-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_16035808-16283049 -reading genomic sequence. ** Processing features (+) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential starts and stops. (strand: +) -loading gene prediction evidence. (strand: +)Valid prediction for pasa_asmbl_44717.p1 Valid prediction for GeneMark_model.22880_t Valid prediction for GeneMark_model.22885_t Valid prediction for CodingQuarry_transcript_52283-T1 Valid prediction for pasa_asmbl_44715.p1 Valid prediction for pasa_asmbl_44704.p1 Couldn't classify 237578, 237805 Couldn't classify 242156, 242299 Sorry, prediction pasa_asmbl_44732.p1 fails validation. (TGG) AC 237578-237805 GT AGG (GCG) AG 237937-238407 GT AGG (CTG) AG 239714-239836 GT GAG (GAC) AG 239999-240094 GT AGG (GAG) AG 240259-240528 GT AGG (GTG) AG 240912-241064 GT AGG (GAG) AG 241244-241371 GT AAG (GTG) AG 241522-241603 GT AGG (TAC) AG 241752-241928 GT AGG (GTG) AG 242156-242299 GG CAG -recovered pasa_asmbl_44732.p1, internal, 237937, 238407 -recovered pasa_asmbl_44732.p1, internal, 239714, 239836 -recovered pasa_asmbl_44732.p1, internal, 239999, 240094 -recovered pasa_asmbl_44732.p1, internal, 240259, 240528 -recovered pasa_asmbl_44732.p1, internal, 240912, 241064 -recovered pasa_asmbl_44732.p1, internal, 241244, 241371 -recovered pasa_asmbl_44732.p1, internal, 241522, 241603 -recovered pasa_asmbl_44732.p1, internal, 241752, 241928 Valid prediction for GlimmerHMM_glimmerT_13621-T1 Couldn't classify 231501, 231515 Couldn't classify 232861, 232913 Sorry, prediction pasa_asmbl_44729.p1 fails validation. (GAG) TG 231501-231515 GT AGG (GTG) AG 231965-232105 GT AGG (CAT) AG 232243-232450 GT AGG (GCG) AG 232587-232688 GT CGG (TCA) AG 232861-232913 TA AGT -recovered pasa_asmbl_44729.p1, internal, 231965, 232105 -recovered pasa_asmbl_44729.p1, internal, 232243, 232450 -recovered pasa_asmbl_44729.p1, internal, 232587, 232688 Couldn't classify 208684, 208908 Couldn't classify 209185, 209262 Sorry, prediction pasa_asmbl_45117.p1 fails validation. (GAT) TG 208684-208908 GT AGG (GTA) AG 209185-209262 CC CCC Valid prediction for GeneMark_model.22853_t Valid prediction for GeneMark_model.22858_t Valid prediction for Augustus_model.g9113.t1 Valid prediction for snap_scaffold_5-snap.2990-T1 Valid prediction for snap_scaffold_5-snap.2997-T1 Valid prediction for snap_scaffold_5-snap.3030-T1 Valid prediction for snap_scaffold_5-snap.3000-T1 Valid prediction for GeneMark_model.22887_t Couldn't classify 242542, 242871 Couldn't classify 244183, 244394 Sorry, prediction pasa_asmbl_44733.p1 fails validation. (GAC) CA 242542-242871 GT AGG (GTG) AG 242994-243189 GT CGG (CGT) AG 243412-243579 GT GGG (CCG) AG 243669-243817 GT ACG (GCT) AG 243900-243966 GT AGG (CCT) AG 244183-244394 CT AGC -recovered pasa_asmbl_44733.p1, internal, 242994, 243189 -recovered pasa_asmbl_44733.p1, internal, 243412, 243579 -recovered pasa_asmbl_44733.p1, internal, 243669, 243817 -recovered pasa_asmbl_44733.p1, internal, 243900, 243966 Valid prediction for GeneMark_model.22851_t Valid prediction for GlimmerHMM_glimmerT_13641-T1 Valid prediction for GlimmerHMM_glimmerT_13640-T1 Valid prediction for snap_scaffold_5-snap.3024-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_13627-T1 Valid prediction for GeneMark_model.22875_t Valid prediction for snap_scaffold_5-snap.3021-T1 Valid prediction for CodingQuarry_transcript_52285-T1 Valid prediction for GlimmerHMM_glimmerT_13625-T1 Valid prediction for snap_scaffold_5-snap.3002-T1 Couldn't classify 35640, 35691 Couldn't classify 36735, 36850 Sorry, prediction pasa_asmbl_44698.p1 fails validation. (GGG) TC 35640-35691 GT AGG (CGC) AG 35822-35892 GT AGG (GAA) AG 36222-36447 GT TGG (TTC) AG 36735-36850 GT AGG -recovered pasa_asmbl_44698.p1, internal, 35822, 35892 -recovered pasa_asmbl_44698.p1, internal, 36222, 36447 -recovered pasa_asmbl_44698.p1, internal, 36735, 36850 Valid prediction for pasa_asmbl_44714.p1 Valid prediction for GeneMark_model.22860_t Valid prediction for snap_scaffold_5-snap.3013-T1 Valid prediction for snap_scaffold_5-snap.3005-T1 Valid prediction for snap_scaffold_5-snap.3016-T1 Valid prediction for GlimmerHMM_glimmerT_13639-T1 Valid prediction for snap_scaffold_5-snap.3020-T1 Valid prediction for snap_scaffold_5-snap.2996-T1 Valid prediction for GeneMark_model.22881_t Valid prediction for snap_scaffold_5-snap.3028-T1 Valid prediction for snap_scaffold_5-snap.2993-T1 Valid prediction for GeneMark_model.22867_t Couldn't classify 234447, 234613 Couldn't classify 235120, 235296 Sorry, prediction pasa_asmbl_44730.p1 fails validation. (GAG) CG 234447-234613 GT CAG (GGT) AG 234829-234886 GT TGG (ATG) AG 235120-235296 GT TGG -recovered pasa_asmbl_44730.p1, initial, 235120, 235296 -recovered pasa_asmbl_44730.p1, internal, 234829, 234886 -recovered pasa_asmbl_44730.p1, internal, 235120, 235296 Valid prediction for GeneMark_model.22870_t Valid prediction for GlimmerHMM_glimmerT_13623-T1 Valid prediction for GeneMark_model.22849_t Valid prediction for GeneMark_model.22862_t Valid prediction for snap_scaffold_5-snap.2998-T1 Valid prediction for snap_scaffold_5-snap.2987-T1 Valid prediction for CodingQuarry_transcript_52277-T1 Valid prediction for Augustus_model.g9109.t1 Valid prediction for snap_scaffold_5-snap.3010-T1 Valid prediction for GlimmerHMM_glimmerT_13622-T1 Valid prediction for GlimmerHMM_glimmerT_13636-T1 Valid prediction for HiQ_model.g9116.t1 Couldn't classify 84926, 84980 Sorry, prediction pasa_asmbl_44706.p2 fails validation. (GAG) GG 84926-84980 GT AGG (GTC) AG 85147-85271 GT AGG (GTG) AG 85827-85955 GC AAG -recovered pasa_asmbl_44706.p2, terminal, 85827, 85955 -recovered pasa_asmbl_44706.p2, internal, 85147, 85271 -recovered pasa_asmbl_44706.p2, internal, 85827, 85955 Valid prediction for GlimmerHMM_glimmerT_13629-T1 Valid prediction for HiQ_model.g9121.t1 Couldn't classify 205122, 205200 Couldn't classify 207361, 207708 Sorry, prediction pasa_asmbl_44721.p1 fails validation. (GCC) AC 205122-205200 GT AGG (ATG) AG 207176-207258 GT AGG (GTC) AG 207361-207708 AA AGA add_exon() Sorry, pasa_asmbl_44721.p1 207176-207258-initial-1 is invalid. -recovered pasa_asmbl_44721.p1, initial, 207176, 207258 -recovered pasa_asmbl_44721.p1, internal, 207176, 207258 Valid prediction for GeneMark_model.22864_t Valid prediction for snap_scaffold_5-snap.3015-T1 Couldn't classify 99313, 99401 Sorry, prediction pasa_asmbl_44709.p1 fails validation. (GAC) CA 99313-99401 GT AAG (AGG) AG 99716-99874 GT AGG (GTT) AG 99973-100098 GT CGG (TGA) AG 100194-100287 GT AGG (GTT) AG 100560-100746 GT TGG (GTG) AG 100924-101156 GT AGG (GAC) AG 102469-102545 GT AGG (TGA) AG 103094-103186 GT AGG (TCG) AG 103427-103517 CA GAC add_exon() Sorry, pasa_asmbl_44709.p1 99716-99874-terminal-1 is invalid. -recovered pasa_asmbl_44709.p1, terminal, 99716, 99874 -recovered pasa_asmbl_44709.p1, terminal, 103427, 103517 -recovered pasa_asmbl_44709.p1, internal, 99716, 99874 -recovered pasa_asmbl_44709.p1, internal, 99973, 100098 -recovered pasa_asmbl_44709.p1, internal, 100194, 100287 -recovered pasa_asmbl_44709.p1, internal, 100560, 100746 -recovered pasa_asmbl_44709.p1, internal, 100924, 101156 -recovered pasa_asmbl_44709.p1, internal, 102469, 102545 -recovered pasa_asmbl_44709.p1, internal, 103094, 103186 Valid prediction for GeneMark_model.22891_t Valid prediction for GlimmerHMM_glimmerT_13615-T1 Valid prediction for CodingQuarry_transcript_52281-T1 Valid prediction for