===== Reading Scaffold from component AGP ===== ./test/scaffold_from_contig_WGS.agp:9:EG1_scaffold2 40449 40548 2 N 100 fragment yes NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty No errors, no warnings, 1 note. Count Code Description 1 w58 assuming AGP version X Objects : 23 - with single component: 13 Scaffolds : 23 - with single component: 13 Components : 95 (W) orientation + : 81 orientation - : 14 orientation ? (formerly 0) : 0 orientation na : 0 Gaps : 72 (N) - do not break scaffold: 72 fragment, linkage yes: 72 (20 or 27.8% of N gaps have length=100) - break it, linkage no : 0 Most frequent N gap_length (27.8% or 20 lines): 100 Object names : 23 EG1_scaffold[1..23]: 23 Component names : 95 AADB[02037551..02037645].1: 95 #Comment line count : 6 ===== Reading Chromosome from scaffold AGP ===== ./test/chr_from_scaffold_WGS.agp:10:chrY 3044 53043 2 N 50000 contig no NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty No errors, no warnings, 1 note. Count Code Description 1 w58 assuming AGP version X Objects : 1 - with single component: 0 Scaffolds : 23 - with single component: 23 Components : 23 (W) orientation + : 20 orientation - : 0 orientation ? (formerly 0) : 3 orientation na : 0 Gaps : 22 (N) - do not break scaffold: 0 - break it, linkage no : 22 contig : 22 (100% of N gaps have length=50000) Most frequent N gap_length (100% or 22 lines): 50000 Object names: 1 chrY : 1 Component names : 23 EG1_scaffold[1..23]: 23 #Comment line count : 8 ===== Reading Scaffold from component AGP ===== ./test/scaffold_from_contig_WGS.agp:9:EG1_scaffold2 40449 40548 2 N 100 fragment yes NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty No errors, no warnings, 1 note. Count Code Description 1 w58 assuming AGP version X Objects : 23 - with single component: 13 Scaffolds : 23 - with single component: 13 Components : 95 (W) orientation + : 81 orientation - : 14 orientation ? (formerly 0) : 0 orientation na : 0 Gaps : 72 (N) - do not break scaffold: 72 fragment, linkage yes: 72 (20 or 27.8% of N gaps have length=100) - break it, linkage no : 0 Most frequent N gap_length (27.8% or 20 lines): 100 Object names : 23 EG1_scaffold[1..23]: 23 Component names : 95 AADB[02037551..02037645].1: 95 #Comment line count : 6 ===== Reading Chromosome from scaffold AGP ===== ./test/chr_from_scaffold_WGS_bad.agp:4:chrY 3044 53043 2 N 50000 contig no NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty ./test/chr_from_scaffold_WGS_bad.agp:41:chrY 10178961 10194983 39 W EG1_scaffold20_mangled 1 16023 + ERROR: scaffold EG1_scaffold20_mangled was not defined in any of "Scaffold from component" files ./test/chr_from_scaffold_WGS_bad.agp:43:chrY 10244974 10901300 41 W EG1_scaffold21 1 656327 + ERROR: component_end greater than sequence length: 656327 > EG1_scaffold21 length = 656317 bp ./test/chr_from_scaffold_WGS_bad.agp:45:chrY 10951301 10955300 43 W EG1_scaffold22 1 4000 + WARNING: in "Chromosome from scaffold" file, scaffold is not used in full (4000 out of 4051 bp) ./test/chr_from_scaffold_WGS_bad.agp:47:chrY 11005301 11009700 45 W EG1_scaffold23 31 4430 + WARNING: in "Chromosome from scaffold" file, scaffold is not used in full (4400 out of 4430 bp) 2 errors, 3 warnings, 1 note. Count Code Description 1 e22 scaffold X was not defined in any of "Scaffold from component" files 1 w58 assuming AGP version X 2 w59 in "Chromosome from scaffold" file, scaffold is not used in full 1 g74 component_end greater than sequence length - - scaffold(s) not found in Chromosome from scaffold AGP Objects : 1 - with single component: 0 Scaffolds : 23 - with single component: 23 Components : 23 (W) orientation + : 20 orientation - : 0 orientation ? (formerly 0) : 3 orientation na : 0 Gaps : 22 (N) - do not break scaffold: 0 - break it, linkage no : 22 contig : 22 (21 or 95.5% of N gaps have length=50000) Most frequent N gap_length (95.5% or 21 lines): 50000 Object names: 1 chrY : 1 Component names : 23 EG1_scaffold[1..23] : 22 EG1_scaffold20_mangled: 1 WARNING -- 1 scaffold not found in Chromosome from scaffold AGP: EG1_scaffold20 #Comment line count : 2