-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_5506280-5669162 -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: +)Couldn't classify 63121, 63243 Sorry, prediction pasa_asmbl_14155.p1 fails validation. (TCG) TG 63121-63243 GT AGG (GTA) AG 63430-63844 GT TGG (GCC) AG 64191-64316 GT AGG (GAC) AG 64448-64465 GT AGG (GGC) AG 64570-64704 GT AGG (GCT) AG 65008-65327 TT GAT -recovered pasa_asmbl_14155.p1, terminal, 65008, 65327 -recovered pasa_asmbl_14155.p1, internal, 63430, 63844 -recovered pasa_asmbl_14155.p1, internal, 64191, 64316 -recovered pasa_asmbl_14155.p1, internal, 64448, 64465 -recovered pasa_asmbl_14155.p1, internal, 64570, 64704 Valid prediction for GeneMark_model.63613_t Valid prediction for GlimmerHMM_glimmerT_36970-T1 Valid prediction for GeneMark_model.63643_t Valid prediction for GlimmerHMM_glimmerT_36971-T1 Valid prediction for GeneMark_model.63627_t Valid prediction for GlimmerHMM_glimmerT_36987-T1 Valid prediction for Augustus_model.g24810.t1 Valid prediction for GeneMark_model.63636_t Valid prediction for snap_scaffold_15-snap.1200-T1 Valid prediction for GeneMark_model.63645_t Valid prediction for Augustus_model.g24818.t1 Valid prediction for snap_scaffold_15-snap.1213-T1 Valid prediction for GlimmerHMM_glimmerT_36991-T1 Valid prediction for Augustus_model.g24809.t1 Valid prediction for Augustus_model.g24815.t1 Valid prediction for GlimmerHMM_glimmerT_36986-T1 Valid prediction for snap_scaffold_15-snap.1196-T1 Valid prediction for GeneMark_model.63626_t Valid prediction for snap_scaffold_15-snap.1220-T1 Valid prediction for snap_scaffold_15-snap.1226-T1 Valid prediction for GeneMark_model.63629_t Valid prediction for CodingQuarry_transcript_17971-T1 Valid prediction for snap_scaffold_15-snap.1221-T1 Valid prediction for GeneMark_model.63620_t Valid prediction for snap_scaffold_15-snap.1211-T1 Valid prediction for HiQ_model.g24827.t1 Valid prediction for GlimmerHMM_glimmerT_36992-T1 Valid prediction for GeneMark_model.63638_t Valid prediction for snap_scaffold_15-snap.1209-T1 Valid prediction for GlimmerHMM_glimmerT_36983-T1 Valid prediction for GlimmerHMM_glimmerT_36984-T1 Valid prediction for Augustus_model.g24822.t1 Valid prediction for GeneMark_model.63618_t Valid prediction for snap_scaffold_15-snap.1198-T1 Valid prediction for GlimmerHMM_glimmerT_36998-T1 Valid prediction for GeneMark_model.63631_t Valid prediction for snap_scaffold_15-snap.1223-T1 Valid prediction for GlimmerHMM_glimmerT_36973-T1 Valid prediction for GlimmerHMM_glimmerT_36982-T1 Valid prediction for GlimmerHMM_glimmerT_36989-T1 Valid prediction for snap_scaffold_15-snap.1216-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for GeneMark_model.63633_t Valid prediction for snap_scaffold_15-snap.1231-T1 Couldn't classify 152212, 152260 Sorry, prediction pasa_asmbl_14159.p1 fails validation. (GGA) GG 152212-152260 GT AGG (CAC) AG 152469-152758 GT AGG (TTC) AG 153117-153296 GT GGG (TTC) AG 153723-153776 GA GAG -recovered pasa_asmbl_14159.p1, terminal, 153723, 153776 -recovered pasa_asmbl_14159.p1, internal, 152469, 152758 -recovered pasa_asmbl_14159.p1, internal, 153117, 153296 Valid prediction for snap_scaffold_15-snap.1204-T1 