Augustus_model.g9123.t1 Valid prediction for snap_scaffold_5-snap.2988-T1 Valid prediction for Augustus_model.g9124.t1 Valid prediction for GeneMark_model.22866_t Valid prediction for Augustus_model.g9111.t1 Valid prediction for HiQ_model.g9108.t1 Valid prediction for GeneMark_model.22899_t Couldn't classify 38057, 38084 Sorry, prediction pasa_asmbl_44699.p1 fails validation. (CTG) TT 38057-38084 GT GAG (TAG) AG 38502-38678 GT AGG (CTC) AG 38947-39060 GT CAG (GTG) AG 39226-39375 GT AGG (GAG) AG 40168-40299 GT AGG (TCA) AG 40562-40634 GT AGG (CGA) AG 41156-41432 AC AAA -recovered pasa_asmbl_44699.p1, terminal, 41156, 41432 -recovered pasa_asmbl_44699.p1, internal, 38502, 38678 -recovered pasa_asmbl_44699.p1, internal, 38947, 39060 -recovered pasa_asmbl_44699.p1, internal, 39226, 39375 -recovered pasa_asmbl_44699.p1, internal, 40168, 40299 -recovered pasa_asmbl_44699.p1, internal, 40562, 40634 Valid prediction for GeneMark_model.22889_t Valid prediction for GlimmerHMM_glimmerT_13628-T1 Valid prediction for HiQ_model.g9118.t1 Valid prediction for GeneMark_model.22900_t Couldn't classify 76826, 76924 Couldn't classify 79114, 79128 Sorry, prediction pasa_asmbl_44705.p1 fails validation. (ACC) GC 76826-76924 GT AGG (GAG) AG 77388-77509 GT AGG (TAT) AG 78819-78930 GT CGG (GAG) AG 79114-79128 CG TGC -recovered pasa_asmbl_44705.p1, internal, 77388, 77509 -recovered pasa_asmbl_44705.p1, internal, 78819, 78930 Valid prediction for pasa_asmbl_44712.p1 Valid prediction for snap_scaffold_5-snap.3017-T1 Valid prediction for GeneMark_model.22872_t Valid prediction for GlimmerHMM_glimmerT_13637-T1 Couldn't classify 56365, 56436 Couldn't classify 56654, 56687 Sorry, prediction CodingQuarry_transcript_52278-T1 fails validation. (ATG) TT 49638-49746 GT TGG (GCA) AG 50188-50376 GT CGG (GGT) AG 50511-50623 GT AAG (GGA) AG 50830-51033 GT AGG (GCT) AG 51159-51397 GT AAG (GGA) AG 51618-51876 GT AGG (GTG) AG 52247-52387 GT AGG (GCC) AG 52469-52551 GT AAG (GCA) AG 52706-52805 GT AGG (GTT) AG 53077-53184 GT TGG (TAC) AG 53340-53525 GT AGG (GTG) AG 53670-53849 GT AGG (ACG) AG 54531-54677 GT AGG (GAG) AG 55083-55220 GT AGG (GAG) AG 55327-55443 GT TGG (GTG) AG 55552-55658 GT CGG (CCT) AG 55742-55883 GT AGG (GAG) AG 56138-56283 GT AAG (GGA) AG 56365-56436 CA CAC (TCC) CG 56654-56687 AG AGA -recovered CodingQuarry_transcript_52278-T1, initial, 49638, 49746 -recovered CodingQuarry_transcript_52278-T1, internal, 50188, 50376 -recovered CodingQuarry_transcript_52278-T1, internal, 50511, 50623 -recovered CodingQuarry_transcript_52278-T1, internal, 50830, 51033 -recovered CodingQuarry_transcript_52278-T1, internal, 51159, 51397 -recovered CodingQuarry_transcript_52278-T1, internal, 51618, 51876 -recovered CodingQuarry_transcript_52278-T1, internal, 52247, 52387 -recovered CodingQuarry_transcript_52278-T1, internal, 52469, 52551 -recovered CodingQuarry_transcript_52278-T1, internal, 52706, 52805 -recovered CodingQuarry_transcript_52278-T1, internal, 53077, 53184 -recovered CodingQuarry_transcript_52278-T1, internal, 53340, 53525 -recovered CodingQuarry_transcript_52278-T1, internal, 53670, 53849 -recovered CodingQuarry_transcript_52278-T1, internal, 54531, 54677 -recovered CodingQuarry_transcript_52278-T1, internal, 55083, 55220 -recovered CodingQuarry_transcript_52278-T1, internal, 55327, 55443 -recovered CodingQuarry_transcript_52278-T1, internal, 55552, 55658 -recovered CodingQuarry_transcript_52278-T1, internal, 55742, 55883 -recovered CodingQuarry_transcript_52278-T1, internal, 56138, 56283 Valid prediction for GeneMark_model.22856_t Valid prediction for CodingQuarry_transcript_52286-T1 Valid prediction for GlimmerHMM_glimmerT_13630-T1 Valid prediction for CodingQuarry_transcript_52279-T1 Valid