-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_5289748-5512525 -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 HiQ_model.g14727.t1 Valid prediction for HiQ_model.g14726.t1 Valid prediction for snap_scaffold_9-snap.1129-T1 Valid prediction for snap_scaffold_9-snap.1133-T1 Valid prediction for Augustus_model.g14729.t1 Valid prediction for snap_scaffold_9-snap.1125-T1 Valid prediction for GlimmerHMM_glimmerT_22160-T1 Valid prediction for Augustus_model.g14721.t1 Valid prediction for CodingQuarry_transcript_62177-T1 Couldn't classify 183564, 183724 Couldn't classify 183999, 184133 Sorry, prediction CodingQuarry_transcript_62182-T1 fails validation. (ATG) AG 182794-182832 GT AAG (TGG) AG 183387-183470 GT AGG (GTC) AG 183564-183724 AT TCA (ATA) AC 183999-184133 GT AGG (GTT) AG 184221-184407 TT AAT -recovered CodingQuarry_transcript_62182-T1, initial, 182794, 182832 -recovered CodingQuarry_transcript_62182-T1, terminal, 184221, 184407 -recovered CodingQuarry_transcript_62182-T1, internal, 182794, 182832 -recovered CodingQuarry_transcript_62182-T1, internal, 183387, 183470 Couldn't classify 101603, 101773 Couldn't classify 103349, 103411 Sorry, prediction pasa_asmbl_54035.p1 fails validation. (CTC) TC 101603-101773 GT AGG (GGG) AG 101885-102042 GT GGG (AGA) AG 102162-102283 GT TGG (ACA) AG 102452-102583 GT AGG (AGA) AG 102771-102882 GT CGG (CCC) AG 103107-103206 GT AGG (GTG) AG 103349-103411 AG ACA -recovered pasa_asmbl_54035.p1, internal, 101885, 102042 -recovered pasa_asmbl_54035.p1, internal, 102162, 102283 -recovered pasa_asmbl_54035.p1, internal, 102452, 102583 -recovered pasa_asmbl_54035.p1, internal, 102771, 102882 -recovered pasa_asmbl_54035.p1, internal, 103107, 103206 Valid prediction for snap_scaffold_9-snap.1132-T1 Valid prediction for snap_scaffold_9-snap.1115-T1 Valid prediction for snap_scaffold_9-snap.1113-T1 Valid prediction for Augustus_model.g14728.t1 Valid prediction for GlimmerHMM_glimmerT_22169-T1 Valid prediction for CodingQuarry_transcript_62180-T1 Valid prediction for snap_scaffold_9-snap.1117-T1 Valid prediction for GlimmerHMM_glimmerT_22162-T1 Valid prediction for snap_scaffold_9-snap.1128-T1 Valid prediction for Augustus_model.g14717.t1 Valid prediction for snap_scaffold_9-snap.1139-T1 Valid prediction for pasa_asmbl_54740.p1 Valid prediction for pasa_asmbl_54034.p1 Valid prediction for snap_scaffold_9-snap.1138-T1 Valid prediction for GlimmerHMM_glimmerT_22166-T1 Valid prediction for GlimmerHMM_glimmerT_22141-T1 Valid prediction for Augustus_model.g14731.t1 Valid prediction for GlimmerHMM_glimmerT_22149-T1 Valid prediction for GlimmerHMM_glimmerT_22158-T1 Valid prediction for GlimmerHMM_glimmerT_22153-T1 Valid prediction for snap_scaffold_9-snap.1121-T1 Valid prediction for snap_scaffold_9-snap.1145-T1 Valid prediction for GlimmerHMM_glimmerT_22156-T1 Valid prediction for GlimmerHMM_glimmerT_22159-T1 Valid prediction for GlimmerHMM_glimmerT_22148-T1 Valid prediction for snap_scaffold_9-snap.1118-T1 Valid prediction for snap_scaffold_9-snap.1141-T1 