Valid prediction for Augustus_model.g24814.t1 Valid prediction for GeneMark_model.63617_t Valid prediction for snap_scaffold_15-snap.1232-T1 Valid prediction for snap_scaffold_15-snap.1208-T1 Valid prediction for snap_scaffold_15-snap.1227-T1 Valid prediction for Augustus_model.g24819.t1 Valid prediction for GeneMark_model.63622_t Valid prediction for snap_scaffold_15-snap.1206-T1 Valid prediction for Augustus_model.g24820.t1 Valid prediction for GeneMark_model.63616_t Valid prediction for GlimmerHMM_glimmerT_36975-T1 Valid prediction for snap_scaffold_15-snap.1202-T1 Sorry, intron length (6) is less than minimum required (10) Couldn't classify 151970, 152148 Sorry, prediction pasa_asmbl_14157.p1 fails validation. (ATG) AA 145507-145996 GT GGG (GGG) AG 147076-147190 GT TGG (GGC) AG 148985-149064 GT CTG (ATA) AG 149283-149422 GT AGG (ATC) AG 149565-149664 GT GGG (GCG) AG 149939-150051 GT TTG (GAC) AG 150197-150460 GT AGG (ATG) AG 150614-150733 GT TGG (ATT) AG 150895-151023 GT ATG (ACC) AG 151492-151660 GT AGG (GGT) AG 151970-152148 GG GCG -recovered pasa_asmbl_14157.p1, initial, 145507, 145996 -recovered pasa_asmbl_14157.p1, initial, 150614, 150733 -recovered pasa_asmbl_14157.p1, internal, 147076, 147190 -recovered pasa_asmbl_14157.p1, internal, 148985, 149064 -recovered pasa_asmbl_14157.p1, internal, 149283, 149422 -recovered pasa_asmbl_14157.p1, internal, 149565, 149664 -recovered pasa_asmbl_14157.p1, internal, 149939, 150051 -recovered pasa_asmbl_14157.p1, internal, 150197, 150460 -recovered pasa_asmbl_14157.p1, internal, 150614, 150733 -recovered pasa_asmbl_14157.p1, internal, 150895, 151023 -recovered pasa_asmbl_14157.p1, internal, 151492, 151660 Valid prediction for GeneMark_model.63641_t Valid prediction for GlimmerHMM_glimmerT_36974-T1 Valid prediction for snap_scaffold_15-snap.1233-T1 Valid prediction for GlimmerHMM_glimmerT_36985-T1 Valid prediction for GlimmerHMM_glimmerT_36988-T1 Couldn't classify 59572, 59693 Couldn't classify 61607, 61664 Sorry, prediction pasa_asmbl_14153.p1 fails validation. (AGG) AC 59572-59693 GT ACG (GTA) AG 60737-60930 GT GGG (GAG) AG 61214-61331 GT CGG (GTC) AG 61607-61664 AC AGA -recovered pasa_asmbl_14153.p1, internal, 60737, 60930 -recovered pasa_asmbl_14153.p1, internal, 61214, 61331 Valid prediction for GeneMark_model.63624_t Couldn't classify 62254, 63033 Sorry, prediction pasa_asmbl_14154.p1 fails validation. (GAC) AG 62254-63033 TT GCT Valid prediction for GeneMark_model.63635_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 Augustus_model.g24826.t1 Valid prediction for snap_scaffold_15-snap.1215-T1 Valid prediction for snap_scaffold_15-snap.1203-T1 Valid prediction for Augustus_model.g24816.t1 Valid prediction for snap_scaffold_15-snap.1222-T1 Valid prediction for GeneMark_model.63615_t Valid prediction for GlimmerHMM_glimmerT_36972-T1 Couldn't classify 42646, 42787 Sorry, prediction pasa_asmbl_15237.p1 fails validation. (AGT) AG 42646-42787 GT CGG (ATG) AG 42984-43192 CC AAC -recovered pasa_asmbl_15237.p1, terminal, 42984, 43192 -recovered pasa_asmbl_15237.p1, internal, 42646, 42787 Valid prediction for GeneMark_model.63623_t Valid prediction for GeneMark_model.63630_t Valid