prediction for GeneMark_model.22874_t Valid prediction for GeneMark_model.22896_t Valid prediction for snap_scaffold_5-snap.3022-T1 Valid prediction for CodingQuarry_transcript_52276-T1 Valid prediction for Augustus_model.g9115.t1 Valid prediction for CodingQuarry_transcript_52287-T1 Valid prediction for Augustus_model.g9112.t1 Couldn't classify 113088, 113171 Couldn't classify 113382, 113568 Sorry, prediction CodingQuarry_transcript_52282-T1 fails validation. (ATG) AA 111847-111885 GT AGG (CTG) AG 112169-112227 GT ATG (GGA) AG 112318-112363 GT TGG (GCT) AG 112440-112555 GT AGG (TAA) AG 112851-112895 GT CAG (GAT) AG 113088-113171 GG GAG (GGT) TG 113382-113568 CG GAC -recovered CodingQuarry_transcript_52282-T1, initial, 111847, 111885 add_exon() Sorry, CodingQuarry_transcript_52282-T1 113088-113171-terminal-1 is invalid. -recovered CodingQuarry_transcript_52282-T1, terminal, 113088, 113171 -recovered CodingQuarry_transcript_52282-T1, internal, 112169, 112227 -recovered CodingQuarry_transcript_52282-T1, internal, 112318, 112363 -recovered CodingQuarry_transcript_52282-T1, internal, 112440, 112555 -recovered CodingQuarry_transcript_52282-T1, internal, 112851, 112895 Valid prediction for snap_scaffold_5-snap.3009-T1 Valid prediction for GlimmerHMM_glimmerT_13635-T1 Valid prediction for GlimmerHMM_glimmerT_13624-T1 Valid prediction for GeneMark_model.22890_t Valid prediction for GeneMark_model.22901_t Couldn't classify 229364, 229483 Couldn't classify 231077, 231157 Sorry, prediction pasa_asmbl_44994.p1 fails validation. (CAG) TG 229364-229483 GT AGG (AGC) AG 229570-229632 GT CGG (AAG) AG 229789-229866 GT AGG (CAG) AG 229975-230025 GT AGG (ATC) AG 230217-230385 GT GGG (TTT) AG 230641-230741 GT TGG (GAC) AG 231077-231157 TG ACT -recovered pasa_asmbl_44994.p1, internal, 229570, 229632 -recovered pasa_asmbl_44994.p1, internal, 229789, 229866 -recovered pasa_asmbl_44994.p1, internal, 229975, 230025 -recovered pasa_asmbl_44994.p1, internal, 230217, 230385 -recovered pasa_asmbl_44994.p1, internal, 230641, 230741 Couldn't classify 229018, 229200 Sorry, prediction pasa_asmbl_44727.p2 fails validation. (ATG) CC 228436-228480 GT CTG (CCT) AG 228603-228701 GT AGG (TGT) AG 229018-229200 AG CCA -recovered pasa_asmbl_44727.p2, initial, 228436, 228480 -recovered pasa_asmbl_44727.p2, internal, 228603, 228701 Couldn't classify 31535, 31553 Couldn't classify 33379, 33506 Sorry, prediction pasa_asmbl_44697.p1 fails validation. (ACA) TC 31535-31553 GT CTG (CTA) AG 32418-32532 GT CTG (CCC) AG 32674-32858 GT AGG (CGG) AG 33074-33205 GT AAG (GCA) AG 33379-33506 AA CCA -recovered pasa_asmbl_44697.p1, internal, 32418, 32532 -recovered pasa_asmbl_44697.p1, internal, 32674, 32858 -recovered pasa_asmbl_44697.p1, internal, 33074, 33205 Valid prediction for snap_scaffold_5-snap.3003-T1 Valid prediction for snap_scaffold_5-snap.3004-T1 Valid prediction for GeneMark_model.22854_t Valid prediction for Augustus_model.g9122.t1 Valid prediction for GeneMark_model.22894_t Valid prediction for snap_scaffold_5-snap.3026-T1 Valid prediction for GeneMark_model.22897_t Couldn't classify 215759, 215811 Sorry, prediction pasa_asmbl_44724.p1 fails validation. (CCC) GC 215759-215811 GT AGG (GTT) AG 216061-216247 GT GGG (GGT) AG 216555-216717 GT AGG (GGT) AG 217240-217327 GT CGG (AGC) AG 217561-217667 GT GGG (GTC) AG 217810-217901 GT AGG (GCC) AG 217996-218085 GT AGG (GAC) AG 218196-218471 GT AGG (TTG) AG 218589-218671 GT GGG (GAA) AG 218845-219017 GT TGG (GTC) AG 219320-219405 GT AGG (GAG) AG 219612-219730 GT AGG (CGA) AG 220151-220497 GT TGG (TCT) AG 220691-220786 GT AGG (CTC) AG 220901-221010 GT AGG (GAG) AG 221146-221500 GT AGG (GTA) AG 221593-221681 GA AAG -recovered pasa_asmbl_44724.p1, terminal, 