-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_4915303-5127056 -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_9-snap.1064-T1 Valid prediction for pasa_asmbl_53975.p1 Valid prediction for GlimmerHMM_glimmerT_22079-T1 Couldn't classify 200797, 200862 Sorry, prediction pasa_asmbl_53996.p1 fails validation. (GAG) CA 200797-200862 GT AGG (GAA) AG 201048-201221 GT AGG (GTC) AG 201320-201425 GT GGG (GGC) AG 201730-201836 GT AGG (GCC) AG 201945-202211 GT AGG (GTC) AG 202316-202501 GT GCG (GAC) AG 202640-202781 GT GGG (AAG) AG 202936-203078 CA GAC -recovered pasa_asmbl_53996.p1, terminal, 202936, 203078 -recovered pasa_asmbl_53996.p1, internal, 201048, 201221 -recovered pasa_asmbl_53996.p1, internal, 201320, 201425 -recovered pasa_asmbl_53996.p1, internal, 201730, 201836 -recovered pasa_asmbl_53996.p1, internal, 201945, 202211 -recovered pasa_asmbl_53996.p1, internal, 202316, 202501 -recovered pasa_asmbl_53996.p1, internal, 202640, 202781 Valid prediction for snap_scaffold_9-snap.1052-T1 Valid prediction for GlimmerHMM_glimmerT_22103-T1 Valid prediction for GlimmerHMM_glimmerT_22087-T1 Valid prediction for Augustus_model.g14679.t1 Valid prediction for snap_scaffold_9-snap.1037-T1 Valid prediction for pasa_asmbl_54685.p2 Valid prediction for snap_scaffold_9-snap.1028-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_22077-T1 Valid prediction for GlimmerHMM_glimmerT_22100-T1 Couldn't classify 113865, 113910 Couldn't classify 114454, 114849 Sorry, prediction pasa_asmbl_53984.p1 fails validation. (ACC) GC 113865-113910 GT AGG (GCA) AG 114263-114336 GC AGG (GCC) AG 114454-114849 AG CCA -recovered pasa_asmbl_53984.p1, internal, 114263, 114336 Valid prediction for Augustus_model.g14692.t1 Valid prediction for snap_scaffold_9-snap.1039-T1 Valid prediction for snap_scaffold_9-snap.1027-T1 Valid prediction for snap_scaffold_9-snap.1041-T1 Valid prediction for CodingQuarry_transcript_62162-T1 Valid prediction for GlimmerHMM_glimmerT_22098-T1 Valid prediction for snap_scaffold_9-snap.1054-T1 Valid prediction for snap_scaffold_9-snap.1031-T1 Valid prediction for GlimmerHMM_glimmerT_22096-T1 Valid prediction for Augustus_model.g14689.t1 Valid prediction for snap_scaffold_9-snap.1043-T1 Valid prediction for CodingQuarry_transcript_62167-T1 Valid prediction for Augustus_model.g14685.t1 Valid prediction for pasa_asmbl_53978.p1 Valid prediction for HiQ_model.g14676.t1 Valid prediction for GlimmerHMM_glimmerT_22082-T1 Couldn't classify 157236, 157409 Sorry, prediction pasa_asmbl_54712.p1 fails validation. (GCC) AG 157236-157409 GT AGG (ATG) AG 157946-158075 GT AGG (AAC) AG 159388-159416 TC AGT -recovered pasa_asmbl_54712.p1, initial, 157946, 158075 -recovered pasa_asmbl_54712.p1, terminal, 157946, 158075 -recovered pasa_asmbl_54712.p1, terminal, 159388, 159416 -recovered pasa_asmbl_54712.p1, internal, 157236, 157409 -recovered pasa_asmbl_54712.p1, internal, 157946, 158075 Valid prediction for snap_scaffold_9-snap.1033-T1 Valid prediction for GlimmerHMM_glimmerT_22099-T1 Valid prediction for HiQ_model.g14677.t1 Valid prediction for