prediction for GeneMark_model.63628_t Valid prediction for Augustus_model.g24824.t1 Valid prediction for snap_scaffold_15-snap.1214-T1 Valid prediction for GlimmerHMM_glimmerT_36981-T1 Valid prediction for pasa_asmbl_15233.p1 Valid prediction for GlimmerHMM_glimmerT_36996-T1 Valid prediction for snap_scaffold_15-snap.1219-T1 Couldn't classify 49893, 49911 Sorry, prediction pasa_asmbl_15235.p1 fails validation. (ATG) CA 45520-45715 GT CAG (GTC) AG 46090-46202 GT CAG (TAC) AG 46456-46536 GT AGG (TTC) AG 46780-46909 GT AGG (GAA) AG 47020-47069 GT AGG (GGC) AG 47192-47322 GT AGG (GGG) AG 47606-47723 GT CTG (GTC) AG 48436-48555 GT CGG (TTC) AG 48829-48885 GT AGG (ATA) AG 49168-49279 GT AGG (AGC) AG 49386-49467 GT GGG (AGG) AG 49893-49911 GG CAG -recovered pasa_asmbl_15235.p1, initial, 45520, 45715 -recovered pasa_asmbl_15235.p1, internal, 46090, 46202 -recovered pasa_asmbl_15235.p1, internal, 46456, 46536 -recovered pasa_asmbl_15235.p1, internal, 46780, 46909 -recovered pasa_asmbl_15235.p1, internal, 47020, 47069 -recovered pasa_asmbl_15235.p1, internal, 47192, 47322 -recovered pasa_asmbl_15235.p1, internal, 47606, 47723 -recovered pasa_asmbl_15235.p1, internal, 48436, 48555 -recovered pasa_asmbl_15235.p1, internal, 48829, 48885 -recovered pasa_asmbl_15235.p1, internal, 49168, 49279 -recovered pasa_asmbl_15235.p1, internal, 49386, 49467 Valid prediction for snap_scaffold_15-snap.1197-T1 Valid prediction for HiQ_model.g24811.t1 Valid prediction for snap_scaffold_15-snap.1230-T1 Valid prediction for Augustus_model.g24812.t1 Valid prediction for snap_scaffold_15-snap.1235-T1 Valid prediction for snap_scaffold_15-snap.1201-T1 Valid prediction for GlimmerHMM_glimmerT_36999-T1 Valid prediction for GeneMark_model.63619_t Valid prediction for snap_scaffold_15-snap.1229-T1 Valid prediction for GeneMark_model.63644_t Valid prediction for GeneMark_model.63612_t Valid prediction for GeneMark_model.63634_t Couldn't classify 37353, 37419 Couldn't classify 41031, 41171 Sorry, prediction pasa_asmbl_15238.p1 fails validation. (TCA) TC 37353-37419 GT AGG (TAG) AG 37663-37760 GT AGG (ATT) AG 39083-39113 GT CTG (ACC) AG 39728-39814 GT GGG (AAA) AG 40082-40193 GT AGG (GAC) AG 40874-40895 GT TGG (AGT) AG 41031-41171 GG AAG -recovered pasa_asmbl_15238.p1, internal, 37663, 37760 -recovered pasa_asmbl_15238.p1, internal, 39083, 39113 -recovered pasa_asmbl_15238.p1, internal, 39728, 39814 -recovered pasa_asmbl_15238.p1, internal, 40082, 40193 -recovered pasa_asmbl_15238.p1, internal, 40874, 40895 Valid prediction for snap_scaffold_15-snap.1228-T1 Valid prediction for GeneMark_model.63632_t Valid prediction for Augustus_model.g24821.t1 Valid prediction for GeneMark_model.63625_t Valid prediction for Augustus_model.g24828.t1 Valid prediction for GlimmerHMM_glimmerT_36993-T1 Valid prediction for GeneMark_model.63621_t Valid prediction for GeneMark_model.63614_t Valid prediction for snap_scaffold_15-snap.1225-T1 Valid prediction for CodingQuarry_transcript_17970-T1 Valid prediction for GeneMark_model.63642_t Valid prediction for GeneMark_model.63639_t Valid prediction for snap_scaffold_15-snap.1218-T1 Valid prediction for HiQ_model.g24823.t1 Valid prediction for