221593, 221681 -recovered pasa_asmbl_44724.p1, internal, 216061, 216247 -recovered pasa_asmbl_44724.p1, internal, 216555, 216717 -recovered pasa_asmbl_44724.p1, internal, 217240, 217327 -recovered pasa_asmbl_44724.p1, internal, 217561, 217667 -recovered pasa_asmbl_44724.p1, internal, 217810, 217901 -recovered pasa_asmbl_44724.p1, internal, 217996, 218085 -recovered pasa_asmbl_44724.p1, internal, 218196, 218471 -recovered pasa_asmbl_44724.p1, internal, 218589, 218671 -recovered pasa_asmbl_44724.p1, internal, 218845, 219017 -recovered pasa_asmbl_44724.p1, internal, 219320, 219405 -recovered pasa_asmbl_44724.p1, internal, 219612, 219730 -recovered pasa_asmbl_44724.p1, internal, 220151, 220497 -recovered pasa_asmbl_44724.p1, internal, 220691, 220786 -recovered pasa_asmbl_44724.p1, internal, 220901, 221010 -recovered pasa_asmbl_44724.p1, internal, 221146, 221500 Valid prediction for GeneMark_model.22892_t Valid prediction for Augustus_model.g9106.t1 Valid prediction for GlimmerHMM_glimmerT_13617-T1 Valid prediction for CodingQuarry_transcript_52284-T1 Valid prediction for GeneMark_model.22878_t -loading the search evidence (protein and EST search results, strand: +) -scoring exons (strand: +) ** Processing features (-) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential starts and stops. (strand: -) -loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_5-snap.3006-T1 Valid prediction for snap_scaffold_5-snap.2985-T1 Valid prediction for Augustus_model.g9105.t1 Valid prediction for snap_scaffold_5-snap.3027-T1 Valid prediction for GlimmerHMM_glimmerT_13616-T1 Valid prediction for snap_scaffold_5-snap.2991-T1 Valid prediction for snap_scaffold_5-snap.3001-T1 Valid prediction for GeneMark_model.22871_t Valid prediction for GeneMark_model.22876_t Valid prediction for snap_scaffold_5-snap.2995-T1 Valid prediction for GeneMark_model.22850_t Valid prediction for snap_scaffold_5-snap.2986-T1 Valid prediction for snap_scaffold_5-snap.3025-T1 Valid prediction for snap_scaffold_5-snap.3007-T1 Valid prediction for GeneMark_model.22898_t Couldn't classify 140855, 140989 Sorry, prediction pasa_asmbl_46373.p1 fails validation. (TGT) CC 140855-140989 GT AGG (TTT) AG 141308-141624 GT AGG (AGT) AG 141962-142076 CC GAC -recovered pasa_asmbl_46373.p1, terminal, 141962, 142076 -recovered pasa_asmbl_46373.p1, internal, 141308, 141624 Valid prediction for GlimmerHMM_glimmerT_13613-T1 Couldn't classify 108310, 108721 Sorry, prediction pasa_asmbl_46125.p1 fails validation. (AAC) TG 108310-108721 GT AGG (GCA) AG 109693-109889 CG GAC -recovered pasa_asmbl_46125.p1, terminal, 109693, 109889 Valid prediction for GeneMark_model.22902_t Valid prediction for GlimmerHMM_glimmerT_13612-T1 Valid prediction for GeneMark_model.22886_t Valid prediction for GeneMark_model.22873_t Valid prediction for snap_scaffold_5-snap.2992-T1 Valid prediction for snap_scaffold_5-snap.2999-T1 Valid prediction for snap_scaffold_5-snap.3031-T1 Valid prediction for snap_scaffold_5-snap.3008-T1 Valid prediction for snap_scaffold_5-snap.3018-T1 Valid prediction for GeneMark_model.22884_t Valid prediction for Augustus_model.g9110.t1 Valid prediction for snap_scaffold_5-snap.3014-T1 Valid prediction for snap_scaffold_5-snap.3011-T1 Valid prediction for GeneMark_model.22861_t Valid prediction for GeneMark_model.22855_t Valid prediction for GeneMark_model.22895_t Valid prediction for GeneMark_model.22863_t Valid prediction for GlimmerHMM_glimmerT_13626-T1 Valid prediction for snap_scaffold_5-snap.3033-T1 Valid prediction for snap_scaffold_5-snap.2994-T1 Valid prediction for GlimmerHMM_glimmerT_13638-T1 Valid prediction for GlimmerHMM_glimmerT_13634-T1 Valid prediction for GeneMark_model.22859_t Valid prediction