Augustus_model.g14687.t1 Valid prediction for snap_scaffold_9-snap.1048-T1 Valid prediction for snap_scaffold_9-snap.1059-T1 Valid prediction for snap_scaffold_9-snap.1066-T1 Valid prediction for snap_scaffold_9-snap.1063-T1 Valid prediction for GlimmerHMM_glimmerT_22076-T1 Couldn't classify 197036, 197551 Sorry, prediction pasa_asmbl_53994.p1 fails validation. (ATG) AA 197036-197551 GA TGG Valid prediction for Augustus_model.g14683.t1 Valid prediction for GlimmerHMM_glimmerT_22095-T1 Couldn't classify 163441, 163554 Sorry, prediction pasa_asmbl_53989.p1 fails validation. (GTG) CA 163441-163554 GT AGG (GCC) AG 166332-166546 GT AGG (CGA) AG 166854-167059 GT AGG (CGG) AG 167817-167984 GT GAG (CCG) AG 169268-169401 GT GAG (GTG) AG 170029-170103 GT AGG (CGC) AG 170465-170623 GT GGG (CCC) AG 171238-171366 GT AGG (GTG) AG 173315-173414 GT CGG (ATG) AG 176389-176562 GT GGG (GCT) AG 179314-179393 GT TGG (GTG) AG 180624-180701 GT TGG (GAA) AG 181646-181801 GT AGG (GTT) AG 182113-182214 TG AGT -recovered pasa_asmbl_53989.p1, initial, 176389, 176562 add_exon() Sorry, pasa_asmbl_53989.p1 167817-167984-terminal-1 is invalid. -recovered pasa_asmbl_53989.p1, terminal, 167817, 167984 -recovered pasa_asmbl_53989.p1, terminal, 182113, 182214 -recovered pasa_asmbl_53989.p1, internal, 166332, 166546 -recovered pasa_asmbl_53989.p1, internal, 166854, 167059 -recovered pasa_asmbl_53989.p1, internal, 167817, 167984 -recovered pasa_asmbl_53989.p1, internal, 169268, 169401 -recovered pasa_asmbl_53989.p1, internal, 170029, 170103 -recovered pasa_asmbl_53989.p1, internal, 170465, 170623 -recovered pasa_asmbl_53989.p1, internal, 171238, 171366 -recovered pasa_asmbl_53989.p1, internal, 173315, 173414 -recovered pasa_asmbl_53989.p1, internal, 176389, 176562 -recovered pasa_asmbl_53989.p1, internal, 179314, 179393 -recovered pasa_asmbl_53989.p1, internal, 180624, 180701 -recovered pasa_asmbl_53989.p1, internal, 181646, 181801 Valid prediction for GlimmerHMM_glimmerT_22105-T1 Valid prediction for HiQ_model.g14684.t1 Valid prediction for GlimmerHMM_glimmerT_22086-T1 Valid prediction for CodingQuarry_transcript_62163-T1 Valid prediction for GlimmerHMM_glimmerT_22101-T1 Valid prediction for GlimmerHMM_glimmerT_22104-T1 Valid prediction for snap_scaffold_9-snap.1050-T1 Valid prediction for Augustus_model.g14690.t1 Valid prediction for Augustus_model.g14693.t1 Valid prediction for GlimmerHMM_glimmerT_22102-T1 Valid prediction for GlimmerHMM_glimmerT_22091-T1 Valid prediction for snap_scaffold_9-snap.1042-T1 Valid prediction for GlimmerHMM_glimmerT_22088-T1 Valid prediction for snap_scaffold_9-snap.1065-T1 Valid prediction for Augustus_model.g14691.t1 Valid prediction for snap_scaffold_9-snap.1045-T1 Valid prediction for snap_scaffold_9-snap.1056-T1 Valid prediction for GlimmerHMM_glimmerT_22078-T1 Valid prediction for snap_scaffold_9-snap.1057-T1 Valid prediction for GlimmerHMM_glimmerT_22089-T1 Valid prediction for snap_scaffold_9-snap.1062-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 snap_scaffold_9-snap.1032-T1 Valid prediction for snap_scaffold_9-snap.1051-T1 Valid