test/bad_test.agp:7:chrY 1 50000 1 N 50000 short_arm yes # comment ERROR, line skipped: invalid linkage "yes" for gap_type short_arm test/bad_test.agp:8:chrY 50001 53043 2 B AADB02037551.1 1 3043 + ERROR, line skipped: invalid value for component_type (column 5) test/bad_test.agp:9:chrY 53044 93491 3 w AADB02037552.1 1 40448 + ERROR, line skipped: invalid value for component_type (column 5) test/bad_test.agp:10:chrY 93492 93591 4 N 100 fragment yes # another comment NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty test/bad_test.agp:11:chrY 93592 170572 5 9 AADB02037553.1 1 76981 + ERROR, line skipped: invalid value for component_type (column 5) test/bad_test.agp:12:chrY 170573 170672 6 n 100 fragment no ERROR, line skipped: invalid value for component_type (column 5) test/bad_test.agp:13:chrY 170673 198341 7 - AADB02037554.1 1 27669 + ERROR, line skipped: invalid value for component_type (column 5) test/bad_test.agp:15:chrY 198442 201393 9 O AADB02037555.1 1 2952 + WARNING: component_id looks like a WGS accession, component_type is not W test/bad_test.agp:17:chrY 201494 205642 11 P AADB02037556.1 1 4149 - WARNING: component_id looks like a WGS accession, component_type is not W test/bad_test.agp:18:chrY 205643 205742 12 u 100 fragment yes ERROR, line skipped: invalid value for component_type (column 5) test/bad_test.agp:19:chrY 205743 211650 13 W AADB02037557.1 1 5908 ? ERROR, line skipped: invalid value for orientation (column 9) test/bad_test.agp:66:chrY 3423628 3473627 60 N 50000 contig yes ERROR, line skipped: invalid linkage "yes" for gap_type contig test/bad_test.agp:67:chrY 3473628 3565954 61 W AADB02037581.1 1 92327 0 ERROR: 'na' or ? (formerly 0) component orientation may only be used in a singleton scaffold test/bad_test.agp:70:chrY 3623105 3673104 64 N 50000 centromere yes ERROR, line skipped: invalid linkage "yes" for gap_type centromere test/bad_test.agp:71:chrY 3673105 3678682 65 W AADB02037583.1 1 5578 ? ERROR, line skipped: invalid value for orientation (column 9) test/bad_test.agp:72:chrY 3678683 3728682 66 N 50000 heterochromatin yes ERROR, line skipped: invalid linkage "yes" for gap_type heterochromatin test/bad_test.agp:107:chrY 6997598 7000631 101 W AADB02037601.1 0 3034 + ERROR, line skipped: component_beg (column 7) must be a positive integer test/bad_test.agp:108:chrY 7000632 7050631 102 N 0 contig no ERROR, line skipped: gap_length (column 6) must be a positive integer test/bad_test.agp:109:chrY 7050632 7053381 103 W AADB02037602.1 1 0 + ERROR, line skipped: component_end (column 8) must be a positive integer test/bad_test.agp:110:chrY 7053382 7103381 0 N 50000 contig no ERROR, line skipped: part_number (column 4) must be a positive integer test/bad_test.agp:111:chrY 0 7107650 105 W AADB02037603.1 1 4269 + ERROR, line skipped: object_beg (column 2) must be a positive integer test/bad_test.agp:112:chrY 7107651 0 106 N 50000 contig no ERROR, line skipped: object_end (column 3) must be a positive integer test/bad_test.agp:121:chrY 18336154 8409082 115 W AADB02037608.1 1 72929 + ERROR, line skipped: object_end is less than object_beg test/bad_test.agp:123:chrY 8451473 8469374 117 W AADB02037609.1 17902 1 + ERROR, line skipped: component_end is less than component_beg test/bad_test.agp:132:chrY 8534243 8534387 126 N 145 fragment yes test/bad_test.agp:133:chrY 8534388 8535698 127 N 1311 fragment yes ERROR: consequtive gaps lines with the same type and linkage test/bad_test.agp:134:chrY 8535699 8535938 128 N 240 fragment yes ERROR: consequtive gaps lines with the same type and linkage test/bad_test.agp:147:chrY 9307071 9315045 141 W AADB02037621.1 1 7975 - test/bad_test.agp:148:chrY 9315045 9322053 142 N 7009 fragment yes ERROR: object_beg != previous object_end + 1 test/bad_test.agp:149:chrY 9322054 9325079 143 W AADB02037622.1 1 3026 + test/bad_test.agp:150:chrY 9325079 9325178 144 N 100 fragment yes ERROR: object_beg != previous object_end + 1 test/bad_test.agp:153:chrY 9332433 9358223 147 W AADB02037624.1 1 25791 + test/bad_test.agp:154:chrY 9358124 9358223 148 N 100 