Augustus_model.g24825.t1 Valid prediction for snap_scaffold_15-snap.1207-T1 Valid prediction for GlimmerHMM_glimmerT_36979-T1 Valid prediction for GlimmerHMM_glimmerT_36977-T1 Valid prediction for GlimmerHMM_glimmerT_36995-T1 Valid prediction for snap_scaffold_15-snap.1210-T1 Valid prediction for snap_scaffold_15-snap.1234-T1 Valid prediction for snap_scaffold_15-snap.1217-T1 Valid prediction for snap_scaffold_15-snap.1224-T1 Valid prediction for snap_scaffold_15-snap.1212-T1 Valid prediction for GlimmerHMM_glimmerT_36990-T1 Valid prediction for GeneMark_model.63640_t Valid prediction for snap_scaffold_15-snap.1199-T1 Valid prediction for GlimmerHMM_glimmerT_36980-T1 Valid prediction for snap_scaffold_15-snap.1205-T1 Valid prediction for GlimmerHMM_glimmerT_36997-T1 Valid prediction for GeneMark_model.63637_t Valid prediction for GlimmerHMM_glimmerT_36994-T1 Valid prediction for GlimmerHMM_glimmerT_36976-T1 Valid prediction for GlimmerHMM_glimmerT_36978-T1 Valid prediction for Augustus_model.g24813.t1 Valid prediction for Augustus_model.g24817.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12946, rend_intergenic: 10292 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 18436, rend_intergenic: 14536 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33401, rend_intergenic: 30211 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46981, rend_intergenic: 38235 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50712, rend_intergenic: 47332 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 65327, rend_intergenic: 58555 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81197, rend_intergenic: 78342 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99593, rend_intergenic: 94116 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105425, rend_intergenic: 101236 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 124001, rend_intergenic: 121246 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 132106, rend_intergenic: 128905 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143193, rend_intergenic: 140854 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 153776, rend_intergenic: 148943 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 162883 -exon list size: 588 building trellis 0.2 0.3 0.5 0.7 0.8 1.0 1.2 1.4 1.5 1.7 1.9 2.0 2.2 2.4 2.5 2.7 2.9 3.1 3.2 3.4 3.6 3.7 3.9 4.1 4.2 4.4 4.6 4.7 4.9 5.1 5.3 5.4 5.6 5.8 5.9 6.1 6.3 6.4 6.6 6.8 6.9 7.1 7.3 7.5 7.6 7.8 8.0 8.1 8.3 8.5 8.6 8.8 9.0 9.2 9.3 9.5 9.7 9.8 10.0 10.2 10.3 10.5 10.7 10.8 11.0 11.2 11.4 11.5 11.7 11.9 12.0 12.2 12.4 12.5 12.7 12.9 13.1 13.2 13.4 13.6 13.7 13.9 14.1 14.2 14.4 14.6 14.7 14.9 15.1 15.3 15.4 15.6 15.8 15.9 16.1 16.3 16.4 16.6 16.8 16.9 17.1 17.3 17.5 17.6 17.8 18.0 18.1 18.3 18.5 18.6 18.8 19.0 19.2 19.3 19.5 19.7 19.8 20.0 20.2 20.3 20.5 20.7 20.8 21.0 21.2 21.4 21.5 21.7 21.9 22.0 22.2 22.4 22.5 22.7 22.9 23.1 23.2 23.4 23.6 23.7 23.9 24.1 24.2 24.4 24.6 24.7 24.9 25.1 25.3 25.4 25.6 25.8 25.9 26.1 26.3 26.4 26.6 26.8 26.9 27.1 27.3 27.5 27.6 27.8 28.0 28.1 28.3 28.5 28.6 28.8 29.0 29.2 29.3 29.5 29.7 29.8 30.0 30.2 30.3 30.5 30.7 30.8 31.0 31.2 31.4 31.5 31.7 31.9 32.0 32.2 32.4 32.5 32.7 32.9 33.1 33.2 33.4 33.6 33.7 