prediction for snap_scaffold_9-snap.1067-T1 Valid prediction for GlimmerHMM_glimmerT_22085-T1 Valid prediction for snap_scaffold_9-snap.1030-T1 Valid prediction for snap_scaffold_9-snap.1049-T1 Valid prediction for snap_scaffold_9-snap.1034-T1 Valid prediction for GlimmerHMM_glimmerT_22083-T1 Valid prediction for Augustus_model.g14678.t1 Valid prediction for GlimmerHMM_glimmerT_22106-T1 Valid prediction for snap_scaffold_9-snap.1047-T1 Valid prediction for GlimmerHMM_glimmerT_22092-T1 Valid prediction for snap_scaffold_9-snap.1061-T1 Valid prediction for Augustus_model.g14686.t1 Valid prediction for snap_scaffold_9-snap.1053-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_22094-T1 Valid prediction for snap_scaffold_9-snap.1055-T1 Valid prediction for snap_scaffold_9-snap.1035-T1 Valid prediction for Augustus_model.g14680.t1 Valid prediction for CodingQuarry_transcript_62168-T1 Valid prediction for GlimmerHMM_glimmerT_22084-T1 Valid prediction for GlimmerHMM_glimmerT_22081-T1 Valid prediction for snap_scaffold_9-snap.1058-T1 Valid prediction for Augustus_model.g14675.t1 Valid prediction for GlimmerHMM_glimmerT_22107-T1 Valid prediction for Augustus_model.g14674.t1 Valid prediction for Augustus_model.g14681.t1 Couldn't classify 87620, 87802 Couldn't classify 88185, 88264 Sorry, prediction pasa_asmbl_55735.p1 fails validation. (GAG) CG 87620-87802 GT AGG (GTG) AG 87945-88017 GT AGG (TGT) AG 88185-88264 CT ACC -recovered pasa_asmbl_55735.p1, internal, 87945, 88017 Valid prediction for Augustus_model.g14682.t1 Valid prediction for GlimmerHMM_glimmerT_22090-T1 Valid prediction for Augustus_model.g14688.t1 Valid prediction for Augustus_model.g14694.t1 Valid prediction for snap_scaffold_9-snap.1040-T1 Valid prediction for snap_scaffold_9-snap.1060-T1 Valid prediction for snap_scaffold_9-snap.1026-T1 Valid prediction for snap_scaffold_9-snap.1046-T1 Valid prediction for snap_scaffold_9-snap.1044-T1 Couldn't classify 204493, 204553 Sorry, prediction pasa_asmbl_55797.p1 fails validation. (ATG) GG 203646-203792 GT AGG (ATC) AG 203988-204163 GT AAG (GTT) AG 204493-204553 AC TGA -recovered pasa_asmbl_55797.p1, initial, 203646, 203792 -recovered pasa_asmbl_55797.p1, internal, 203988, 204163 Couldn't classify 176247, 176254 Couldn't classify 176297, 176420 Sorry, prediction CodingQuarry_transcript_62164-T1 fails validation. (ATG) TC 176247-176254 CT GCC (CTG) GC 176297-176420 CT GAC Couldn't classify 86002, 86073 Couldn't classify 86635, 86775 Sorry, prediction pasa_asmbl_55786.p1 fails validation. (GGG) AT 86002-86073 GT AGG (ACA) AG 86247-86306 GC AGG (GTG) AG 86418-86522 GT AGG (GGG) AG 86635-86775 GA TGG -recovered pasa_asmbl_55786.p1, internal, 86247, 86306 -recovered pasa_asmbl_55786.p1, internal, 86418, 86522 Valid prediction for snap_scaffold_9-snap.1036-T1 Valid prediction for GlimmerHMM_glimmerT_22097-T1 Valid prediction for GlimmerHMM_glimmerT_22075-T1 Valid prediction for GlimmerHMM_glimmerT_22080-T1 Couldn't classify 172918, 172995 Sorry, prediction pasa_asmbl_54982.p1 fails validation. (GAT) CA 172918-172995 GT CGG (CTG) AG 173288-173363 