-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_5760022-6306536 -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 snap_scaffold_3-snap.1218-T1 Valid prediction for snap_scaffold_3-snap.1281-T1 Couldn't classify 106913, 107781 Sorry, prediction pasa_asmbl_40085.p1 fails validation. (ATG) CA 105971-105998 GT AGG (GCG) AG 106182-106392 GT AGG (TGC) AG 106623-106705 GT AGG (ATC) AG 106913-107781 AG CCA -recovered pasa_asmbl_40085.p1, initial, 105971, 105998 -recovered pasa_asmbl_40085.p1, internal, 106182, 106392 -recovered pasa_asmbl_40085.p1, internal, 106623, 106705 Valid prediction for GlimmerHMM_glimmerT_6603-T1 Valid prediction for GlimmerHMM_glimmerT_6616-T1 Valid prediction for GlimmerHMM_glimmerT_6601-T1 Valid prediction for Augustus_model.g4299.t1 Valid prediction for snap_scaffold_3-snap.1231-T1 Couldn't classify 107926, 109037 Sorry, prediction pasa_asmbl_40087.p1 fails validation. (CTC) GG 107926-109037 GT AGG (GTC) AG 109190-109647 GT CGG (ACA) AG 109836-110311 GT AGG (AAG) AG 110434-110508 TG AGT -recovered pasa_asmbl_40087.p1, terminal, 110434, 110508 -recovered pasa_asmbl_40087.p1, internal, 109190, 109647 -recovered pasa_asmbl_40087.p1, internal, 109836, 110311 Valid prediction for snap_scaffold_3-snap.1278-T1 Valid prediction for Augustus_model.g4289.t1 Valid prediction for GlimmerHMM_glimmerT_6624-T1 Valid prediction for snap_scaffold_3-snap.1215-T1 Valid prediction for Augustus_model.g4287.t1 Valid prediction for snap_scaffold_3-snap.1216-T1 Valid prediction for GlimmerHMM_glimmerT_6609-T1 Valid prediction for GlimmerHMM_glimmerT_6598-T1 Valid prediction for GlimmerHMM_glimmerT_6610-T1 Valid prediction for Augustus_model.g4285.t1 Valid prediction for GlimmerHMM_glimmerT_6634-T1 Couldn't classify 141659, 142276 Sorry, prediction pasa_asmbl_40090.p1 fails validation. (GCA) AA 141659-142276 AA AAA Valid prediction for snap_scaffold_3-snap.1219-T1 Valid prediction for snap_scaffold_3-snap.1213-T1 Valid prediction for Augustus_model.g4293.t1 Valid prediction for snap_scaffold_3-snap.1212-T1 Valid prediction for Augustus_model.g4292.t1 Valid prediction for GlimmerHMM_glimmerT_6604-T1 Couldn't classify 11463, 11661 Sorry, prediction pasa_asmbl_40083.p1 fails validation. (GGC) CG 11463-11661 GT AGG (GTT) AG 12639-12742 CT AGC -recovered pasa_asmbl_40083.p1, terminal, 12639, 12742 Valid prediction for snap_scaffold_3-snap.1226-T1 Valid prediction for Augustus_model.g4291.t1 Valid prediction for snap_scaffold_3-snap.1282-T1 Valid prediction for snap_scaffold_3-snap.1225-T1 Valid prediction for snap_scaffold_3-snap.1224-T1 Valid prediction for GlimmerHMM_glimmerT_6607-T1 Valid prediction for GlimmerHMM_glimmerT_6635-T1 Valid prediction for snap_scaffold_3-snap.1276-T1 Valid prediction for snap_scaffold_3-snap.1214-T1 Valid prediction for snap_scaffold_3-snap.1222-T1 Valid prediction for GlimmerHMM_glimmerT_6608-T1 Valid prediction for Augustus_model.g4288.t1 Valid prediction for Augustus_model.g4311.t1 Valid prediction for GlimmerHMM_glimmerT_6615-T1 Valid prediction for snap_scaffold_3-snap.1209-T1 Valid prediction for Augustus_model.g4295.t1 Valid prediction for snap_scaffold_3-snap.1229-T1 Valid prediction for snap_scaffold_3-snap.1269-T1 Valid prediction for snap_scaffold_3-snap.1220-T1 -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 GlimmerHMM_glimmerT_6631-T1 Valid prediction for snap_scaffold_3-snap.1279-T1 Valid prediction for GlimmerHMM_glimmerT_6617-T1 Valid prediction for snap_scaffold_3-snap.1274-T1 Valid prediction for snap_scaffold_3-snap.1254-T1 Valid prediction for snap_scaffold_3-snap.1228-T1 Valid prediction for pasa_asmbl_38872.p1 Valid prediction for CodingQuarry_transcript_46184-T1 Valid prediction for snap_scaffold_3-snap.1277-T1 Valid prediction for snap_scaffold_3-snap.1208-T1 Valid prediction for GlimmerHMM_glimmerT_6621-T1 Valid prediction for