for GeneMark_model.22879_t Valid prediction for GeneMark_model.22852_t Valid prediction for GlimmerHMM_glimmerT_13614-T1 Valid prediction for GeneMark_model.22882_t Valid prediction for GeneMark_model.22877_t Valid prediction for GeneMark_model.22857_t Valid prediction for GlimmerHMM_glimmerT_13631-T1 Valid prediction for snap_scaffold_5-snap.2989-T1 Valid prediction for HiQ_model.g9120.t1 Valid prediction for snap_scaffold_5-snap.3019-T1 Valid prediction for GlimmerHMM_glimmerT_13633-T1 Valid prediction for Augustus_model.g9107.t1 Valid prediction for GeneMark_model.22868_t Valid prediction for GeneMark_model.22883_t Valid prediction for GeneMark_model.22865_t Valid prediction for snap_scaffold_5-snap.3029-T1 Couldn't classify 79376, 79465 Sorry, prediction pasa_asmbl_46127.p1 fails validation. (TCA) TC 79376-79465 GT AAG (ATT) AG 79897-79956 GT ATG (CCT) AG 80511-80608 GT AGG (GTT) AG 80757-80872 GT AGG (GTA) AG 80972-81032 GT CGG (CAC) AG 81134-81266 GT AGG (AGT) AG 81414-81547 GT ATG (GAA) AG 81694-81796 GT AGG (CTG) AG 81876-82022 GT CGG (GCC) AG 82193-82287 GT AAG (GCT) AG 82507-82567 GT GGG (TTG) AG 82907-83008 AC AAA add_exon() Sorry, pasa_asmbl_46127.p1 82193-82287-terminal-2 is invalid. -recovered pasa_asmbl_46127.p1, terminal, 82193, 82287 -recovered pasa_asmbl_46127.p1, terminal, 82907, 83008 -recovered pasa_asmbl_46127.p1, internal, 79897, 79956 -recovered pasa_asmbl_46127.p1, internal, 80511, 80608 -recovered pasa_asmbl_46127.p1, internal, 80757, 80872 -recovered pasa_asmbl_46127.p1, internal, 80972, 81032 -recovered pasa_asmbl_46127.p1, internal, 81134, 81266 -recovered pasa_asmbl_46127.p1, internal, 81414, 81547 -recovered pasa_asmbl_46127.p1, internal, 81694, 81796 -recovered pasa_asmbl_46127.p1, internal, 81876, 82022 -recovered pasa_asmbl_46127.p1, internal, 82193, 82287 -recovered pasa_asmbl_46127.p1, internal, 82507, 82567 Valid prediction for Augustus_model.g9114.t1 Valid prediction for GlimmerHMM_glimmerT_13618-T1 Valid prediction for snap_scaffold_5-snap.3023-T1 Valid prediction for GeneMark_model.22869_t Valid prediction for GlimmerHMM_glimmerT_13632-T1 Valid prediction for GlimmerHMM_glimmerT_13619-T1 Valid prediction for GlimmerHMM_glimmerT_13620-T1 Valid prediction for Augustus_model.g9119.t1 Valid prediction for CodingQuarry_transcript_52280-T1 Valid prediction for GeneMark_model.22888_t Valid prediction for Augustus_model.g9117.t1 Valid prediction for snap_scaffold_5-snap.3012-T1 Valid prediction for GeneMark_model.22893_t -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18776, rend_intergenic: 8226 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21061, rend_intergenic: 19291 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24551, rend_intergenic: 21204 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27111, rend_intergenic: 25109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41432, rend_intergenic: 30217 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74382, rend_intergenic: 73294 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 82326, rend_intergenic: 74650 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107171, rend_intergenic: 100920 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123421, rend_intergenic: 118414 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 187988, rend_intergenic: 186384 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192855, rend_intergenic: 188726 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197693, rend_intergenic: 194172 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 198181, rend_intergenic: 197969 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 203841, rend_intergenic: 200712 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 