fragment yes ERROR: object_beg != previous object_end + 1 test/bad_test.agp:155:chrY 9358324 9364423 149 W AADB02037625.1 1 6100 + ERROR: object_beg != previous object_end + 1 test/bad_test.agp:176:chrY 10128961 10178960 170 N 50000 scaffold no ERROR, line skipped: invalid value for gap_type (column 7) test/bad_test.agp:178:chrY 10194984 10244983 172 N 50000 contig ? ERROR, line skipped: invalid value for linkage (column 8) test/bad_test.agp:186:chrY 10507047 10507146 180 N 100 fragment yes test/bad_test.agp:187:chrY 10507147 10509939 180 W AADB02037641.1 1 2793 -# modified ERROR: part number (column 4) != previous part number + 1 test/bad_test.agp:188:chrY 10509940 10517020 182 N 100 fragment yes # modified ERROR, line skipped: object range length not equal to the gap length: 7081 != 100 test/bad_test.agp:192:chrY 10901301 10951300 186 N 50000 telomere yes ERROR, line skipped: invalid linkage "yes" for gap_type telomere test/bad_test.agp:195:chrX 1001 2000 1 W AADB02037645.1 1 1000 + ERROR: first line of an object must have object_beg=1 test/bad_test.agp:196:chrX 2002 3001 2 W AADB02037646.1 1 1000 + ERROR: object_beg != previous object_end + 1 test/bad_test.agp:197:chrZ 1 1000 3 W AADB02037647.1 1 1000 + ERROR: first line of an object must have part_number=1 test/bad_test.agp:198:chrX 1 100 1 W AADB02037645.1 1 1000 + ERROR, line skipped: object range length not equal to component range length: 100 != 1000 test/bad_test.agp:199:chrX 2002 3001 2 W AADB02037646.1 1 1000 + ERROR: duplicate object chrX WARNING: the span overlaps a previous span for this component: 1..1000 at test/bad_test.agp:196 WARNING: same component_id found on different scaffolds; previous occurance at line 196, in another object test/bad_test.agp:200: 1 1000 1 W AADB02037648.1 1 1000 + ERROR, line skipped: column 1 is empty test/bad_test.agp:201:chrA 2000 2 W AADB02037649.1 1 1000 + ERROR, line skipped: column 2 is empty test/bad_test.agp:202:chrA 2001 3 W AADB02037650.1 1 1000 + ERROR, line skipped: column 3 is empty test/bad_test.agp:203:chrA 3001 4000 W AADB02037651.1 1 1000 + ERROR, line skipped: column 4 is empty test/bad_test.agp:204:chrA 4001 5000 5 AADB02037652.1 1 1000 + ERROR, line skipped: column 5 is empty test/bad_test.agp:205:chrA 5001 6000 6 W 1 1000 + ERROR, line skipped: column 6 is empty test/bad_test.agp:206:chrA 6001 7000 7 W AADB02037654.1 1000 + ERROR, line skipped: column 7 is empty test/bad_test.agp:207:chrA 7001 8000 8 W AADB02037655.1 1 + ERROR, line skipped: column 8 is empty test/bad_test.agp:208:chrA 8001 9000 9 W AADB02037656.1 1 1000 ERROR, line skipped: invalid value for orientation (column 9) test/bad_test.agp:210:chrA 10001 11000 11 W AADB02037658.1 1 1000 ERROR, line skipped: expecting 9 tab-separated columns, found 8 test/bad_test.agp:212:chrA 12001 13000 13 W AADB02037660.1 1 1000 + ERROR, line skipped: expecting 9 tab-separated columns, found 11 test/bad_test.agp:213:chrB 1 100 1 N 100 fragment yes WARNING: gap at the end of object (OK if chrB is the circular chromosome/plasmid) WARNING: no components in object chrB test/bad_test.agp:214:chrY 1 177051 1 D AC163727.2 1 177051 + ERROR: duplicate object chrY test/bad_test.agp:219:chrY 218658 223697 6 F AC163728.2 4033 9072 - WARNING: duplicate component with non-draft type; preceding span: 9173..32729 at test/bad_test.agp:217 test/bad_test.agp:221:chrY 223798 277847 8 F AC163728.2 65081 119130 - WARNING: component span appears out of order; preceding span: 4033..9072 at test/bad_test.agp:219 test/bad_test.agp:222:chrY 277848 443135 9 F AC16371.2 1 165288 + WARNING: component_id AC16371.2 is not an HTG accession, but is used with component_type A, D, or F test/bad_test.agp:225:chrY 452891 462370 12 F AC158542.1 11304 20783 + WARNING: duplicate component with non-draft type; preceding span: 1549..11203 at test/bad_test.agp:223 test/bad_test.agp:227:chrY 462471 471917 14 F AC158542.1 20884 30330 + WARNING: duplicate component with non-draft type; preceding span: 1549..11203 at test/bad_test.agp:223 test/bad_test.agp:229:chrY 472018 564686 16 F AC158542.1 