Augustus_model.g4300.t1 Valid prediction for snap_scaffold_3-snap.1270-T1 Valid prediction for Augustus_model.g4290.t1 Valid prediction for GlimmerHMM_glimmerT_6614-T1 Valid prediction for Augustus_model.g4312.t1 Valid prediction for snap_scaffold_3-snap.1246-T1 Valid prediction for GlimmerHMM_glimmerT_6632-T1 Valid prediction for GlimmerHMM_glimmerT_6626-T1 Valid prediction for CodingQuarry_transcript_46185-T1 Valid prediction for pasa_asmbl_38929.p1 Valid prediction for snap_scaffold_3-snap.1234-T1 Valid prediction for CodingQuarry_transcript_46189-T1 Valid prediction for snap_scaffold_3-snap.1247-T1 Valid prediction for CodingQuarry_transcript_46177-T1 Valid prediction for snap_scaffold_3-snap.1252-T1 Valid prediction for CodingQuarry_transcript_46178-T1 Valid prediction for GlimmerHMM_glimmerT_6623-T1 Valid prediction for GlimmerHMM_glimmerT_6600-T1 Couldn't classify 123874, 123971 Sorry, prediction pasa_asmbl_38910.p1 fails validation. (ATG) AA 110223-110352 GT AGG (AGC) AG 110469-110750 GT AGG (AGC) AG 110835-111113 GT AGG (ATA) AG 111199-111486 GT AGG (AGC) AG 111594-111872 GT AGG (AAT) AG 111976-112257 GT CGG (AAC) AG 112366-112644 GT AGG (AGG) AG 112766-113053 GT AGG (AAC) AG 113175-113462 GT AGG (AAC) AG 113626-113916 GT TGG (AGC) AG 114145-114432 GT AGG (AGA) AG 114512-114628 GT GAG (AGG) AG 115051-115336 GT AAG (GAC) AG 115437-115620 GT AGG (GAA) AG 115815-115898 GT AGG (CCT) AG 116031-116298 GT GGG (AAG) AG 116414-116449 GT CGG (TCC) AG 119031-119102 GT AGG (ATT) AG 119484-119558 GT AGG (CCA) AG 119739-119810 GT AGG (AAT) AG 120057-120143 GT AGG (ATG) AG 120499-120645 GT AGG (TCC) AG 120869-121462 GT AGG (TGC) AG 121978-122088 GT AGG (AAA) AG 123874-123971 CA TGC -recovered pasa_asmbl_38910.p1, initial, 110223, 110352 add_exon() Sorry, pasa_asmbl_38910.p1 120499-120645-initial-1 is invalid. -recovered pasa_asmbl_38910.p1, initial, 120499, 120645 add_exon() Sorry, pasa_asmbl_38910.p1 110469-110750-terminal-1 is invalid. -recovered pasa_asmbl_38910.p1, terminal, 110469, 110750 add_exon() Sorry, pasa_asmbl_38910.p1 110835-111113-terminal-1 is invalid. -recovered pasa_asmbl_38910.p1, terminal, 110835, 111113 -recovered pasa_asmbl_38910.p1, internal, 110469, 110750 -recovered pasa_asmbl_38910.p1, internal, 110835, 111113 -recovered pasa_asmbl_38910.p1, internal, 111199, 111486 -recovered pasa_asmbl_38910.p1, internal, 111594, 111872 -recovered pasa_asmbl_38910.p1, internal, 111976, 112257 -recovered pasa_asmbl_38910.p1, internal, 112366, 112644 -recovered pasa_asmbl_38910.p1, internal, 112766, 113053 -recovered pasa_asmbl_38910.p1, internal, 113175, 113462 -recovered pasa_asmbl_38910.p1, internal, 113626, 113916 -recovered pasa_asmbl_38910.p1, internal, 114145, 114432 -recovered pasa_asmbl_38910.p1, internal, 114512, 114628 -recovered pasa_asmbl_38910.p1, internal, 115051, 115336 -recovered pasa_asmbl_38910.p1, internal, 115437, 115620 -recovered pasa_asmbl_38910.p1, internal, 115815, 115898 -recovered pasa_asmbl_38910.p1, internal, 116031, 116298 -recovered pasa_asmbl_38910.p1, internal, 116414, 116449 -recovered pasa_asmbl_38910.p1, internal, 119031, 119102 -recovered pasa_asmbl_38910.p1, internal, 119484, 119558 -recovered pasa_asmbl_38910.p1, internal, 119739, 119810 -recovered pasa_asmbl_38910.p1, internal, 120057, 120143 -recovered pasa_asmbl_38910.p1, internal, 120499, 120645 -recovered pasa_asmbl_38910.p1, internal, 120869, 121462 -recovered pasa_asmbl_38910.p1, internal, 121978, 122088 Valid prediction for GlimmerHMM_glimmerT_6627-T1 Valid prediction for GlimmerHMM_glimmerT_6599-T1 Couldn't classify 3683, 3729 Sorry, prediction pasa_asmbl_38947.p1 fails validation. (ATG) AA 162-294 GT AGG (ATG) AG 544-669 GT GGG (CTG) AG 926-1063 GT AAG (ACC) AG 1216-1347 GT CGG (CGG) AG 1470-1607 GT AAG (ACC) AG 2391-2549 GT GGG (GCA) AG 2773-2970 GT GGG (AGG) AG 3097-3279 GT CGG (TCA) AG 3683-3729 TT