209793, rend_intergenic: 204530 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 221681, rend_intergenic: 214432 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 247242 -exon list size: 948 building trellis 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 9.9 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 10.8 10.9 11.1 11.2 11.3 11.4 11.5 11.6 11.7 11.8 11.9 12.0 12.1 12.2 12.3 12.4 12.5 12.6 12.7 12.8 12.9 13.1 13.2 13.3 13.4 13.5 13.6 13.7 13.8 13.9 14.0 14.1 14.2 14.3 14.4 14.5 14.6 14.7 14.8 14.9 15.1 15.2 15.3 15.4 15.5 15.6 15.7 15.8 15.9 16.0 16.1 16.2 16.3 16.4 16.5 16.6 16.7 16.8 16.9 17.1 17.2 17.3 17.4 17.5 17.6 17.7 17.8 17.9 18.0 18.1 18.2 18.3 18.4 18.5 18.6 18.7 18.8 18.9 19.1 19.2 19.3 19.4 19.5 19.6 19.7 19.8 19.9 20.0 20.1 20.2 20.3 20.4 20.5 20.6 20.7 20.8 20.9 21.1 21.2 21.3 21.4 21.5 21.6 21.7 21.8 21.9 22.0 22.1 22.2 22.3 22.4 22.5 22.6 22.7 22.8 22.9 23.1 23.2 23.3 23.4 23.5 23.6 23.7 23.8 23.9 24.0 24.1 24.2 24.3 24.4 24.5 24.6 24.7 24.8 24.9 25.1 25.2 25.3 25.4 25.5 25.6 25.7 25.8 25.9 26.0 26.1 26.2 26.3 26.4 26.5 26.6 26.7 26.8 26.9 27.1 27.2 27.3 27.4 27.5 27.6 27.7 27.8 27.9 28.0 28.1 28.2 28.3 28.4 28.5 28.6 28.7 28.8 28.9 29.1 29.2 29.3 29.4 29.5 29.6 29.7 29.8 29.9 30.0 30.1 30.2 30.3 30.4 30.5 30.6 30.7 30.8 30.9 31.1 31.2 31.3 31.4 31.5 31.6 31.7 31.8 31.9 32.0 32.1 32.2 32.3 32.4 32.5 32.6 32.7 32.8 32.9 33.1 33.2 33.3 33.4 33.5 33.6 33.7 33.8 33.9 34.0 34.1 34.2 34.3 34.4 34.5 34.6 34.7 34.8 34.9 35.1 35.2 35.3 35.4 35.5 35.6 35.7 35.8 35.9 36.0 36.1 36.2 36.3 36.4 36.5 36.6 36.7 36.8 36.9 37.1 37.2 37.3 37.4 37.5 37.6 37.7 37.8 37.9 38.0 38.1 38.2 38.3 38.4 38.5 38.6 38.7 38.8 38.9 39.1 39.2 39.3 39.4 39.5 39.6 39.7 39.8 39.9 40.0 40.1 40.2 40.3 40.4 40.5 40.6 40.7 40.8 40.9 41.1 41.2 41.3 41.4 41.5 41.6 41.7 41.8 41.9 42.0 42.1 42.2 42.3 42.4 42.5 42.6 42.7 42.8 42.9 43.1 43.2 43.3 43.4 43.5 43.6 43.7 43.8 43.9 44.0 44.1 44.2 44.3 44.4 44.5 44.6 44.7 44.8 44.9 45.1 45.2 45.3 45.4 45.5 45.6 45.7 45.8 45.9 46.0 46.1 46.2 46.3 46.4 46.5 46.6 46.7 46.8 46.9 47.1 47.2 47.3 47.4 47.5 47.6 47.7 47.8 47.9 48.0 48.1 48.2 48.3 48.4 48.5 48.6 48.7 48.8 48.9 49.1 49.2 49.3 49.4 49.5 49.6 49.7 49.8 49.9 50.0 50.1 50.2 50.3 50.4 50.5 50.6 50.7 50.8 50.9 51.1 51.2 51.3 51.4 51.5 51.6 51.7 51.8 51.9 52.0 52.1 52.2 52.3 52.4 52.5 52.6 52.7 52.8 52.9 53.1 53.2 53.3 53.4 53.5 53.6 53.7 53.8 53.9 54.0 54.1 54.2 54.3 54.4 54.5 54.6 54.7 54.8 54.9 55.1 55.2 55.3 55.4 55.5 55.6 55.7 55.8 55.9 56.0 56.1 56.2 56.3 56.4 56.5 56.6 56.7 56.8 56.9 57.1 57.2 57.3 57.4 57.5 57.6 57.7 57.8 57.9 58.0 58.1 58.2 58.3 58.4 58.5 58.6 58.7 58.8 58.9 59.1 59.2 59.3 59.4 59.5 59.6 59.7 59.8 59.9 60.0 60.1 60.2 60.3 60.4 60.5 60.6 60.7 60.8 60.9 61.1 61.2 61.3 61.4 61.5 61.6 61.7 61.8 61.9 62.0 62.1 62.2 62.3 62.4 62.5 62.6 62.7 62.8 62.9 63.1 63.2 63.3 63.4 63.5 63.6 63.7 63.8 63.9 64.0 64.1 64.2 64.3 64.4 64.5 64.6 64.7 64.8 64.9 65.1 65.2 65.3 65.4 65.5 65.6 65.7 65.8 65.9 66.0 66.1 66.2 66.3 66.4 66.5 66.6 66.7 66.8 66.9 67.1 67.2 67.3 67.4 67.5 67.6 67.7 67.8 67.9 68.0 68.1 68.2 68.3 68.4 68.5 68.6 68.7 68.8 68.9 69.1 69.2 69.3 69.4 69.5 69.6 69.7 69.8 69.9 70.0 70.1 70.2 70.3 70.4 70.5 70.6 70.7 70.8 70.9 71.1 71.2 71.3 71.4 71.5 71.6 71.7 71.8 71.9 72.0 72.1 72.2 72.3 72.4 72.5 72.6 72.7 72.8 72.9 73.1 73.2 73.3 73.4 73.5 73.6 73.7 73.8 73.9 74.0 74.1 74.2 74.3 74.4 74.5 74.6 74.7 74.8 74.9 75.1 75.2 75.3 75.4 75.5 75.6 75.7 75.8 75.9 76.0 76.1 76.2 76.3 76.4 76.5 76.6 76.7 76.8 76.9 77.1 77.2 77.3 77.4 77.5 77.6 77.7 77.8 77.9 78.0 78.1 78.2 78.3 78.4 78.5 78.6 78.7 78.8 78.9 79.1 79.2 79.3 79.4 79.5 79.6 79.7 79.8 79.9 80.0 80.1 80.2 80.3 80.4 80.5 80.6 80.7 80.8 80.9 81.1 81.2 81.3 81.4 81.5 81.6 81.7 81.8 81.9 82.0 