33.9 34.1 34.2 34.4 34.6 34.7 34.9 35.1 35.3 35.4 35.6 35.8 35.9 36.1 36.3 36.4 36.6 36.8 36.9 37.1 37.3 37.5 37.6 37.8 38.0 38.1 38.3 38.5 38.6 38.8 39.0 39.2 39.3 39.5 39.7 39.8 40.0 40.2 40.3 40.5 40.7 40.8 41.0 41.2 41.4 41.5 41.7 41.9 42.0 42.2 42.4 42.5 42.7 42.9 43.1 43.2 43.4 43.6 43.7 43.9 44.1 44.2 44.4 44.6 44.7 44.9 45.1 45.3 45.4 45.6 45.8 45.9 46.1 46.3 46.4 46.6 46.8 46.9 47.1 47.3 47.5 47.6 47.8 48.0 48.1 48.3 48.5 48.6 48.8 49.0 49.2 49.3 49.5 49.7 49.8 50.0 50.2 50.3 50.5 50.7 50.8 51.0 51.2 51.4 51.5 51.7 51.9 52.0 52.2 52.4 52.5 52.7 52.9 53.1 53.2 53.4 53.6 53.7 53.9 54.1 54.2 54.4 54.6 54.7 54.9 55.1 55.3 55.4 55.6 55.8 55.9 56.1 56.3 56.4 56.6 56.8 56.9 57.1 57.3 57.5 57.6 57.8 58.0 58.1 58.3 58.5 58.6 58.8 59.0 59.2 59.3 59.5 59.7 59.8 60.0 60.2 60.3 60.5 60.7 60.8 61.0 61.2 61.4 61.5 61.7 61.9 62.0 62.2 62.4 62.5 62.7 62.9 63.1 63.2 63.4 63.6 63.7 63.9 64.1 64.2 64.4 64.6 64.7 64.9 65.1 65.3 65.4 65.6 65.8 65.9 66.1 66.3 66.4 66.6 66.8 66.9 67.1 67.3 67.5 67.6 67.8 68.0 68.1 68.3 68.5 68.6 68.8 69.0 69.2 69.3 69.5 69.7 69.8 70.0 70.2 70.3 70.5 70.7 70.8 71.0 71.2 71.4 71.5 71.7 71.9 72.0 72.2 72.4 72.5 72.7 72.9 73.1 73.2 73.4 73.6 73.7 73.9 74.1 74.2 74.4 74.6 74.7 74.9 75.1 75.3 75.4 75.6 75.8 75.9 76.1 76.3 76.4 76.6 76.8 76.9 77.1 77.3 77.5 77.6 77.8 78.0 78.1 78.3 78.5 78.6 78.8 79.0 79.2 79.3 79.5 79.7 79.8 80.0 80.2 80.3 80.5 80.7 80.8 81.0 81.2 81.4 81.5 81.7 81.9 82.0 82.2 82.4 82.5 82.7 82.9 83.1 83.2 83.4 83.6 83.7 83.9 84.1 84.2 84.4 84.6 84.7 84.9 85.1 85.3 85.4 85.6 85.8 85.9 86.1 86.3 86.4 86.6 86.8 86.9 87.1 87.3 87.5 87.6 87.8 88.0 88.1 88.3 88.5 88.6 88.8 89.0 89.2 89.3 89.5 89.7 89.8 90.0 90.2 90.3 90.5 90.7 90.8 91.0 91.2 91.4 91.5 91.7 91.9 92.0 92.2 92.4 92.5 92.7 92.9 93.1 93.2 93.4 93.6 93.7 93.9 94.1 94.2 94.4 94.6 94.7 94.9 95.1 95.3 95.4 95.6 95.8 95.9 96.1 96.3 96.4 96.6 96.8 96.9 97.1 97.3 97.5 97.6 97.8 98.0 98.1 98.3 98.5 98.6 98.8 99.0 99.2 99.3 99.5 99.7 99.8 -found 29 predictions from path traversal Error with prediction: snap lend_intergenic: 12946, rend_intergenic: 10292 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 18436, rend_intergenic: 14536 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33401, rend_intergenic: 30211 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46981, rend_intergenic: 38235 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50712, rend_intergenic: 47332 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 65327, rend_intergenic: 58555 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81197, rend_intergenic: 78342 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99593, rend_intergenic: 94116 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105425, rend_intergenic: 101236 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 124001, rend_intergenic: 121246 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 132106, rend_intergenic: 128905 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143193, rend_intergenic: 140854 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 153776, rend_intergenic: 148943 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 17 predictions persist after filtering for low support