AGT -recovered pasa_asmbl_38947.p1, initial, 162, 294 add_exon() Sorry, pasa_asmbl_38947.p1 544-669-initial-1 is invalid. -recovered pasa_asmbl_38947.p1, initial, 544, 669 -recovered pasa_asmbl_38947.p1, internal, 544, 669 -recovered pasa_asmbl_38947.p1, internal, 926, 1063 -recovered pasa_asmbl_38947.p1, internal, 1216, 1347 -recovered pasa_asmbl_38947.p1, internal, 1470, 1607 -recovered pasa_asmbl_38947.p1, internal, 2391, 2549 -recovered pasa_asmbl_38947.p1, internal, 2773, 2970 -recovered pasa_asmbl_38947.p1, internal, 3097, 3279 Couldn't classify 103004, 103215 Sorry, prediction pasa_asmbl_38922.p1 fails validation. (ATG) CA 102213-102354 GT AGG (AGC) AG 102625-102906 GT AGG (AGC) AG 103004-103215 GA GGG -recovered pasa_asmbl_38922.p1, initial, 102213, 102354 -recovered pasa_asmbl_38922.p1, internal, 102625, 102906 Valid prediction for snap_scaffold_3-snap.1264-T1 Couldn't classify 249367, 249485 Sorry, prediction pasa_asmbl_38892.p1 fails validation. (ATG) AA 249014-249263 GT AGG (AAC) AG 249367-249485 GA CAG -recovered pasa_asmbl_38892.p1, initial, 249014, 249263 Valid prediction for pasa_asmbl_38887.p1 Valid prediction for Augustus_model.g4308.t1 Valid prediction for GlimmerHMM_glimmerT_6622-T1 Valid prediction for snap_scaffold_3-snap.1280-T1 Valid prediction for pasa_asmbl_38941.p1 Valid prediction for GlimmerHMM_glimmerT_6602-T1 Valid prediction for HiQ_model.g4310.t1 Valid prediction for snap_scaffold_3-snap.1262-T1 Valid prediction for snap_scaffold_3-snap.1250-T1 Valid prediction for snap_scaffold_3-snap.1249-T1 Valid prediction for snap_scaffold_3-snap.1283-T1 Valid prediction for GlimmerHMM_glimmerT_6629-T1 Valid prediction for CodingQuarry_transcript_46172-T1 Valid prediction for snap_scaffold_3-snap.1248-T1 Valid prediction for snap_scaffold_3-snap.1272-T1 Valid prediction for snap_scaffold_3-snap.1275-T1 Valid prediction for HiQ_model.g4302.t1 Valid prediction for CodingQuarry_transcript_46173-T1 Couldn't classify 100722, 100767 Couldn't classify 101791, 101852 Sorry, prediction pasa_asmbl_38923.p1 fails validation. (GCT) AA 100722-100767 GT AGG (TAC) AG 101330-101608 GT GGG (AAA) AG 101791-101852 GC AAG -recovered pasa_asmbl_38923.p1, internal, 101330, 101608 -recovered pasa_asmbl_38923.p1, internal, 101791, 101852 Valid prediction for snap_scaffold_3-snap.1221-T1 Valid prediction for CodingQuarry_transcript_46182-T1 Valid prediction for Augustus_model.g4307.t1 Valid prediction for snap_scaffold_3-snap.1260-T1 Valid prediction for snap_scaffold_3-snap.1267-T1 Valid prediction for HiQ_model.g4309.t1 Valid prediction for Augustus_model.g4303.t1 Valid prediction for snap_scaffold_3-snap.1239-T1 Valid prediction for snap_scaffold_3-snap.1284-T1 Valid prediction for snap_scaffold_3-snap.1261-T1 Valid prediction for Augustus_model.g4296.t1 Couldn't classify 5662, 5791 Couldn't classify 7794, 7927 Sorry, prediction pasa_asmbl_39783.p1 fails validation. (GAC) TA 5662-5791 GT TGG (ATC) AG 5888-6031 GT AGG (GTG) AG 7794-7927 AG GCA -recovered pasa_asmbl_39783.p1, internal, 5888, 6031 Valid prediction for GlimmerHMM_glimmerT_6637-T1 Couldn't classify 247294, 247573 Couldn't classify 247808, 248304 Sorry, prediction pasa_asmbl_38893.p1 fails validation. (GTG) CA 247294-247573 GT AGG (AAC) AG 247808-248304 GG CAG Valid prediction for pasa_asmbl_38859.p1 Valid prediction for snap_scaffold_3-snap.1244-T1 Valid prediction for snap_scaffold_3-snap.1227-T1 Valid prediction for CodingQuarry_transcript_46169-T1 Valid prediction for HiQ_model.g4297.t1 Valid prediction for GlimmerHMM_glimmerT_6606-T1 Valid prediction for snap_scaffold_3-snap.1255-T1 Valid prediction for snap_scaffold_3-snap.1223-T1 Valid prediction for GlimmerHMM_glimmerT_6597-T1 Valid prediction for snap_scaffold_3-snap.1217-T1 Couldn't classify 107184, 107442 Couldn't classify 107552, 107814 Sorry, prediction pasa_asmbl_38918.p1 