-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_10574270-10755279 -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.2109-T1 Couldn't classify 9072, 9132 Sorry, prediction pasa_asmbl_40277.p1 fails validation. (GGC) AT 9072-9132 GT AGG (GGG) AG 9264-9420 GT AGG (GTT) AG 11601-11709 GT AGG (GCC) AG 13958-14083 GT AGG (CTC) AG 14542-14700 GT AGG (TAT) AG 15813-15911 GT AGG (AAC) AG 16036-16274 GT AGG (ACT) AG 16872-16980 GA GAG -recovered pasa_asmbl_40277.p1, terminal, 16872, 16980 -recovered pasa_asmbl_40277.p1, internal, 9264, 9420 -recovered pasa_asmbl_40277.p1, internal, 11601, 11709 -recovered pasa_asmbl_40277.p1, internal, 13958, 14083 -recovered pasa_asmbl_40277.p1, internal, 14542, 14700 -recovered pasa_asmbl_40277.p1, internal, 15813, 15911 -recovered pasa_asmbl_40277.p1, internal, 16036, 16274 Valid prediction for snap_scaffold_3-snap.2102-T1 Valid prediction for snap_scaffold_3-snap.2122-T1 Valid prediction for GlimmerHMM_glimmerT_7256-T1 Valid prediction for CodingQuarry_transcript_46259-T1 Valid prediction for GlimmerHMM_glimmerT_7253-T1 Valid prediction for snap_scaffold_3-snap.2116-T1 Valid prediction for snap_scaffold_3-snap.2133-T1 Valid prediction for GlimmerHMM_glimmerT_7257-T1 Valid prediction for GlimmerHMM_glimmerT_7258-T1 Valid prediction for GlimmerHMM_glimmerT_7247-T1 Valid prediction for snap_scaffold_3-snap.2136-T1 Valid prediction for CodingQuarry_transcript_46256-T1 Valid prediction for GlimmerHMM_glimmerT_7265-T1 Valid prediction for snap_scaffold_3-snap.2105-T1 Valid prediction for snap_scaffold_3-snap.2127-T1 Valid prediction for snap_scaffold_3-snap.2117-T1 Valid prediction for Augustus_model.g4723.t1 Valid prediction for CodingQuarry_transcript_46258-T1 Couldn't classify 1624, 1881 Sorry, prediction pasa_asmbl_40276.p1 fails validation. (CTC) TT 1624-1881 GT TGG (TCC) AG 2074-2281 GT AGG (ACG) AG 2394-2475 GT CGG (GTC) AG 2564-2819 CG GAC -recovered pasa_asmbl_40276.p1, terminal, 2564, 2819 -recovered pasa_asmbl_40276.p1, internal, 2074, 2281 -recovered pasa_asmbl_40276.p1, internal, 2394, 2475 Valid prediction for snap_scaffold_3-snap.2132-T1 Valid prediction for CodingQuarry_transcript_46260-T1 Valid prediction for pasa_asmbl_40286.p1 Valid prediction for GlimmerHMM_glimmerT_7238-T1 Valid prediction for GlimmerHMM_glimmerT_7239-T1 Valid prediction for CodingQuarry_transcript_46255-T1 Valid prediction for snap_scaffold_3-snap.2123-T1 Valid prediction for Augustus_model.g4715.t1 Valid prediction for Augustus_model.g4722.t1 Valid prediction for snap_scaffold_3-snap.2098-T1 Valid prediction for snap_scaffold_3-snap.2129-T1 Valid prediction for GlimmerHMM_glimmerT_7254-T1 Valid prediction for snap_scaffold_3-snap.2135-T1 Valid prediction for Augustus_model.g4720.t1 Valid prediction for snap_scaffold_3-snap.2103-T1 Valid prediction for HiQ_model.g4718.t1 Valid prediction for GlimmerHMM_glimmerT_7251-T1 Valid prediction for snap_scaffold_3-snap.2113-T1 Valid prediction for snap_scaffold_3-snap.2130-T1 Valid prediction for snap_scaffold_3-snap.2111-T1 Valid prediction for Augustus_model.g4714.t1 Valid prediction for snap_scaffold_3-snap.2095-T1 Valid prediction for Augustus_model.g4721.t1 Valid prediction for snap_scaffold_3-snap.2120-T1 Valid prediction for CodingQuarry_transcript_46257-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: -)Couldn't classify 16072, 16176 Couldn't classify 19349, 19465 Sorry, prediction pasa_asmbl_39110.p1 fails validation. (AGT) AC 16072-16176 GT AGG (GCC) AG 18402-18494 GT AGG (AGT) AG 18810-18887 GT AGG (CTC) AG 19095-19202 GT AGG (ATG) AG 19349-19465 CC CCC -recovered pasa_asmbl_39110.p1, internal, 18402, 18494 -recovered pasa_asmbl_39110.p1, internal, 18810, 18887 -recovered