GT GGG (TGA) AG 173661-173773 GT AGG (GTG) AG 174492-174611 AC GAA -recovered pasa_asmbl_54982.p1, terminal, 174492, 174611 -recovered pasa_asmbl_54982.p1, internal, 173288, 173363 -recovered pasa_asmbl_54982.p1, internal, 173661, 173773 Valid prediction for GlimmerHMM_glimmerT_22093-T1 Valid prediction for snap_scaffold_9-snap.1038-T1 Valid prediction for snap_scaffold_9-snap.1029-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8109, rend_intergenic: 1891 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 17560, rend_intergenic: 12525 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20717, rend_intergenic: 17593 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 26301, rend_intergenic: 23803 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41628, rend_intergenic: 37088 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 45444, rend_intergenic: 44095 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46543, rend_intergenic: 45985 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 79484, rend_intergenic: 46598 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81811, rend_intergenic: 79885 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95143, rend_intergenic: 83829 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 122613, rend_intergenic: 119458 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 141211, rend_intergenic: 137538 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 156695, rend_intergenic: 141410 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160617, rend_intergenic: 156858 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 162830, rend_intergenic: 161050 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 173518, rend_intergenic: 168884 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 176620, rend_intergenic: 173671 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 211754 -exon list size: 547 building trellis 0.2 0.4 0.5 0.7 0.9 1.1 1.3 1.5 1.6 1.8 2.0 2.2 2.4 2.6 2.7 2.9 3.1 3.3 3.5 3.6 3.8 4.0 4.2 4.4 4.6 4.7 4.9 5.1 5.3 5.5 5.6 5.8 6.0 6.2 6.4 6.6 6.7 6.9 7.1 7.3 7.5 7.7 7.8 8.0 8.2 8.4 8.6 8.7 8.9 9.1 9.3 9.5 9.7 9.8 10.0 10.2 10.4 10.6 10.7 10.9 11.1 11.3 11.5 11.7 11.8 12.0 12.2 12.4 12.6 12.8 12.9 13.1 13.3 13.5 13.7 13.8 14.0 14.2 14.4 14.6 14.8 14.9 15.1 15.3 15.5 15.7 15.8 16.0 16.2 16.4 16.6 16.8 16.9 17.1 17.3 17.5 17.7 17.9 18.0 18.2 18.4 18.6 18.8 18.9 19.1 19.3 19.5 19.7 19.9 20.0 20.2 20.4 20.6 20.8 20.9 21.1 21.3 21.5 21.7 21.9 22.0 22.2 22.4 22.6 22.8 23.0 23.1 23.3 23.5 23.7 23.9 24.0 24.2 24.4 24.6 24.8 25.0 25.1 25.3 25.5 25.7 25.9 26.0 26.2 26.4 26.6 26.8 27.0 27.1 27.3 27.5 27.7 27.9 28.1 28.2 28.4 28.6 28.8 29.0 29.1 29.3 29.5 29.7 29.9 30.1 30.2 30.4 30.6 30.8 31.0 31.1 31.3 31.5 31.7 31.9 32.1 32.2 32.4 32.6 32.8 33.0 33.2 33.3 33.5 33.7 33.9 34.1 34.2 34.4 34.6 34.8 35.0 35.2 35.3 35.5 35.7 35.9 36.1 36.2 36.4 36.6 36.8 37.0 37.2 37.3 37.5 37.7 37.9 38.1 38.3 38.4 38.6 38.8 39.0 39.2 39.3 39.5 39.7 39.9 40.1 40.3 40.4 40.6 40.8 41.0 41.2 41.3 41.5 41.7 41.9 42.1 42.3 42.4 42.6 42.8 43.0 43.2 43.4 43.5 43.7 43.9 44.1 44.3 44.4 44.6 