fails validation. (CCT) CT 107184-107442 GT AGG (AGC) AG 107552-107814 AC CTA Valid prediction for snap_scaffold_3-snap.1265-T1 Valid prediction for snap_scaffold_3-snap.1237-T1 Valid prediction for snap_scaffold_3-snap.1259-T1 Valid prediction for snap_scaffold_3-snap.1271-T1 Valid prediction for CodingQuarry_transcript_46171-T1 Valid prediction for snap_scaffold_3-snap.1266-T1 Valid prediction for CodingQuarry_transcript_46188-T1 Valid prediction for snap_scaffold_3-snap.1253-T1 Valid prediction for snap_scaffold_3-snap.1210-T1 Valid prediction for pasa_asmbl_38907.p1 Couldn't classify 88186, 88186 Sorry, prediction CodingQuarry_transcript_46183-T1 fails validation. (ATG) AA 70449-70539 GT TGG (GTT) AG 70999-71202 GT AGG (CGG) AG 71390-71677 GT GGG (GTG) AG 72217-72302 GT GGG (AAA) AG 72386-72612 GT AGG (GCC) AG 72716-72971 GT AGG (GCA) AG 75647-75712 GT CTG (GCT) AG 75828-76086 GT AGG (TGT) AG 76191-76257 GT CAG (CTT) AG 76364-76585 GT AGG (ATA) AG 76680-76822 GT AGG (AGG) AG 76908-77077 GT AGG (GAA) AG 77210-77440 GT AGG (ATC) AG 77581-77822 GT AGG (GTC) AG 77929-78149 GT TGG (GAC) AG 78238-78402 GT AGG (CTA) AG 78521-78689 GT AAG (GAT) AG 78767-80466 GT AGG (GCA) AG 80596-80877 GT AGG (GTG) AG 80968-81234 GT ATG (TGC) AG 81391-81663 GT AAG (CCA) AG 81761-82024 GT AAG (AAA) AG 82136-82396 GT AGG (GTG) AG 82506-82766 GT AGG (CTG) AG 82853-83116 GT AAG (CCA) AG 83240-83500 GT GGG (CTC) AG 83657-83917 GT CTG (CTA) AG 84015-84275 GT AGG (CTC) AG 84367-84508 GT AGG (ATA) AG 84615-84783 GT CTG (GTT) AG 84866-85097 GT CAG (TCC) AG 85205-85489 GT AGG (TTT) AG 85575-85700 GT AGG (ATG) AG 85826-86014 GT TGG (TAT) AG 87134-87178 GT AGG (AAG) AG 87952-88045 GT TGG (AGT) AG 88186-88186 GT GAG -recovered CodingQuarry_transcript_46183-T1, initial, 70449, 70539 add_exon() Sorry, CodingQuarry_transcript_46183-T1 85826-86014-initial-1 is invalid. -recovered CodingQuarry_transcript_46183-T1, initial, 85826, 86014 add_exon() Sorry, CodingQuarry_transcript_46183-T1 77581-77822-terminal-2 is invalid. -recovered CodingQuarry_transcript_46183-T1, terminal, 77581, 77822 -recovered CodingQuarry_transcript_46183-T1, internal, 70999, 71202 -recovered CodingQuarry_transcript_46183-T1, internal, 71390, 71677 -recovered CodingQuarry_transcript_46183-T1, internal, 72217, 72302 -recovered CodingQuarry_transcript_46183-T1, internal, 72386, 72612 -recovered CodingQuarry_transcript_46183-T1, internal, 72716, 72971 -recovered CodingQuarry_transcript_46183-T1, internal, 75647, 75712 -recovered CodingQuarry_transcript_46183-T1, internal, 75828, 76086 -recovered CodingQuarry_transcript_46183-T1, internal, 76191, 76257 -recovered CodingQuarry_transcript_46183-T1, internal, 76364, 76585 -recovered CodingQuarry_transcript_46183-T1, internal, 76680, 76822 -recovered CodingQuarry_transcript_46183-T1, internal, 76908, 77077 -recovered CodingQuarry_transcript_46183-T1, internal, 77210, 77440 -recovered CodingQuarry_transcript_46183-T1, internal, 77581, 77822 -recovered CodingQuarry_transcript_46183-T1, internal, 77929, 78149 -recovered CodingQuarry_transcript_46183-T1, internal, 78238, 78402 -recovered CodingQuarry_transcript_46183-T1, internal, 78521, 78689 -recovered CodingQuarry_transcript_46183-T1, internal, 78767, 80466 -recovered CodingQuarry_transcript_46183-T1, internal, 80596, 80877 -recovered CodingQuarry_transcript_46183-T1, internal, 80968, 81234 -recovered CodingQuarry_transcript_46183-T1, internal, 81391, 81663 -recovered CodingQuarry_transcript_46183-T1, internal, 81761, 82024 -recovered CodingQuarry_transcript_46183-T1, internal, 82136, 82396 -recovered CodingQuarry_transcript_46183-T1, internal, 82506, 82766 -recovered CodingQuarry_transcript_46183-T1, internal, 82853, 83116 -recovered CodingQuarry_transcript_46183-T1, internal, 83240, 83500 -recovered CodingQuarry_transcript_46183-T1, internal, 83657, 83917 -recovered