Valid prediction for GlimmerHMM_glimmerT_22167-T1 Valid prediction for GlimmerHMM_glimmerT_22144-T1 Valid prediction for snap_scaffold_9-snap.1111-T1 Valid prediction for GlimmerHMM_glimmerT_22157-T1 Couldn't classify 111679, 111750 Sorry, prediction pasa_asmbl_54039.p1 fails validation. (GGC) CA 111679-111750 GT CGG (GGG) AG 111979-112050 GT AGG (CTC) AG 112669-112789 GT GTG (GTG) AG 112934-113039 GT AGG (GGC) AG 115024-115173 GT AGG (AGC) AG 115645-115692 GT AGG (TCC) AG 117410-117511 GT AGG (CTC) AG 118072-118165 AC GAA add_exon() Sorry, pasa_asmbl_54039.p1 112934-113039-terminal-3 is invalid. -recovered pasa_asmbl_54039.p1, terminal, 112934, 113039 -recovered pasa_asmbl_54039.p1, terminal, 118072, 118165 -recovered pasa_asmbl_54039.p1, internal, 111979, 112050 -recovered pasa_asmbl_54039.p1, internal, 112669, 112789 -recovered pasa_asmbl_54039.p1, internal, 112934, 113039 -recovered pasa_asmbl_54039.p1, internal, 115024, 115173 -recovered pasa_asmbl_54039.p1, internal, 115645, 115692 -recovered pasa_asmbl_54039.p1, internal, 117410, 117511 Valid prediction for snap_scaffold_9-snap.1144-T1 Valid prediction for GlimmerHMM_glimmerT_22168-T1 Valid prediction for snap_scaffold_9-snap.1147-T1 Valid prediction for snap_scaffold_9-snap.1116-T1 Valid prediction for snap_scaffold_9-snap.1119-T1 Valid prediction for snap_scaffold_9-snap.1136-T1 Couldn't classify 63954, 64250 Sorry, prediction pasa_asmbl_54703.p2 fails validation. (ATG) CC 63954-64250 CA AGC Valid prediction for Augustus_model.g14735.t1 Valid prediction for snap_scaffold_9-snap.1146-T1 Valid prediction for GlimmerHMM_glimmerT_22150-T1 Valid prediction for Augustus_model.g14730.t1 Valid prediction for pasa_asmbl_54670.p1 Valid prediction for Augustus_model.g14723.t1 Valid prediction for snap_scaffold_9-snap.1126-T1 Couldn't classify 7963, 8130 Sorry, prediction pasa_asmbl_54024.p1 fails validation. (TGC) CG 7963-8130 GT AGG (ACC) AG 8258-8358 GT ATG (GTT) AG 8480-8531 GT AGG (GAG) AG 8727-8822 TG AGT -recovered pasa_asmbl_54024.p1, terminal, 8727, 8822 -recovered pasa_asmbl_54024.p1, internal, 8258, 8358 -recovered pasa_asmbl_54024.p1, internal, 8480, 8531 Valid prediction for snap_scaffold_9-snap.1140-T1 Valid prediction for HiQ_model.g14734.t1 Valid prediction for snap_scaffold_9-snap.1134-T1 Valid prediction for pasa_asmbl_54045.p1 Valid prediction for GlimmerHMM_glimmerT_22165-T1 Valid prediction for Augustus_model.g14724.t1 Valid prediction for GlimmerHMM_glimmerT_22161-T1 Valid prediction for Augustus_model.g14720.t1 Valid prediction for CodingQuarry_transcript_62179-T1 Valid prediction for Augustus_model.g14733.t1 Couldn't classify 110235, 110274 Sorry, prediction pasa_asmbl_54037.p1 fails validation. (ATG) TT 106752-106908 GT ATG (ATA) AG 107306-107375 GT AGG (ATT) AG 107479-107560 GT AGG (TTG) AG 107800-107873 GT AGG (ATT) AG 108129-108380 GT AGG (AGC) AG 108765-108830 GT GTG (AGG) AG 109192-109281 GT AGG (GTC) AG 109417-109470 GT GAG (AAG) AG 110235-110274 GA AGG -recovered pasa_asmbl_54037.p1, initial, 106752, 