pasa_asmbl_39110.p1, internal, 19095, 19202 Valid prediction for GlimmerHMM_glimmerT_7245-T1 Valid prediction for snap_scaffold_3-snap.2125-T1 Couldn't classify 23635, 23783 Sorry, prediction Augustus_model.g4726.t1 fails validation. (ATG) CC 1958-2127 GT AGG (TTC) AG 2262-2325 GT AGG (GCA) AG 4869-4977 GT AGG (CAT) AG 5469-5518 GT AGG (TTT) AG 5732-5868 GT TGG (GGC) AG 7707-7827 GT AGG (GAT) AG 8019-8231 GT TGG (CAT) AG 10648-10702 GT GAG (TTC) AG 11260-11294 GT AGG (AAG) AG 12294-12387 GT AGG (GCT) AG 13881-14007 GT AGG (GTG) AG 14757-14855 GT GGG (GGT) AG 15301-15520 GT AGG (GCT) AG 16030-16176 GT AGG (GCC) AG 18402-18494 GT AGG (AGT) AG 18810-18887 GT AGG (CTC) AG 19095-19202 GT AGG (ATG) AG 19349-19747 GT AGG (CAG) AG 19982-20089 GT AGG (GGG) AG 20442-21349 GT AGG (GAA) AG 21675-21804 GT ACG (CTG) AG 22168-22273 GT GGG (ACC) AG 22881-23086 GT GGG (GAG) AG 23182-23228 GT AAG (TGC) AG 23358-23432 GT AAG (GTG) AG 23635-23783 GT AGG -recovered Augustus_model.g4726.t1, initial, 1958, 2127 -recovered Augustus_model.g4726.t1, initial, 19349, 19747 add_exon() Sorry, Augustus_model.g4726.t1 12294-12387-terminal-3 is invalid. -recovered Augustus_model.g4726.t1, terminal, 12294, 12387 -recovered Augustus_model.g4726.t1, internal, 2262, 2325 -recovered Augustus_model.g4726.t1, internal, 4869, 4977 -recovered Augustus_model.g4726.t1, internal, 5469, 5518 -recovered Augustus_model.g4726.t1, internal, 5732, 5868 -recovered Augustus_model.g4726.t1, internal, 7707, 7827 -recovered Augustus_model.g4726.t1, internal, 8019, 8231 -recovered Augustus_model.g4726.t1, internal, 10648, 10702 -recovered Augustus_model.g4726.t1, internal, 11260, 11294 -recovered Augustus_model.g4726.t1, internal, 12294, 12387 -recovered Augustus_model.g4726.t1, internal, 13881, 14007 -recovered Augustus_model.g4726.t1, internal, 14757, 14855 -recovered Augustus_model.g4726.t1, internal, 15301, 15520 -recovered Augustus_model.g4726.t1, internal, 16030, 16176 -recovered Augustus_model.g4726.t1, internal, 18402, 18494 -recovered Augustus_model.g4726.t1, internal, 18810, 18887 -recovered Augustus_model.g4726.t1, internal, 19095, 19202 -recovered Augustus_model.g4726.t1, internal, 19349, 19747 -recovered Augustus_model.g4726.t1, internal, 19982, 20089 -recovered Augustus_model.g4726.t1, internal, 20442, 21349 -recovered Augustus_model.g4726.t1, internal, 21675, 21804 -recovered Augustus_model.g4726.t1, internal, 22168, 22273 -recovered Augustus_model.g4726.t1, internal, 22881, 23086 -recovered Augustus_model.g4726.t1, internal, 23182, 23228 -recovered Augustus_model.g4726.t1, internal, 23358, 23432 -recovered Augustus_model.g4726.t1, internal, 23635, 23783 Valid prediction for GlimmerHMM_glimmerT_7263-T1 Valid prediction for snap_scaffold_3-snap.2093-T1 Valid prediction for snap_scaffold_3-snap.2128-T1 Valid prediction for GlimmerHMM_glimmerT_7267-T1 Valid prediction for GlimmerHMM_glimmerT_7262-T1 Valid prediction for snap_scaffold_3-snap.2115-T1 Valid prediction for CodingQuarry_transcript_46252-T1 Valid prediction for snap_scaffold_3-snap.2096-T1 Valid prediction for snap_scaffold_3-snap.2137-T1 Valid prediction for snap_scaffold_3-snap.2118-T1 Valid prediction for snap_scaffold_3-snap.2101-T1 Valid prediction for snap_scaffold_3-snap.2097-T1 Valid prediction for Augustus_model.g4724.t1 Valid prediction for snap_scaffold_3-snap.2092-T1 Valid prediction for GlimmerHMM_glimmerT_7260-T1 Valid prediction for snap_scaffold_3-snap.2119-T1 Valid prediction for CodingQuarry_transcript_46253-T1 Valid prediction for GlimmerHMM_glimmerT_7248-T1 Valid prediction for GlimmerHMM_glimmerT_7240-T1 Valid prediction for snap_scaffold_3-snap.2094-T1 Valid prediction for GlimmerHMM_glimmerT_7249-T1 Valid prediction