CodingQuarry_transcript_46183-T1, internal, 84015, 84275 -recovered CodingQuarry_transcript_46183-T1, internal, 84367, 84508 -recovered CodingQuarry_transcript_46183-T1, internal, 84615, 84783 -recovered CodingQuarry_transcript_46183-T1, internal, 84866, 85097 -recovered CodingQuarry_transcript_46183-T1, internal, 85205, 85489 -recovered CodingQuarry_transcript_46183-T1, internal, 85575, 85700 -recovered CodingQuarry_transcript_46183-T1, internal, 85826, 86014 -recovered CodingQuarry_transcript_46183-T1, internal, 87134, 87178 -recovered CodingQuarry_transcript_46183-T1, internal, 87952, 88045 -recovered CodingQuarry_transcript_46183-T1, internal, 88186, 88186 Valid prediction for GlimmerHMM_glimmerT_6628-T1 Valid prediction for CodingQuarry_transcript_46176-T1 Valid prediction for GlimmerHMM_glimmerT_6633-T1 Valid prediction for snap_scaffold_3-snap.1268-T1 Couldn't classify 395258, 395283 Sorry, prediction pasa_asmbl_38868.p1 fails validation. (CTT) AT 395258-395283 GT AGG (GCT) AG 395400-395521 GT AAG (GTG) AG 395615-396009 CC GAC -recovered pasa_asmbl_38868.p1, terminal, 395615, 396009 -recovered pasa_asmbl_38868.p1, internal, 395400, 395521 Couldn't classify 8274, 8388 Couldn't classify 8702, 8769 Sorry, prediction pasa_asmbl_38946.p2 fails validation. (ACA) TG 8274-8388 GT CGG (ATC) AG 8494-8622 GT TGG (CTC) AG 8702-8769 AA ACA -recovered pasa_asmbl_38946.p2, internal, 8494, 8622 Valid prediction for CodingQuarry_transcript_46187-T1 Valid prediction for Augustus_model.g4284.t1 Valid prediction for snap_scaffold_3-snap.1236-T1 Valid prediction for snap_scaffold_3-snap.1263-T1 Valid prediction for pasa_asmbl_38934.p3 Valid prediction for CodingQuarry_transcript_46170-T1 Valid prediction for snap_scaffold_3-snap.1251-T1 Valid prediction for snap_scaffold_3-snap.1211-T1 Valid prediction for GlimmerHMM_glimmerT_6625-T1 Valid prediction for snap_scaffold_3-snap.1240-T1 Couldn't classify 105389, 105563 Couldn't classify 106394, 106521 Sorry, prediction pasa_asmbl_38921.p1 fails validation. (TTT) CT 105389-105563 GT AGG (AAC) AG 105651-105929 GT AGG (AAC) AG 106027-106305 GT CGG (ATC) AG 106394-106521 AA AGA -recovered pasa_asmbl_38921.p1, internal, 105651, 105929 -recovered pasa_asmbl_38921.p1, internal, 106027, 106305 Valid prediction for Augustus_model.g4304.t1 Valid prediction for snap_scaffold_3-snap.1256-T1 Valid prediction for GlimmerHMM_glimmerT_6630-T1 Valid prediction for CodingQuarry_transcript_46168-T1 Valid prediction for GlimmerHMM_glimmerT_6613-T1 Valid prediction for snap_scaffold_3-snap.1245-T1 Valid prediction for CodingQuarry_transcript_46186-T1 Valid prediction for GlimmerHMM_glimmerT_6618-T1 Valid prediction for snap_scaffold_3-snap.1233-T1 Valid prediction for HiQ_model.g4301.t1 Valid prediction for HiQ_model.g4298.t1 Valid prediction for snap_scaffold_3-snap.1241-T1 Valid prediction for snap_scaffold_3-snap.1230-T1 Valid prediction for pasa_asmbl_38894.p1 Valid prediction for snap_scaffold_3-snap.1242-T1 Couldn't classify 14280, 14484 Sorry, prediction pasa_asmbl_38943.p1 fails validation. (TGG) AC 14280-14484 GT CAG (TCT) AG 14647-14763 GT CGG (GAG) AG 14935-15099 GT AGG (ACA) AG 15227-15382 GT AGG (ACC) AG 15514-15627 GT CCG (CCC) AG 15739-16026 GT AGG (CGA) AG 16176-16363 GT TGG (ATT) AG 17160-17247 GT CAG (CCA) AG 17414-17593 GT AGG (GTT) AG 17724-17813 GT AGG (CCA) AG 17956-18147 GT GGG (GTC) AG 18246-18335 GT TCG (AGC) AG 18697-18793 GT AAG (CAG) AG 18900-19272 GT AGG (ATG) AG 19542-19680 GT CGG (TCC) AG 19873-20034 GT CAG (AAT) AG 20677-20802 GT ACG (ATG) AG 20939-21045 GT AGG (GGC) AG 21251-21370 GT TGG (AAC) AG 21458-21526 AG AGA -recovered pasa_asmbl_38943.p1, initial, 19542, 19680 -recovered pasa_asmbl_38943.p1, initial, 20939, 21045 -recovered pasa_asmbl_38943.p1, terminal, 21458, 21526 -recovered pasa_asmbl_38943.p1, internal, 14647, 14763 -recovered pasa_asmbl_38943.p1, internal, 