106908 add_exon() Sorry, pasa_asmbl_54037.p1 107306-107375-terminal-3 is invalid. -recovered pasa_asmbl_54037.p1, terminal, 107306, 107375 add_exon() Sorry, pasa_asmbl_54037.p1 109417-109470-terminal-1 is invalid. -recovered pasa_asmbl_54037.p1, terminal, 109417, 109470 -recovered pasa_asmbl_54037.p1, internal, 107306, 107375 -recovered pasa_asmbl_54037.p1, internal, 107479, 107560 -recovered pasa_asmbl_54037.p1, internal, 107800, 107873 -recovered pasa_asmbl_54037.p1, internal, 108129, 108380 -recovered pasa_asmbl_54037.p1, internal, 108765, 108830 -recovered pasa_asmbl_54037.p1, internal, 109192, 109281 -recovered pasa_asmbl_54037.p1, internal, 109417, 109470 Valid prediction for GlimmerHMM_glimmerT_22142-T1 Valid prediction for GlimmerHMM_glimmerT_22155-T1 Couldn't classify 183564, 183724 Couldn't classify 183999, 184133 Sorry, prediction pasa_asmbl_54046.p1 fails validation. (ATG) AG 182794-182832 GT AAG (TGG) AG 183387-183470 GT AGG (GTC) AG 183564-183724 AT TCA (ATA) AC 183999-184133 GT AGG (GTT) AG 184221-184407 TT AAT -recovered pasa_asmbl_54046.p1, initial, 182794, 182832 -recovered pasa_asmbl_54046.p1, terminal, 184221, 184407 -recovered pasa_asmbl_54046.p1, internal, 182794, 182832 -recovered pasa_asmbl_54046.p1, internal, 183387, 183470 Couldn't classify 53512, 53659 Couldn't classify 54916, 55010 Sorry, prediction pasa_asmbl_54031.p1 fails validation. (TCC) AT 53512-53659 GT AGG (AGC) AG 53763-53950 GT AGG (GGA) AG 54388-54529 GT AGG (GAA) AG 54916-55010 GG GCG -recovered pasa_asmbl_54031.p1, internal, 53763, 53950 -recovered pasa_asmbl_54031.p1, internal, 54388, 54529 -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_22147-T1 Couldn't classify 189271, 189465 Sorry, prediction pasa_asmbl_55005.p1 fails validation. (ATG) TA 180424-180505 GT AGG (AGC) AG 183412-183622 GT AGG (GAT) AG 183969-184069 GT GGG (GTC) AG 184627-184809 GT AGG (GTT) AG 187111-187191 GT TGG (TTC) AG 187312-187427 GT AGG (ACA) AG 189271-189465 GG GAG -recovered pasa_asmbl_55005.p1, initial, 180424, 180505 -recovered pasa_asmbl_55005.p1, internal, 183412, 183622 -recovered pasa_asmbl_55005.p1, internal, 183969, 184069 -recovered pasa_asmbl_55005.p1, internal, 184627, 184809 -recovered pasa_asmbl_55005.p1, internal, 187111, 187191 -recovered pasa_asmbl_55005.p1, internal, 187312, 187427 Valid prediction for GlimmerHMM_glimmerT_22154-T1 Valid prediction for snap_scaffold_9-snap.1124-T1 Valid prediction for GlimmerHMM_glimmerT_22151-T1 Valid prediction for HiQ_model.g14718.t1 Valid prediction for snap_scaffold_9-snap.1143-T1 Valid prediction for Augustus_model.g14725.t1 Valid prediction for snap_scaffold_9-snap.1114-T1 Valid prediction for snap_scaffold_9-snap.1123-T1 Valid prediction for snap_scaffold_9-snap.1120-T1 Valid prediction for snap_scaffold_9-snap.1122-T1 Valid prediction for HiQ_model.g14732.t1 Valid prediction for pasa_asmbl_55008.p1 Valid prediction for snap_scaffold_9-snap.1127-T1 Valid prediction for snap_scaffold_9-snap.1135-T1 Valid prediction for snap_scaffold_9-snap.1142-T1 Valid