for snap_scaffold_3-snap.2121-T1 Valid prediction for GlimmerHMM_glimmerT_7243-T1 Couldn't classify 22189, 22273 Sorry, prediction pasa_asmbl_39108.p1 fails validation. (TTC) CC 22189-22273 GT GGG (ACC) AG 22881-23086 GT GGG (GAG) AG 23182-23228 GT AAG (TGC) AG 23358-23432 GT AAG (GTG) AG 23635-23783 GT AGG (GCC) AG 23983-24097 GT AAG (GAA) AG 24404-24591 GT TGG (CAC) AG 25746-25887 GT AAG (GTA) AG 26109-26235 GT AGG (GTG) AG 26850-27020 GT TCG (GCT) AG 27705-27728 CA GAC -recovered pasa_asmbl_39108.p1, terminal, 27705, 27728 -recovered pasa_asmbl_39108.p1, internal, 22881, 23086 -recovered pasa_asmbl_39108.p1, internal, 23182, 23228 -recovered pasa_asmbl_39108.p1, internal, 23358, 23432 -recovered pasa_asmbl_39108.p1, internal, 23635, 23783 -recovered pasa_asmbl_39108.p1, internal, 23983, 24097 -recovered pasa_asmbl_39108.p1, internal, 24404, 24591 -recovered pasa_asmbl_39108.p1, internal, 25746, 25887 -recovered pasa_asmbl_39108.p1, internal, 26109, 26235 -recovered pasa_asmbl_39108.p1, internal, 26850, 27020 Valid prediction for GlimmerHMM_glimmerT_7266-T1 Valid prediction for GlimmerHMM_glimmerT_7242-T1 Valid prediction for GlimmerHMM_glimmerT_7244-T1 Couldn't classify 141696, 141878 Sorry, prediction pasa_asmbl_39105.p1 fails validation. (TTC) AG 141696-141878 GT AGG (GTG) AG 142143-142289 AA GAA -recovered pasa_asmbl_39105.p1, terminal, 142143, 142289 -recovered pasa_asmbl_39105.p1, internal, 141696, 141878 Valid prediction for CodingQuarry_transcript_46254-T1 Valid prediction for snap_scaffold_3-snap.2106-T1 Valid prediction for CodingQuarry_transcript_46262-T1 Valid prediction for snap_scaffold_3-snap.2112-T1 Valid prediction for snap_scaffold_3-snap.2110-T1 Valid prediction for GlimmerHMM_glimmerT_7252-T1 Valid prediction for GlimmerHMM_glimmerT_7241-T1 Valid prediction for Augustus_model.g4725.t1 Valid prediction for snap_scaffold_3-snap.2126-T1 Valid prediction for Augustus_model.g4717.t1 Valid prediction for GlimmerHMM_glimmerT_7255-T1 Valid prediction for snap_scaffold_3-snap.2131-T1 Valid prediction for snap_scaffold_3-snap.2124-T1 Valid prediction for Augustus_model.g4719.t1 Valid prediction for snap_scaffold_3-snap.2099-T1 Valid prediction for snap_scaffold_3-snap.2107-T1 Valid prediction for snap_scaffold_3-snap.2104-T1 Valid prediction for snap_scaffold_3-snap.2134-T1 Valid prediction for GlimmerHMM_glimmerT_7259-T1 Valid prediction for snap_scaffold_3-snap.2114-T1 Valid prediction for GlimmerHMM_glimmerT_7261-T1 Valid prediction for HiQ_model.g4716.t1 Valid prediction for GlimmerHMM_glimmerT_7246-T1 Valid prediction for GlimmerHMM_glimmerT_7250-T1 Couldn't classify 20685, 21089 Sorry, prediction pasa_asmbl_39109.p1 fails validation. (ACC) AC 20685-21089 GC CAG Valid prediction for snap_scaffold_3-snap.2100-T1 Valid prediction for snap_scaffold_3-snap.2091-T1 Valid prediction for GlimmerHMM_glimmerT_7264-T1 Valid prediction for pasa_asmbl_39101.p2 Valid prediction for snap_scaffold_3-snap.2108-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30914, rend_intergenic: 28051 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36817, rend_intergenic: 32704 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67924, rend_intergenic: 63517 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90437, rend_intergenic: 85440 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 97596, rend_intergenic: 95105 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 122767, rend_intergenic: 118483 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129972, rend_intergenic: 124064 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137016, rend_intergenic: 130615 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140599, rend_intergenic: 