2:ps1010rel4_chr1 1 1889 1 W ps1010rel4_chr1 1 1889 + WARNING: object name (column 1) is the same as component_id (column 6) 3:ps1010rel4_chr100000 1 433 1 W ps1010rel4_chr100000 1 433 + WARNING: object name (column 1) is the same as component_id (column 6) 4:ps1010rel4_chr100002 1 138 1 W ps1010rel4_chr100002 1 138 + WARNING: object name (column 1) is the same as component_id (column 6) 5:ps1010rel4_chr100003 1 146 1 W ps1010rel4_chr100003 1 146 + WARNING: object name (column 1) is the same as component_id (column 6) 6:ps1010rel4_chr100004 1 248 1 W ps1010rel4_chr100004 1 248 + WARNING: object name (column 1) is the same as component_id (column 6) 7:ps1010rel4_chr100014 1 158 1 W ps1010rel4_chr100014 1 158 + WARNING: object name (column 1) is the same as component_id (column 6) 9:ps1010rel4_chr100016 319 364 2 N 46 fragment yes NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty 23:LACBIscaffold_1 1104 3435 2 U 2332 fragment yes WARNING: gap length (column 6) is not 100 for a gap of unknown size (an INSDC standard) 25:LACBIscaffold_1 4637 5256 4 N 620 contig no ERROR: in "Scaffold from component" file, invalid scaffold-breaking gap 24:LACBIscaffold_1 3436 4636 3 W LACBIscaffold_1_Cont2 1 1201 + 26:LACBIscaffold_1 5257 6500 5 W LACBIscaffold_1_Cont2 1202 2445 + WARNING: duplicate component with non-draft type; preceding span: 1..1201 at line 24 WARNING: same component_id found on different scaffolds (a scaffold-breaking gap in between) WARNING: in unplaced singleton scaffold, component is not used in full 28:LACBIscaffold_2 1 1103 1 W LACBIscaffold_2_Cont1 1 1103 - WARNING: in unplaced singleton scaffold, component orientation is not "+" 30:LACBIscaffold_3 1 1103 1 W LACBIscaffold_3_Cont1 1 1103 - WARNING: in unplaced singleton scaffold, component orientation is not "+" 1 error, 12 warnings, 1 note. Count Code Description 1 e20 in "Scaffold from component" file, invalid scaffold-breaking gap 1 w37 duplicate component with non-draft type 6 w47 object name (column 1) is the same as component_id (column 6) 1 w48 gap length (column 6) is not 100 for a gap of unknown size (an INSDC standard) 1 w49 same component_id found on different scaffolds 1 w50 in unplaced singleton scaffold, component is not used in full 2 w51 in unplaced singleton scaffold, component orientation is not "+" 1 w58 assuming AGP version X Objects : 13 - with single component: 9 Scaffolds : 14 - with single component: 10 Components : 20 (W) orientation + : 18 orientation - : 2 orientation ? (formerly 0) : 0 orientation na : 0 Gaps : 7 (N:6, U:1) - do not break scaffold: 6 fragment, linkage yes: 6 - break it, linkage no : 1 contig : 1 Object names : 13 ps1010rel4_chr[1..100022]: 9 LACBIscaffold_[1..3] : 3 scaffold_0 : 1 Component names : 19 ----------------- Nucleotide accessions: 1 AAGU02000001.1 : 1 ----------------- OTHER identifiers : 18 ps1010rel4_chr[100016..100022]_[1..4]: 8 (local or misspelled) ps1010rel4_chr[1..100014] : 6 (local or misspelled) LACBIscaffold_[1..3]_Cont[1,2] : 4 (local or misspelled) Use -g or "-show all" to print lines with suspicious accessions. 6 names are used both as object and as component_id: ps1010rel4_chr1, ps1010rel4_chr100000, ps1010rel4_chr100002, ... #Comment line count : 3 End of line #comments : 1