14935, 15099 -recovered pasa_asmbl_38943.p1, internal, 15227, 15382 -recovered pasa_asmbl_38943.p1, internal, 15514, 15627 -recovered pasa_asmbl_38943.p1, internal, 15739, 16026 -recovered pasa_asmbl_38943.p1, internal, 16176, 16363 -recovered pasa_asmbl_38943.p1, internal, 17160, 17247 -recovered pasa_asmbl_38943.p1, internal, 17414, 17593 -recovered pasa_asmbl_38943.p1, internal, 17724, 17813 -recovered pasa_asmbl_38943.p1, internal, 17956, 18147 -recovered pasa_asmbl_38943.p1, internal, 18246, 18335 -recovered pasa_asmbl_38943.p1, internal, 18697, 18793 -recovered pasa_asmbl_38943.p1, internal, 18900, 19272 -recovered pasa_asmbl_38943.p1, internal, 19542, 19680 -recovered pasa_asmbl_38943.p1, internal, 19873, 20034 -recovered pasa_asmbl_38943.p1, internal, 20677, 20802 -recovered pasa_asmbl_38943.p1, internal, 20939, 21045 -recovered pasa_asmbl_38943.p1, internal, 21251, 21370 Valid prediction for snap_scaffold_3-snap.1238-T1 Valid prediction for GlimmerHMM_glimmerT_6605-T1 Valid prediction for snap_scaffold_3-snap.1273-T1 Valid prediction for Augustus_model.g4306.t1 Valid prediction for snap_scaffold_3-snap.1257-T1 Valid prediction for CodingQuarry_transcript_46179-T1 Valid prediction for pasa_asmbl_38902.p1 Valid prediction for snap_scaffold_3-snap.1258-T1 Couldn't classify 389913, 389965 Sorry, prediction pasa_asmbl_38870.p1 fails validation. (ATG) TC 382962-383022 GT AGG (AAG) AG 385578-385607 GT GGG (ATG) AG 385783-386238 GT AGG (AAG) AG 386355-386384 GT AGG (ATC) AG 387140-387163 GT AGG (GTG) AG 387280-387363 GT GGG (CTC) AG 388562-388585 GT AGG (ATG) AG 388724-388744 GT AGG (AGG) AG 389717-389836 GT GGG (AAG) AG 389913-389965 GG AGG -recovered pasa_asmbl_38870.p1, initial, 382962, 383022 add_exon() Sorry, pasa_asmbl_38870.p1 385783-386238-initial-1 is invalid. -recovered pasa_asmbl_38870.p1, initial, 385783, 386238 -recovered pasa_asmbl_38870.p1, initial, 388724, 388744 -recovered pasa_asmbl_38870.p1, internal, 385578, 385607 -recovered pasa_asmbl_38870.p1, internal, 385783, 386238 -recovered pasa_asmbl_38870.p1, internal, 386355, 386384 -recovered pasa_asmbl_38870.p1, internal, 387140, 387163 -recovered pasa_asmbl_38870.p1, internal, 387280, 387363 -recovered pasa_asmbl_38870.p1, internal, 388562, 388585 -recovered pasa_asmbl_38870.p1, internal, 388724, 388744 -recovered pasa_asmbl_38870.p1, internal, 389717, 389836 Valid prediction for snap_scaffold_3-snap.1243-T1 Valid prediction for GlimmerHMM_glimmerT_6636-T1 Valid prediction for GlimmerHMM_glimmerT_6612-T1 Valid prediction for GlimmerHMM_glimmerT_6611-T1 Valid prediction for snap_scaffold_3-snap.1232-T1 Valid prediction for pasa_asmbl_38883.p1 Valid prediction for HiQ_model.g4305.t1 Valid prediction for snap_scaffold_3-snap.1235-T1 Couldn't classify 12103, 12187 Couldn't classify 14003, 14061 Sorry, prediction pasa_asmbl_38945.p1 fails validation. (TTG) CT 12103-12187 GT AGG (ACA) AG 12344-12535 GT AGG (ATG) AG 13039-13311 GT TGG (CTG) AG 13680-13871 GT GAG (ACC) AG 14003-14061 AG AGA add_exon() Sorry, pasa_asmbl_38945.p1 13039-13311-initial-1 is invalid. -recovered pasa_asmbl_38945.p1, initial, 13039, 13311 -recovered pasa_asmbl_38945.p1, internal, 12344, 12535 -recovered pasa_asmbl_38945.p1, internal, 13039, 13311 -recovered pasa_asmbl_38945.p1, internal, 13680, 13871 Valid prediction for GlimmerHMM_glimmerT_6620-T1 Valid prediction for HiQ_model.g4286.t1 Valid prediction for GlimmerHMM_glimmerT_6619-T1 Valid prediction for Augustus_model.g4294.t1 Couldn't classify 250156, 250384 Couldn't classify 250503, 250747 Sorry, prediction pasa_asmbl_38891.p1 fails validation. (AAC) GA 250156-250384 GT AGG (AAC) AG 250503-250747 AA GGA -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 127732, rend_intergenic: 124284 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133811, rend_intergenic: 133688 