85272 177940 + WARNING: duplicate component with non-draft type; preceding span: 1549..11203 at test/bad_test.agp:223 test/bad_test.agp:231:chrY 564787 567081 18 F AC158542.1 38856 41150 + WARNING: component span appears out of order; preceding span: 85272..177940 at test/bad_test.agp:229 test/bad_test.agp:233:chrC 1 100 1 W AADB02037644.1 4051 4150 + WARNING: the span overlaps a previous span for this component: 1..4051 at test/bad_test.agp:193 WARNING: same component_id found on different scaffolds; previous occurance at line 193, in another object test/bad_test.agp:234:chrC 101 200 2 W AADB02037645.1 1000 1099 - WARNING: the span overlaps a previous span for this component: 1..1000 at test/bad_test.agp:195 WARNING: same component_id found on different scaffolds; previous occurance at line 195, in another object test/bad_test.agp:235:chrC 201 300 3 W AADB02037646.1 1 100 - WARNING: the span overlaps a previous span for this component: 1..1000 at test/bad_test.agp:196 WARNING: same component_id found on different scaffolds; previous occurance at line 199, in another object test/bad_test.agp:236: ERROR, line skipped: empty line test/alt_bad_test.agp:2:scaffold_0 2107 4201 2 N 2095 fragment yes NOTE: assuming AGP version 1.1 since linkage evidence (column 9) is empty test/alt_bad_test.agp:20:scaffold_0 62232 62557 20 N 326 fragment yes WARNING: gap at the end of object (OK if scaffold_0 is the circular chromosome/plasmid) 50 errors, 21 warnings, 2 notes; 1 not printed. Count Code Description 2 e01 expecting 9 tab-separated columns 8 e02 column X is empty 1 e03 empty line 11 e04 invalid value for X 5 e05 invalid linkage 6 e06 X must be a positive integer 1 e08 object_end is less than object_beg 1 e09 component_end is less than component_beg 1 e10 object range length not equal to the gap length 1 e11 object range length not equal to component range length 2 e12 duplicate object 1 e13 first line of an object must have object_beg=1 1 e14 first line of an object must have part_number=1 1 e15 part number (column 4) != previous part number + 1 1 e16 'na' or ? (formerly 0) component orientation may only be used in a singleton scaffold 5 e17 object_beg != previous object_end + 1 2 e19 consequtive gaps lines with the same type and linkage 2 w31 gap at the end of object (OK if X is the circular chromosome/plasmid) 1 w34 no components in object 4 w35 the span overlaps a previous span for this component 2 w36 component span appears out of order 4 w37 duplicate component with non-draft type 1 w40 extra tab or space at the end of line 2 w45 component_id looks like a WGS accession, component_type is not W (Use -g to print lines with WGS component_id/component_type mismatch.) 4 w49 same component_id found on different scaffolds 2 w58 assuming AGP version X 1 w64 component_id X is not an HTG accession, but is used with component_type A, D, or F NOTE: 37 invalid lines were skipped (not subjected to all the checks, not included in most of the counts below). Objects : 9 - with single component: 2 Scaffolds : 19 - with single component: 5 ***no components, gaps only: 2 Components : 113 (W:99, F:10, D:2, O:1, P:1) orientation + : 92 orientation - : 19 orientation ? (formerly 0) : 1 orientation na : 1 Gaps : 100 (N) - do not break scaffold: 89 clone , linkage yes: 1 fragment, linkage yes: 87 (26 or 29.9% of N gaps have length=100) repeat , linkage yes: 1 - break it, linkage no : 11 clone : 1 repeat : 1 contig : 8 (100% of N gaps have length=50000) telomere : 1 Most frequent N gap_length (26.0% or 26 lines): 100 Object names: 7 scaffold_0: 1 chrZ : 1 chrY : 1 chrX : 1 chrC : 1 chrB : 1 chrA : 1 Component names : 102 ------ Nucleotide accessions: 97 AADB[02037555..02037659].1: 86 AAGU[02000002..02990008] : 6 NT_165199 : 1 AC163726 : 1 ABRQ01000007 : 1 AAGU02000001.15 : 1 AAAA01999999.1 : 1 ------ OTHER identifiers : 5 AC[16371..163728].[1,2] : 4 (some local or misspelled) AAAGU02000003 : 1 (local or misspelled) Use -g or "-show all" to print lines with suspicious accessions. #Comment line count : 6 End of line #comments : 11