;;; --- PGDB Incremental Update --- ;;; --- Parse Results for Brachypodium distachyon --- ;;; ;;; This report summarizes the findings of the PathoLogic parser for ;;; the annotation files for all updated genetic elements. Through ;;; inspection of this report, the user can tell whether features of major ;;; importance were not recognized, possibly due to syntax errors or other ;;; problems in the updated annotation files. If you want to change ;;; annotation file(s) to improve their parsability, update the files ;; then re-run the Update. ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_1.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_1.pf gene-IDs : 7732 gene-name : 7732 gene-startbase : 7732 gene-endbase : 7732 gene-product-type : 7732 gene-Proteins : 7732 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 7732 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 2456 genes with 1 EC number : 1739 genes with >1 EC numbers : 428 total GO terms linked to reactions : 2022 genes with 1 GO term linked to reactions : 1227 genes with >1 GO terms linked to reactions : 464 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_2.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_2.pf gene-IDs : 5990 gene-name : 5990 gene-startbase : 5990 gene-endbase : 5990 gene-product-type : 5990 gene-Proteins : 5990 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 5990 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 1974 genes with 1 EC number : 1354 genes with >1 EC numbers : 366 total GO terms linked to reactions : 1542 genes with 1 GO term linked to reactions : 948 genes with >1 GO terms linked to reactions : 347 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_3.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_3.pf gene-IDs : 5884 gene-name : 5884 gene-startbase : 5884 gene-endbase : 5884 gene-product-type : 5884 gene-Proteins : 5884 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 5884 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 1891 genes with 1 EC number : 1341 genes with >1 EC numbers : 333 total GO terms linked to reactions : 1406 genes with 1 GO term linked to reactions : 867 genes with >1 GO terms linked to reactions : 327 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_4.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_4.pf gene-IDs : 4368 gene-name : 4368 gene-startbase : 4368 gene-endbase : 4368 gene-product-type : 4368 gene-Proteins : 4368 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 4368 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 1298 genes with 1 EC number : 918 genes with >1 EC numbers : 227 total GO terms linked to reactions : 1127 genes with 1 GO term linked to reactions : 663 genes with >1 GO terms linked to reactions : 267 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_5.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\chr_5.pf gene-IDs : 2549 gene-name : 2549 gene-startbase : 2549 gene-endbase : 2549 gene-product-type : 2549 gene-Proteins : 2549 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 2549 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 871 genes with 1 EC number : 583 genes with >1 EC numbers : 165 total GO terms linked to reactions : 673 genes with 1 GO term linked to reactions : 409 genes with >1 GO terms linked to reactions : 158 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\plastid-1.gb ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\plastid-1.gb gene-IDs : 118 gene-name : 118 gene-startbase : 126 gene-endbase : 126 gene-product-type : 126 gene-Proteins : 80 gene-tRNAs : 38 gene-rRNAs : 8 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 126 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_7.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_7.pf gene-IDs : 4 gene-name : 4 gene-startbase : 4 gene-endbase : 4 gene-product-type : 4 gene-Proteins : 4 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 4 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_9.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_9.pf gene-IDs : 6 gene-name : 6 gene-startbase : 6 gene-endbase : 6 gene-product-type : 6 gene-Proteins : 6 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 6 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_12.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_12.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_14.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_14.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_15.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_15.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_16.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_16.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_18.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_18.pf gene-IDs : 2 gene-name : 2 gene-startbase : 2 gene-endbase : 2 gene-product-type : 2 gene-Proteins : 2 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 2 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_19.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_19.pf gene-IDs : 2 gene-name : 2 gene-startbase : 2 gene-endbase : 2 gene-product-type : 2 gene-Proteins : 2 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 2 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_23.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_23.pf gene-IDs : 3 gene-name : 3 gene-startbase : 3 gene-endbase : 3 gene-product-type : 3 gene-Proteins : 3 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 3 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_26.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_26.pf gene-IDs : 3 gene-name : 3 gene-startbase : 3 gene-endbase : 3 gene-product-type : 3 gene-Proteins : 3 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 3 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_27.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_27.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_38.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_38.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_40.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_40.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_68.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_68.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_98.pf ;;; ;;; The annotation file used by the parser is: ;;; C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\input\scaffold_98.pf gene-IDs : 1 gene-name : 1 gene-startbase : 1 gene-endbase : 1 gene-product-type : 1 gene-Proteins : 1 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 0 genes with 1 EC number : 0 genes with >1 EC numbers : 0 total GO terms linked to reactions : 0 genes with 1 GO term linked to reactions : 0 genes with >1 GO terms linked to reactions : 0 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0