== Classifying modified proteins as such ==== ===== Updating molecular weights of polypeptides from amino acid sequences ==== Updated 0 protein molecular weights from sequence == Done with protein updates == ===== Checking compound structures for redundancy ===== Checking Compound structures for redundant bonds == Done checking compound structure redundancies == ====Recomputing statistics for database sorghumcyc==== Recomputed statistics are as follows: (PSEUDOGENE-NUMBER 0 ENZYMATIC-REACTION-NUMBER 1846 CITATION-COUNT 167 GENOME-LENGTH 700981858 MAPPED-GENE-NUMBER 36338 UN-MAPPED-GENE-NUMBER 0 PROTEIN-GENE-NUMBER 36338 RNA-GENE-NUMBER 0 ORF-GENE-NUMBER 0 REACTION-NUMBER 1876 NO-EC-REACTION-NUMBER 494 ORGANISM-REACTION-NUMBER 1876 TRANSPORT-REACTION-NUMBER 8 POLYPEPTIDE-NUMBER 36351 COMPLEX-NUMBER 2 ENZYME-NUMBER 10636 TRANSPORTER-NUMBER 258 CPD-NUMBER 1414 TOTAL-GENE-NUMBER 36338 OPERON-NUMBER 0 TRNA-NUMBER 0 LAST-TIME-STAMP 28-Jul-2009 01:11:25) == Done recomputing statistics for database sorghumcyc == The report from this consistency checker run can be found at /usr/local/pathway-tools/ptools-local/pgdbs/user/sorghumcyc/1.0/reports/consistency-checker-report-2009-07-28_01-10-45.txt