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 138939, rend_intergenic: 134108 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 151112, rend_intergenic: 150374 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 163551, rend_intergenic: 159901 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 484667, rend_intergenic: 482066 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 497496, rend_intergenic: 494828 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 511539, rend_intergenic: 502879 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 546515 -exon list size: 1289 building trellis 0.1 0.2 0.2 0.3 0.4 0.5 0.5 0.6 0.7 0.8 0.9 0.9 1.0 1.1 1.2 1.2 1.3 1.4 1.5 1.5 1.6 1.7 1.8 1.9 1.9 2.0 2.1 2.2 2.2 2.3 2.4 2.5 2.6 2.6 2.7 2.8 2.9 2.9 3.0 3.1 3.2 3.3 3.3 3.4 3.5 3.6 3.6 3.7 3.8 3.9 4.0 4.0 4.1 4.2 4.3 4.3 4.4 4.5 4.6 4.6 4.7 4.8 4.9 5.0 5.0 5.1 5.2 5.3 5.3 5.4 5.5 5.6 5.7 5.7 5.8 5.9 6.0 6.0 6.1 6.2 6.3 6.4 6.4 6.5 6.6 6.7 6.7 6.8 6.9 7.0 7.0 7.1 7.2 7.3 7.4 7.4 7.5 7.6 7.7 7.7 7.8 7.9 8.0 8.1 8.1 8.2 8.3 8.4 8.4 8.5 8.6 8.7 8.8 8.8 8.9 9.0 9.1 9.1 9.2 9.3 9.4 9.5 9.5 9.6 9.7 9.8 9.8 9.9 10.0 10.1 10.1 10.2 10.3 10.4 10.5 10.5 10.6 10.7 10.8 10.8 10.9 11.0 11.1 11.2 11.2 11.3 11.4 11.5 11.5 11.6 11.7 11.8 11.9 11.9 12.0 12.1 12.2 12.2 12.3 12.4 12.5 12.5 12.6 12.7 12.8 12.9 12.9 13.0 13.1 13.2 13.2 13.3 13.4 13.5 13.6 13.6 13.7 13.8 13.9 13.9 14.0 14.1 14.2 14.3 14.3 14.4 14.5 14.6 14.6 14.7 14.8 14.9 14.9 15.0 15.1 15.2 15.3 15.3 15.4 15.5 15.6 15.6 15.7 15.8 15.9 16.0 16.0 16.1 16.2 16.3 16.3 16.4 16.5 16.6 16.7 16.7 16.8 16.9 17.0 17.0 17.1 17.2 17.3 17.4 17.4 17.5 17.6 17.7 17.7 17.8 17.9 18.0 18.0 18.1 18.2 18.3 18.4 18.4 18.5 18.6 18.7 18.7 18.8 18.9 19.0 19.1 19.1 19.2 19.3 19.4 19.4 19.5 19.6 19.7 19.8 19.8 19.9 20.0 20.1 20.1 20.2 20.3 20.4 20.4 20.5 20.6 20.7 20.8 20.8 20.9 21.0 21.1 21.1 21.2 21.3 21.4 21.5 21.5 21.6 21.7 21.8 21.8 21.9 22.0 22.1 22.2 22.2 22.3 22.4 22.5 22.5 22.6 22.7 22.8 22.9 22.9 23.0 23.1 23.2 23.2 23.3 23.4 23.5 23.5 23.6 23.7 23.8 23.9 23.9 24.0 24.1 24.2 24.2 24.3 24.4 24.5 24.6 24.6 24.7 24.8 24.9 24.9 25.0 25.1 25.2 25.3 25.3 25.4 25.5 25.6 25.6 25.7 25.8 25.9 25.9 26.0 26.1 26.2 26.3 26.3 26.4 26.5 26.6 26.6 26.7 26.8 26.9 27.0 27.0 27.1 27.2 27.3 27.3 27.4 27.5 27.6 27.7 27.7 27.8 27.9 28.0 28.0 28.1 28.2 28.3 28.4 28.4 28.5 28.6 28.7 28.7 28.8 28.9 29.0 29.0 29.1 29.2 29.3 29.4 29.4 29.5 29.6 29.7 29.7 29.8 29.9 30.0 30.1 30.1 30.2 30.3 30.4 30.4 30.5 30.6 30.7 30.8 30.8 30.9 31.0 31.1 31.1 31.2 31.3 31.4 31.4 31.5 31.6 31.7 31.8 31.8 31.9 32.0 32.1 32.1 32.2 32.3 32.4 32.5 32.5 32.6 32.7 32.8 32.8 32.9 33.0 33.1 33.2 33.2 33.3 33.4 33.5 33.5 33.6 33.7 33.8 33.8 33.9 34.0 34.1 34.2 34.2 34.3 34.4 34.5 34.5 34.6 34.7 34.8 34.9 34.9 35.0 35.1 35.2 35.2 35.3 35.4 35.5 35.6 35.6 35.7 35.8 35.9 35.9 36.0 36.1 36.2 36.3 36.3 36.4 36.5 36.6 36.6 36.7 36.8 36.9 36.9 37.0 37.1 37.2 37.3 37.3 37.4 37.5 37.6 37.6 37.7 37.8 37.9 38.0 38.0 38.1 38.2 38.3 38.3 38.4 38.5 38.6 38.7 38.7 38.8 38.9 39.0 39.0 39.1 39.2 39.3 39.3 39.4 39.5 39.6 39.7 39.7 39.8 39.9 40.0 40.0 40.1 40.2 40.3 40.4 40.4 40.5 40.6 40.7 40.7 40.8 40.9 41.0 41.1 41.1 41.2 41.3 41.4 41.4 41.5 41.6 41.7 41.8 41.8 41.9 42.0 42.1 42.1 42.2 42.3 42.4 42.4 42.5 42.6 42.7 42.8 42.8 42.9 43.0 43.1 43.1 43.2 43.3 43.4 43.5 43.5 43.6 43.7 43.8 43.8 43.9 44.0 44.1 44.2 44.2 44.3 44.4 44.5 44.5 44.6 44.7 44.8 44.8 44.9 45.0 45.1 45.2 45.2 45.3 45.4 45.5 45.5 45.6 45.7 45.8 45.9 45.9 46.0 46.1 46.2 46.2 46.3 46.4 46.5 46.6 46.6 46.7 46.8 46.9 46.9 47.0 47.1 47.2 47.3 47.3 47.4 47.5 47.6 47.6 47.7 47.8 47.9 47.9 48.0 48.1 48.2 48.3 48.3 48.4 48.5 48.6 48.6 48.7 48.8 48.9 49.0 49.0 49.1 49.2 49.3 49.3 49.4 49.5 49.6 49.7 49.7 49.8 49.9 50.0 50.0 50.1 50.2 50.3 50.3 50.4 50.5 50.6 50.7 50.7 50.8 50.9 51.0 51.0 51.1 51.2 51.3 51.4 51.4 51.5 51.6 51.7 51.7 51.8 51.9 52.0 52.1 52.1 52.2 52.3 52.4 52.4 52.5 52.6 52.7 52.7 52.8 