One CDS exon does not begin properly after the previous CDS exon

[Niohuruzh]

Hi,
When I use Augustus=3.5.0 installed via conda, I encounter an issue with the script and am unsure what is causing it. I would appreciate your help.

[Aug 22 10:48 AM]: Training Augustus using BUSCO gene models
Error: In sequence scaffold_1_115029-121883: One CDS exon does not begin properly after the previous CDS exon.6254 >= 6252
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_157538-160146: One CDS exon does not begin properly after the previous CDS exon.2008 >= 2006
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_333491-339501: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_432109-434199: One CDS exon does not begin properly after the previous CDS exon.1490 >= 1488
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_754865-757016: One CDS exon does not begin properly after the previous CDS exon.1551 >= 1549
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_808924-812682: One CDS exon does not begin properly after the previous CDS exon.3158 >= 3156
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_987640-991533: One CDS exon does not begin properly after the previous CDS exon.3293 >= 3291
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_8923-10693: One CDS exon does not begin properly after the previous CDS exon.1170 >= 1168
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_87818-91422: One CDS exon does not begin properly after the previous CDS exon.3004 >= 3002
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_141403-144751: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_423339-428624: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_670429-672279: One CDS exon does not begin properly after the previous CDS exon.1250 >= 1248
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_69226-72031: One CDS exon does not begin properly after the previous CDS exon.2205 >= 2203
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_225326-228274: One CDS exon does not begin properly after the previous CDS exon.2441 >= 2439
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_808038-811589: One CDS exon does not begin properly after the previous CDS exon.3131 >= 3129
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_811590-815105: One CDS exon does not begin properly after the previous CDS exon.422 >= 420
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_815169-820912: One CDS exon does not begin properly after the previous CDS exon.5143 >= 5141
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_64786-68029: One CDS exon does not begin properly after the previous CDS exon.2643 >= 2641
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_98609-111025: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_507904-510468: One CDS exon does not begin properly after the previous CDS exon.1964 >= 1962
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_691192-693802: One CDS exon does not begin properly after the previous CDS exon.2010 >= 2008
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_724875-728147: One CDS exon does not begin properly after the previous CDS exon.2672 >= 2670
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_145897-151632: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_313847-321526: One CDS exon does not begin properly after the previous CDS exon.7079 >= 7077
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_589249-591735: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_529921-532765: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_578055-584807: One CDS exon does not begin properly after the previous CDS exon.6152 >= 6150
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_12078-15212: One CDS exon does not begin properly after the previous CDS exon.2534 >= 2532
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_48381-51044: One CDS exon does not begin properly after the previous CDS exon.2063 >= 2061
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_532999-534888: One CDS exon does not begin properly after the previous CDS exon.1289 >= 1287
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_10_117854-122338: One CDS exon does not begin properly after the previous CDS exon.4415 >= 4413
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_10_372706-375392: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_12_288985-290921: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_12_369090-371305: One CDS exon does not begin properly after the previous CDS exon.1615 >= 1613
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_12_407139-410804: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_14_413546-418838: One CDS exon does not begin properly after the previous CDS exon.4692 >= 4690
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_16_370915-373770: One CDS exon does not begin properly after the previous CDS exon.2732 >= 2730
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_17_77362-81623: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_18_112117-114640: One CDS exon does not begin properly after the previous CDS exon.1923 >= 1921
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_18_191972-194455: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_21_121473-126355: One CDS exon does not begin properly after the previous CDS exon.4282 >= 4280
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_21_259560-261799: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_21_291863-295967: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_22_82142-86608: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_22_157683-161339: One CDS exon does not begin properly after the previous CDS exon.3056 >= 3054
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_22_164836-166745: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_24_314189-321179: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_25_60541-63983: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_25_210027-213104: One CDS exon does not begin properly after the previous CDS exon.2958 >= 2956
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_27_42911-44983: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_27_87684-90499: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_27_283924-286873: One CDS exon does not begin properly after the previous CDS exon.2349 >= 2347
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_27_309760-315507: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_28_119832-123765: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_28_179654-182288: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_28_212419-214635: One CDS exon does not begin properly after the previous CDS exon.1616 >= 1614
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_28_274213-277575: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_29_47950-49689: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_30_31229-33784: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_30_77896-80137: One CDS exon does not begin properly after the previous CDS exon.1641 >= 1639
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_30_208828-210962: One CDS exon does not begin properly after the previous CDS exon.1534 >= 1532
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_30_284296-287316: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_31_71983-74431: One CDS exon does not begin properly after the previous CDS exon.1848 >= 1846
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_31_103694-108430: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_32_238183-241439: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_33_266485-268244: One CDS exon does not begin properly after the previous CDS exon.1159 >= 1157
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_35_64851-68419: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_36_19982-21819: One CDS exon does not begin properly after the previous CDS exon.1237 >= 1235
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_36_190708-196006: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_39_224402-226513: One CDS exon does not begin properly after the previous CDS exon.1511 >= 1509
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_42_213272-215519: One CDS exon does not begin properly after the previous CDS exon.1647 >= 1645
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_43_216536-218490: One CDS exon does not begin properly after the previous CDS exon.1354 >= 1352
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_47_54541-59464: One CDS exon does not begin properly after the previous CDS exon.4323 >= 4321
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_48_113458-117920: One CDS exon does not begin properly after the previous CDS exon.3862 >= 3860
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_48_202311-204525: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_49_123296-124877: One CDS exon does not begin properly after the previous CDS exon.92 >= 90
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_51_35768-38663: One CDS exon does not begin properly after the previous CDS exon.2295 >= 2293
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_53_145835-147835: One CDS exon does not begin properly after the previous CDS exon.389 >= 387
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_61_17980-20200: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_61_80774-83016: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_63_97761-105945: One CDS exon does not begin properly after the previous CDS exon.7584 >= 7582
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_64_18367-21382: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_65_146232-149768: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_67_160950-163409: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_73_148611-151447: One CDS exon does not begin properly after the previous CDS exon.2236 >= 2234
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_75_92913-96490: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_80_7506-10161: One CDS exon does not begin properly after the previous CDS exon.2055 >= 2053
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_81_66042-69200: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_83_44802-47025: One CDS exon does not begin properly after the previous CDS exon.2044 >= 2042
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_89_22304-26299: One CDS exon does not begin properly after the previous CDS exon.179 >= 177
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_94_39935-43905: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_98_92175-95682: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_99_109345-111265: One CDS exon does not begin properly after the previous CDS exon.1320 >= 1318
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_126_20724-26468: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_150_34436-38688: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_155_9319-13829: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_155_48534-50447: One CDS exon does not begin properly after the previous CDS exon.1313 >= 1311
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_157_26860-29609: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_162_42656-46767: One CDS exon does not begin properly after the previous CDS exon.3511 >= 3509
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_241_9611-14729: One CDS exon does not begin properly after the previous CDS exon.4518 >= 4516
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.

augustus: ERROR
No genbank sequences found.