prediction for snap_scaffold_9-snap.1137-T1 Valid prediction for snap_scaffold_9-snap.1131-T1 Valid prediction for snap_scaffold_9-snap.1130-T1 Valid prediction for CodingQuarry_transcript_62181-T1 Valid prediction for Augustus_model.g14719.t1 Valid prediction for GlimmerHMM_glimmerT_22143-T1 Valid prediction for GlimmerHMM_glimmerT_22164-T1 Valid prediction for Augustus_model.g14722.t1 Valid prediction for GlimmerHMM_glimmerT_22146-T1 Couldn't classify 196770, 196904 Sorry, prediction pasa_asmbl_55003.p1 fails validation. (GAG) CA 196770-196904 GT AGG (ACG) AG 197168-197312 GT TGG (AAA) AG 197495-197518 GT AGG (GCC) AG 198529-198658 GT GGG (TGA) AG 199066-199157 GT CTG (TGA) AG 201112-201207 GT AGG (GGG) AG 201536-201613 GT GAG (TCG) AG 201886-201978 GT AGG (GTG) AG 202164-202285 GT TGG (TAC) AG 203083-203192 GT ATG (GCT) AG 203524-203683 GT TGG (TGG) AG 204066-204202 GT ATG (CTA) AG 204315-204768 TG AGT add_exon() Sorry, pasa_asmbl_55003.p1 201886-201978-terminal-1 is invalid. -recovered pasa_asmbl_55003.p1, terminal, 201886, 201978 -recovered pasa_asmbl_55003.p1, terminal, 204315, 204768 -recovered pasa_asmbl_55003.p1, internal, 197168, 197312 -recovered pasa_asmbl_55003.p1, internal, 197495, 197518 -recovered pasa_asmbl_55003.p1, internal, 198529, 198658 -recovered pasa_asmbl_55003.p1, internal, 199066, 199157 -recovered pasa_asmbl_55003.p1, internal, 201112, 201207 -recovered pasa_asmbl_55003.p1, internal, 201536, 201613 -recovered pasa_asmbl_55003.p1, internal, 201886, 201978 -recovered pasa_asmbl_55003.p1, internal, 202164, 202285 -recovered pasa_asmbl_55003.p1, internal, 203083, 203192 -recovered pasa_asmbl_55003.p1, internal, 203524, 203683 -recovered pasa_asmbl_55003.p1, internal, 204066, 204202 Valid prediction for GlimmerHMM_glimmerT_22163-T1 Valid prediction for GlimmerHMM_glimmerT_22170-T1 Valid prediction for GlimmerHMM_glimmerT_22171-T1 Valid prediction for GlimmerHMM_glimmerT_22152-T1 Valid prediction for snap_scaffold_9-snap.1112-T1 Valid prediction for GlimmerHMM_glimmerT_22145-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8822, rend_intergenic: 5993 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34067, rend_intergenic: 17592 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38145, rend_intergenic: 37281 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41422, rend_intergenic: 38195 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50197, rend_intergenic: 47499 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58778, rend_intergenic: 56984 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 71113, rend_intergenic: 67982 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105691, rend_intergenic: 101495 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115941, rend_intergenic: 111205 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 222778 -exon list size: 452 building trellis 0.2 0.4 0.7 0.9 1.1 1.3 1.5 1.8 2.0 2.2 2.4 2.6 2.9 3.1 3.3 3.5 3.7 4.0 4.2 4.4 4.6 4.8 5.1 5.3 5.5 5.7 5.9 6.2 6.4 6.6 6.8 7.0 7.3 7.5 7.7 7.9 8.1 8.4 