52.9 53.0 53.1 53.1 53.2 53.3 53.4 53.4 53.5 53.6 53.7 53.8 53.8 53.9 54.0 54.1 54.1 54.2 54.3 54.4 54.5 54.5 54.6 54.7 54.8 54.8 54.9 55.0 55.1 55.2 55.2 55.3 55.4 55.5 55.5 55.6 55.7 55.8 55.8 55.9 56.0 56.1 56.2 56.2 56.3 56.4 56.5 56.5 56.6 56.7 56.8 56.9 56.9 57.0 57.1 57.2 57.2 57.3 57.4 57.5 57.6 57.6 57.7 57.8 57.9 57.9 58.0 58.1 58.2 58.2 58.3 58.4 58.5 58.6 58.6 58.7 58.8 58.9 58.9 59.0 59.1 59.2 59.3 59.3 59.4 59.5 59.6 59.6 59.7 59.8 59.9 60.0 60.0 60.1 60.2 60.3 60.3 60.4 60.5 60.6 60.7 60.7 60.8 60.9 61.0 61.0 61.1 61.2 61.3 61.3 61.4 61.5 61.6 61.7 61.7 61.8 61.9 62.0 62.0 62.1 62.2 62.3 62.4 62.4 62.5 62.6 62.7 62.7 62.8 62.9 63.0 63.1 63.1 63.2 63.3 63.4 63.4 63.5 63.6 63.7 63.7 63.8 63.9 64.0 64.1 64.1 64.2 64.3 64.4 64.4 64.5 64.6 64.7 64.8 64.8 64.9 65.0 65.1 65.1 65.2 65.3 65.4 65.5 65.5 65.6 65.7 65.8 65.8 65.9 66.0 66.1 66.2 66.2 66.3 66.4 66.5 66.5 66.6 66.7 66.8 66.8 66.9 67.0 67.1 67.2 67.2 67.3 67.4 67.5 67.5 67.6 67.7 67.8 67.9 67.9 68.0 68.1 68.2 68.2 68.3 68.4 68.5 68.6 68.6 68.7 68.8 68.9 68.9 69.0 69.1 69.2 69.2 69.3 69.4 69.5 69.6 69.6 69.7 69.8 69.9 69.9 70.0 70.1 70.2 70.3 70.3 70.4 70.5 70.6 70.6 70.7 70.8 70.9 71.0 71.0 71.1 71.2 71.3 71.3 71.4 71.5 71.6 71.6 71.7 71.8 71.9 72.0 72.0 72.1 72.2 72.3 72.3 72.4 72.5 72.6 72.7 72.7 72.8 72.9 73.0 73.0 73.1 73.2 73.3 73.4 73.4 73.5 73.6 73.7 73.7 73.8 73.9 74.0 74.1 74.1 74.2 74.3 74.4 74.4 74.5 74.6 74.7 74.7 74.8 74.9 75.0 75.1 75.1 75.2 75.3 75.4 75.4 75.5 75.6 75.7 75.8 75.8 75.9 76.0 76.1 76.1 76.2 76.3 76.4 76.5 76.5 76.6 76.7 76.8 76.8 76.9 77.0 77.1 77.1 77.2 77.3 77.4 77.5 77.5 77.6 77.7 77.8 77.8 77.9 78.0 78.1 78.2 78.2 78.3 78.4 78.5 78.5 78.6 78.7 78.8 78.9 78.9 79.0 79.1 79.2 79.2 79.3 79.4 79.5 79.6 79.6 79.7 79.8 79.9 79.9 80.0 80.1 80.2 80.2 80.3 80.4 80.5 80.6 80.6 80.7 80.8 80.9 80.9 81.0 81.1 81.2 81.3 81.3 81.4 81.5 81.6 81.6 81.7 81.8 81.9 82.0 82.0 82.1 82.2 82.3 82.3 82.4 82.5 82.6 82.6 82.7 82.8 82.9 83.0 83.0 83.1 83.2 83.3 83.3 83.4 83.5 83.6 83.7 83.7 83.8 83.9 84.0 84.0 84.1 84.2 84.3 84.4 84.4 84.5 84.6 84.7 84.7 84.8 84.9 85.0 85.1 85.1 85.2 85.3 85.4 85.4 85.5 85.6 85.7 85.7 85.8 85.9 86.0 86.1 86.1 86.2 86.3 86.4 86.4 86.5 86.6 86.7 86.8 86.8 86.9 87.0 87.1 87.1 87.2 87.3 87.4 87.5 87.5 87.6 87.7 87.8 87.8 87.9 88.0 88.1 88.1 88.2 88.3 88.4 88.5 88.5 88.6 88.7 88.8 88.8 88.9 89.0 89.1 89.2 89.2 89.3 89.4 89.5 89.5 89.6 89.7 89.8 89.9 89.9 90.0 90.1 90.2 90.2 90.3 90.4 90.5 90.5 90.6 90.7 90.8 90.9 90.9 91.0 91.1 91.2 91.2 91.3 91.4 91.5 91.6 91.6 91.7 91.8 91.9 91.9 92.0 92.1 92.2 92.3 92.3 92.4 92.5 92.6 92.6 92.7 92.8 92.9 93.0 93.0 93.1 93.2 93.3 93.3 93.4 93.5 93.6 93.6 93.7 93.8 93.9 94.0 94.0 94.1 94.2 94.3 94.3 94.4 94.5 94.6 94.7 94.7 94.8 94.9 95.0 95.0 95.1 95.2 95.3 95.4 95.4 95.5 95.6 95.7 95.7 95.8 95.9 96.0 96.0 96.1 96.2 96.3 96.4 96.4 96.5 96.6 96.7 96.7 96.8 96.9 97.0 97.1 97.1 97.2 97.3 97.4 97.4 97.5 97.6 97.7 97.8 97.8 97.9 98.0 98.1 98.1 98.2 98.3 98.4 98.5 98.5 98.6 98.7 98.8 98.8 98.9 99.0 99.1 99.1 99.2 99.3 99.4 99.5 99.5 99.6 99.7 99.8 99.8 99.9 -found 38 predictions from path traversal Error with prediction: snap lend_intergenic: 127732, rend_intergenic: 124284 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133811, rend_intergenic: 133688 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 138939, rend_intergenic: 134108 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 151112, rend_intergenic: 150374 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 163551, rend_intergenic: 159901 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 484667, rend_intergenic: 482066 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 497496, rend_intergenic: 494828 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 511539, rend_intergenic: 502879 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 36 predictions persist after filtering for low support