139092 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 163044, rend_intergenic: 154096 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 172998, rend_intergenic: 165335 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 173085, rend_intergenic: 173082 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 119465, rend_intergenic: 119462 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 181010 -exon list size: 409 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 1.9 2.2 2.4 2.7 2.9 3.2 3.4 3.6 3.9 4.1 4.4 4.6 4.9 5.1 5.4 5.6 5.8 6.1 6.3 6.6 6.8 7.1 7.3 7.5 7.8 8.0 8.3 8.5 8.8 9.0 9.2 9.5 9.7 10.0 10.2 10.5 10.7 10.9 11.2 11.4 11.7 11.9 12.2 12.4 12.7 12.9 13.1 13.4 13.6 13.9 14.1 14.4 14.6 14.8 15.1 15.3 15.6 15.8 16.1 16.3 16.5 16.8 17.0 17.3 17.5 17.8 18.0 18.2 18.5 18.7 19.0 19.2 19.5 19.7 20.0 20.2 20.4 20.7 20.9 21.2 21.4 21.7 21.9 22.1 22.4 22.6 22.9 23.1 23.4 23.6 23.8 24.1 24.3 24.6 24.8 25.1 25.3 25.5 25.8 26.0 26.3 26.5 26.8 27.0 27.3 27.5 27.7 28.0 28.2 28.5 28.7 29.0 29.2 29.4 29.7 29.9 30.2 30.4 30.7 30.9 31.1 31.4 31.6 31.9 32.1 32.4 32.6 32.8 33.1 33.3 33.6 33.8 34.1 34.3 34.5 34.8 35.0 35.3 35.5 35.8 36.0 36.3 36.5 36.7 37.0 37.2 37.5 37.7 38.0 38.2 38.4 38.7 38.9 39.2 39.4 39.7 39.9 40.1 40.4 40.6 40.9 41.1 41.4 41.6 41.8 42.1 42.3 42.6 42.8 43.1 43.3 43.6 43.8 44.0 44.3 44.5 44.8 45.0 45.3 45.5 45.7 46.0 46.2 46.5 46.7 47.0 47.2 47.4 47.7 47.9 48.2 48.4 48.7 48.9 49.1 49.4 49.6 49.9 50.1 50.4 50.6 50.9 51.1 51.3 51.6 51.8 52.1 52.3 52.6 52.8 53.0 53.3 53.5 53.8 54.0 54.3 54.5 54.7 55.0 55.2 55.5 55.7 56.0 56.2 56.4 56.7 56.9 57.2 57.4 57.7 57.9 58.2 58.4 58.6 58.9 59.1 59.4 59.6 59.9 60.1 60.3 60.6 60.8 61.1 61.3 61.6 61.8 62.0 62.3 62.5 62.8 63.0 63.3 63.5 63.7 64.0 64.2 64.5 64.7 65.0 65.2 65.5 65.7 65.9 66.2 66.4 66.7 66.9 67.2 67.4 67.6 67.9 68.1 68.4 68.6 68.9 69.1 69.3 69.6 69.8 70.1 70.3 70.6 70.8 71.0 71.3 71.5 71.8 72.0 72.3 72.5 72.7 73.0 73.2 73.5 73.7 74.0 74.2 74.5 74.7 74.9 75.2 75.4 75.7 75.9 76.2 76.4 76.6 76.9 77.1 77.4 77.6 77.9 78.1 78.3 78.6 78.8 79.1 79.3 79.6 79.8 80.0 80.3 80.5 80.8 81.0 81.3 81.5 81.8 82.0 82.2 82.5 82.7 83.0 83.2 83.5 83.7 83.9 84.2 84.4 84.7 84.9 85.2 85.4 85.6 85.9 86.1 86.4 86.6 86.9 87.1 87.3 87.6 87.8 88.1 88.3 88.6 88.8 89.1 89.3 89.5 89.8 90.0 90.3 90.5 90.8 91.0 91.2 91.5 91.7 92.0 92.2 92.5 92.7 92.9 93.2 93.4 93.7 93.9 94.2 94.4 94.6 94.9 95.1 95.4 95.6 95.9 96.1 96.4 96.6 96.8 97.1 97.3 97.6 97.8 98.1 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 32 predictions from path traversal Error with prediction: snap lend_intergenic: 30914, rend_intergenic: 28051 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36817, rend_intergenic: 32704 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67924, rend_intergenic: 63517 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90437, rend_intergenic: 85440 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 97596, rend_intergenic: 95105 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 122767, rend_intergenic: 118483 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129972, rend_intergenic: 124064 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137016, rend_intergenic: 130615 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140599, rend_intergenic: 139092 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 163044, rend_intergenic: 154096 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 172998, rend_intergenic: 165335 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 173085, rend_intergenic: 173082 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 119465, rend_intergenic: 119462 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 19 predictions persist after filtering for low support