8.6 8.8 9.0 9.3 9.5 9.7 9.9 10.1 10.4 10.6 10.8 11.0 11.2 11.5 11.7 11.9 12.1 12.3 12.6 12.8 13.0 13.2 13.4 13.7 13.9 14.1 14.3 14.5 14.8 15.0 15.2 15.4 15.6 15.9 16.1 16.3 16.5 16.7 17.0 17.2 17.4 17.6 17.8 18.1 18.3 18.5 18.7 18.9 19.2 19.4 19.6 19.8 20.0 20.3 20.5 20.7 20.9 21.1 21.4 21.6 21.8 22.0 22.2 22.5 22.7 22.9 23.1 23.3 23.6 23.8 24.0 24.2 24.4 24.7 24.9 25.1 25.3 25.6 25.8 26.0 26.2 26.4 26.7 26.9 27.1 27.3 27.5 27.8 28.0 28.2 28.4 28.6 28.9 29.1 29.3 29.5 29.7 30.0 30.2 30.4 30.6 30.8 31.1 31.3 31.5 31.7 31.9 32.2 32.4 32.6 32.8 33.0 33.3 33.5 33.7 33.9 34.1 34.4 34.6 34.8 35.0 35.2 35.5 35.7 35.9 36.1 36.3 36.6 36.8 37.0 37.2 37.4 37.7 37.9 38.1 38.3 38.5 38.8 39.0 39.2 39.4 39.6 39.9 40.1 40.3 40.5 40.7 41.0 41.2 41.4 41.6 41.9 42.1 42.3 42.5 42.7 43.0 43.2 43.4 43.6 43.8 44.1 44.3 44.5 44.7 44.9 45.2 45.4 45.6 45.8 46.0 46.3 46.5 46.7 46.9 47.1 47.4 47.6 47.8 48.0 48.2 48.5 48.7 48.9 49.1 49.3 49.6 49.8 50.0 50.2 50.4 50.7 50.9 51.1 51.3 51.5 51.8 52.0 52.2 52.4 52.6 52.9 53.1 53.3 53.5 53.7 54.0 54.2 54.4 54.6 54.8 55.1 55.3 55.5 55.7 55.9 56.2 56.4 56.6 56.8 57.0 57.3 57.5 57.7 57.9 58.1 58.4 58.6 58.8 59.0 59.3 59.5 59.7 59.9 60.1 60.4 60.6 60.8 61.0 61.2 61.5 61.7 61.9 62.1 62.3 62.6 62.8 63.0 63.2 63.4 63.7 63.9 64.1 64.3 64.5 64.8 65.0 65.2 65.4 65.6 65.9 66.1 66.3 66.5 66.7 67.0 67.2 67.4 67.6 67.8 68.1 68.3 68.5 68.7 68.9 69.2 69.4 69.6 69.8 70.0 70.3 70.5 70.7 70.9 71.1 71.4 71.6 71.8 72.0 72.2 72.5 72.7 72.9 73.1 73.3 73.6 73.8 74.0 74.2 74.4 74.7 74.9 75.1 75.3 75.6 75.8 76.0 76.2 76.4 76.7 76.9 77.1 77.3 77.5 77.8 78.0 78.2 78.4 78.6 78.9 79.1 79.3 79.5 79.7 80.0 80.2 80.4 80.6 80.8 81.1 81.3 81.5 81.7 81.9 82.2 82.4 82.6 82.8 83.0 83.3 83.5 83.7 83.9 84.1 84.4 84.6 84.8 85.0 85.2 85.5 85.7 85.9 86.1 86.3 86.6 86.8 87.0 87.2 87.4 87.7 87.9 88.1 88.3 88.5 88.8 89.0 89.2 89.4 89.6 89.9 90.1 90.3 90.5 90.7 91.0 91.2 91.4 91.6 91.9 92.1 92.3 92.5 92.7 93.0 93.2 93.4 93.6 93.8 94.1 94.3 94.5 94.7 94.9 95.2 95.4 95.6 95.8 96.0 96.3 96.5 96.7 96.9 97.1 97.4 97.6 97.8 98.0 98.2 98.5 98.7 98.9 99.1 99.3 99.6 99.8 -found 28 predictions from path traversal Error with prediction: snap lend_intergenic: 8822, rend_intergenic: 5993 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34067, rend_intergenic: 17592 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38145, rend_intergenic: 37281 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41422, rend_intergenic: 38195 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50197, rend_intergenic: 47499 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58778, rend_intergenic: 56984 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 71113, rend_intergenic: 67982 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105691, rend_intergenic: 101495 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115941, rend_intergenic: 111205 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 210643 - 222778 -exon list size: 4 building trellis 16.7 33.3 50.0 66.7 83.3 -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