82.1 82.2 82.3 82.4 82.5 82.6 82.7 82.8 82.9 83.1 83.2 83.3 83.4 83.5 83.6 83.7 83.8 83.9 84.0 84.1 84.2 84.3 84.4 84.5 84.6 84.7 84.8 84.9 85.1 85.2 85.3 85.4 85.5 85.6 85.7 85.8 85.9 86.0 86.1 86.2 86.3 86.4 86.5 86.6 86.7 86.8 86.9 87.1 87.2 87.3 87.4 87.5 87.6 87.7 87.8 87.9 88.0 88.1 88.2 88.3 88.4 88.5 88.6 88.7 88.8 88.9 89.1 89.2 89.3 89.4 89.5 89.6 89.7 89.8 89.9 90.0 90.1 90.2 90.3 90.4 90.5 90.6 90.7 90.8 90.9 91.1 91.2 91.3 91.4 91.5 91.6 91.7 91.8 91.9 92.0 92.1 92.2 92.3 92.4 92.5 92.6 92.7 92.8 92.9 93.1 93.2 93.3 93.4 93.5 93.6 93.7 93.8 93.9 94.0 94.1 94.2 94.3 94.4 94.5 94.6 94.7 94.8 94.9 95.1 95.2 95.3 95.4 95.5 95.6 95.7 95.8 95.9 96.0 96.1 96.2 96.3 96.4 96.5 96.6 96.7 96.8 96.9 97.1 97.2 97.3 97.4 97.5 97.6 97.7 97.8 97.9 98.0 98.1 98.2 98.3 98.4 98.5 98.6 98.7 98.8 98.9 99.1 99.2 99.3 99.4 99.5 99.6 99.7 99.8 99.9 -found 35 predictions from path traversal Error with prediction: snap lend_intergenic: 18776, rend_intergenic: 8226 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21061, rend_intergenic: 19291 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24551, rend_intergenic: 21204 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27111, rend_intergenic: 25109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41432, rend_intergenic: 30217 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74382, rend_intergenic: 73294 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 82326, rend_intergenic: 74650 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107171, rend_intergenic: 100920 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123421, rend_intergenic: 118414 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 187988, rend_intergenic: 186384 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192855, rend_intergenic: 188726 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 197693, rend_intergenic: 194172 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 198181, rend_intergenic: 197969 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 203841, rend_intergenic: 200712 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 209793, rend_intergenic: 204530 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 221681, rend_intergenic: 214432 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 26 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 13832 -exon list size: 52 building trellis 1.9 3.7 5.6 7.4 9.3 11.1 13.0 14.8 16.7 18.5 20.4 22.2 24.1 25.9 27.8 29.6 31.5 33.3 35.2 37.0 38.9 40.7 42.6 44.4 46.3 48.1 50.0 51.9 53.7 55.6 57.4 59.3 61.1 63.0 64.8 66.7 68.5 70.4 72.2 74.1 75.9 77.8 79.6 81.5 83.3 85.2 87.0 88.9 90.7 92.6 94.4 96.3 98.1 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 12775 -exon list size: 46 building trellis 2.1 4.2 6.2 8.3 10.4 12.5 14.6 16.7 18.8 20.8 22.9 25.0 27.1 29.2 31.2 33.3 35.4 37.5 39.6 41.7 43.8 45.8 47.9 50.0 52.1 54.2 56.2 58.3 60.4 62.5 64.6 66.7 68.8 70.8 72.9 75.0 77.1 79.2 81.2 83.3 85.4 87.5 89.6 91.7 93.8 95.8 97.9 -found 2 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 11569 -exon list size: 39 building trellis 2.4 4.9 7.3 9.8 12.2 14.6 17.1 19.5 22.0 24.4 26.8 29.3 31.7 34.1 36.6 39.0 41.5 43.9 46.3 48.8 51.2 53.7 56.1 58.5 61.0 63.4 65.9 68.3 70.7 73.2 75.6 78.0 80.5 82.9 85.4 87.8 90.2 92.7 95.1 97.6 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 235297 - 247242 -exon list size: 45 building trellis 2.1 4.3 6.4 8.5 10.6 12.8 14.9 17.0 19.1 21.3 23.4 25.5 27.7 29.8 31.9 34.0 36.2 38.3 40.4 42.6 44.7 46.8 48.9 51.1 53.2 55.3 57.4 59.6 61.7 63.8 66.0 68.1 70.2 72.3 74.5 76.6 78.7 80.9 83.0 85.1 87.2 89.4 91.5 93.6 95.7 97.9 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 1 predictions persist after filtering for low support