44.8 45.0 45.2 45.4 45.5 45.7 45.9 46.1 46.3 46.4 46.6 46.8 47.0 47.2 47.4 47.5 47.7 47.9 48.1 48.3 48.5 48.6 48.8 49.0 49.2 49.4 49.5 49.7 49.9 50.1 50.3 50.5 50.6 50.8 51.0 51.2 51.4 51.5 51.7 51.9 52.1 52.3 52.5 52.6 52.8 53.0 53.2 53.4 53.6 53.7 53.9 54.1 54.3 54.5 54.6 54.8 55.0 55.2 55.4 55.6 55.7 55.9 56.1 56.3 56.5 56.6 56.8 57.0 57.2 57.4 57.6 57.7 57.9 58.1 58.3 58.5 58.7 58.8 59.0 59.2 59.4 59.6 59.7 59.9 60.1 60.3 60.5 60.7 60.8 61.0 61.2 61.4 61.6 61.7 61.9 62.1 62.3 62.5 62.7 62.8 63.0 63.2 63.4 63.6 63.8 63.9 64.1 64.3 64.5 64.7 64.8 65.0 65.2 65.4 65.6 65.8 65.9 66.1 66.3 66.5 66.7 66.8 67.0 67.2 67.4 67.6 67.8 67.9 68.1 68.3 68.5 68.7 68.9 69.0 69.2 69.4 69.6 69.8 69.9 70.1 70.3 70.5 70.7 70.9 71.0 71.2 71.4 71.6 71.8 71.9 72.1 72.3 72.5 72.7 72.9 73.0 73.2 73.4 73.6 73.8 74.0 74.1 74.3 74.5 74.7 74.9 75.0 75.2 75.4 75.6 75.8 76.0 76.1 76.3 76.5 76.7 76.9 77.0 77.2 77.4 77.6 77.8 78.0 78.1 78.3 78.5 78.7 78.9 79.1 79.2 79.4 79.6 79.8 80.0 80.1 80.3 80.5 80.7 80.9 81.1 81.2 81.4 81.6 81.8 82.0 82.1 82.3 82.5 82.7 82.9 83.1 83.2 83.4 83.6 83.8 84.0 84.2 84.3 84.5 84.7 84.9 85.1 85.2 85.4 85.6 85.8 86.0 86.2 86.3 86.5 86.7 86.9 87.1 87.2 87.4 87.6 87.8 88.0 88.2 88.3 88.5 88.7 88.9 89.1 89.3 89.4 89.6 89.8 90.0 90.2 90.3 90.5 90.7 90.9 91.1 91.3 91.4 91.6 91.8 92.0 92.2 92.3 92.5 92.7 92.9 93.1 93.3 93.4 93.6 93.8 94.0 94.2 94.4 94.5 94.7 94.9 95.1 95.3 95.4 95.6 95.8 96.0 96.2 96.4 96.5 96.7 96.9 97.1 97.3 97.4 97.6 97.8 98.0 98.2 98.4 98.5 98.7 98.9 99.1 99.3 99.5 99.6 99.8 -found 33 predictions from path traversal Error with prediction: snap lend_intergenic: 8109, rend_intergenic: 1891 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 17560, rend_intergenic: 12525 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20717, rend_intergenic: 17593 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 26301, rend_intergenic: 23803 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41628, rend_intergenic: 37088 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 45444, rend_intergenic: 44095 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46543, rend_intergenic: 45985 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 79484, rend_intergenic: 46598 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81811, rend_intergenic: 79885 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95143, rend_intergenic: 83829 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 122613, rend_intergenic: 119458 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 141211, rend_intergenic: 137538 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 156695, rend_intergenic: 141410 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160617, rend_intergenic: 156858 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 162830, rend_intergenic: 161050 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 173518, rend_intergenic: 168884 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 176620, rend_intergenic: 173671 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 27 predictions persist after filtering for low support