-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_15391280-15615653 -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_7-snap.2928-T1 Valid prediction for GlimmerHMM_glimmerT_18624-T1 Valid prediction for snap_scaffold_7-snap.2931-T1 Valid prediction for snap_scaffold_7-snap.2935-T1 Couldn't classify 206831, 206945 Sorry, prediction pasa_asmbl_50451.p1 fails validation. (CCC) CT 206831-206945 GT AGG (ACG) AG 207116-207261 GT AGG (TCC) AG 208445-208561 TT AAT -recovered pasa_asmbl_50451.p1, terminal, 208445, 208561 -recovered pasa_asmbl_50451.p1, internal, 207116, 207261 Valid prediction for snap_scaffold_7-snap.2917-T1 Valid prediction for snap_scaffold_7-snap.2919-T1 Valid prediction for snap_scaffold_7-snap.2900-T1 Valid prediction for snap_scaffold_7-snap.2895-T1 Valid prediction for snap_scaffold_7-snap.2926-T1 Valid prediction for GlimmerHMM_glimmerT_18612-T1 Couldn't classify 10841, 11410 Sorry, prediction pasa_asmbl_50445.p2 fails validation. (AGA) CT 10841-11410 TG AGT Valid prediction for HiQ_model.g12554.t1 Valid prediction for GlimmerHMM_glimmerT_18639-T1 Valid prediction for snap_scaffold_7-snap.2915-T1 Valid prediction for GlimmerHMM_glimmerT_18614-T1 Valid prediction for GlimmerHMM_glimmerT_18636-T1 Valid prediction for snap_scaffold_7-snap.2901-T1 Valid prediction for snap_scaffold_7-snap.2913-T1 Valid prediction for snap_scaffold_7-snap.2904-T1 Valid prediction for snap_scaffold_7-snap.2911-T1 Valid prediction for Augustus_model.g12552.t1 Valid prediction for GlimmerHMM_glimmerT_18617-T1 Valid prediction for GlimmerHMM_glimmerT_18623-T1 Couldn't classify 208920, 209136 Sorry, prediction CodingQuarry_transcript_57733-T1 fails validation. (ATG) AG 208920-209136 CT CTC (ACC) AG 209455-209477 CC GAC -recovered CodingQuarry_transcript_57733-T1, terminal, 209455, 209477 Couldn't classify 205876, 205907 Couldn't classify 206764, 206827 Sorry, prediction pasa_asmbl_50607.p1 fails validation. (CAG) GT 205876-205907 GT CGG (GAT) AG 206137-206295 GT GAG (GCT) AG 206516-206668 GT CTG (GGA) AG 206764-206827 TC TGT -recovered pasa_asmbl_50607.p1, internal, 206137, 206295 -recovered pasa_asmbl_50607.p1, internal, 206516, 206668 Valid prediction for snap_scaffold_7-snap.2903-T1 Valid prediction for GlimmerHMM_glimmerT_18640-T1 Couldn't classify 205762, 205821 Sorry, prediction pasa_asmbl_50449.p1 fails validation. (ATG) AG 204672-204814 GT AGG (CTC) AG 205128-205272 GT ATG (GAG) AG 205762-205821 CT AGC -recovered pasa_asmbl_50449.p1, initial, 204672, 204814 -recovered pasa_asmbl_50449.p1, internal, 204672, 204814 -recovered pasa_asmbl_50449.p1, internal, 205128, 205272 Valid prediction for Augustus_model.g12542.t1 Valid prediction for GlimmerHMM_glimmerT_18622-T1 Valid prediction for snap_scaffold_7-snap.2924-T1 Valid prediction for snap_scaffold_7-snap.2921-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_18628-T1 Valid prediction for snap_scaffold_7-snap.2929-T1 Valid prediction for snap_scaffold_7-snap.2908-T1 Valid prediction for GlimmerHMM_glimmerT_18619-T1 Valid prediction for snap_scaffold_7-snap.2894-T1 Valid prediction for GlimmerHMM_glimmerT_18630-T1 Valid prediction for GlimmerHMM_glimmerT_18621-T1 Valid prediction for CodingQuarry_transcript_57732-T1 Valid prediction for snap_scaffold_7-snap.2916-T1 Valid prediction for GlimmerHMM_glimmerT_18632-T1 Couldn't classify 44047, 44128 Sorry, prediction pasa_asmbl_51383.p1 fails validation. (CTG) AG 44047-44128 GT AGG (GTC) AG 44311-44407 GT CAG (TTG) AG 44512-44663 GT CGG (GGT) AG 44884-45021 GT TGG (GGG) AG 45186-45425 GT AGG (ACC) AG 45698-45906 GT TGG (ACA) AG 46024-46200 GT GGG (CTA) AG 47583-47653 GT AGG (TGC) AG 49437-49536 GT AGG (GTT) AG 49627-49680 GT GGG (AAA) AG 49785-49850 GT ACG (ATG) AG 49941-50009 GT AGG (GGT) AG 50315-50411 GT GGG (TAT) AG 50646-50716 TG GAT -recovered pasa_asmbl_51383.p1, initial, 49941, 50009 add_exon() Sorry, pasa_asmbl_51383.p1 44047-44128-terminal-3 is invalid. -recovered pasa_asmbl_51383.p1, terminal, 44047, 44128 add_exon() Sorry, pasa_asmbl_51383.p1 45186-45425-terminal-1 is invalid. -recovered pasa_asmbl_51383.p1, terminal, 45186, 45425 -recovered pasa_asmbl_51383.p1, terminal, 50646, 50716 -recovered pasa_asmbl_51383.p1, internal, 44047, 44128 -recovered pasa_asmbl_51383.p1, internal, 44311, 44407 -recovered pasa_asmbl_51383.p1, internal, 44512, 44663 -recovered pasa_asmbl_51383.p1, internal, 44884, 45021 -recovered pasa_asmbl_51383.p1, internal, 45186, 45425 -recovered pasa_asmbl_51383.p1, internal, 45698, 45906 -recovered pasa_asmbl_51383.p1, internal, 46024, 46200 -recovered pasa_asmbl_51383.p1, internal, 47583, 47653 -recovered pasa_asmbl_51383.p1, internal, 49437, 49536 -recovered pasa_asmbl_51383.p1, internal, 49627, 49680 -recovered pasa_asmbl_51383.p1, internal, 49785, 49850 -recovered pasa_asmbl_51383.p1, internal, 49941, 50009 -recovered pasa_asmbl_51383.p1, internal, 50315, 50411 Valid prediction for GlimmerHMM_glimmerT_18615-T1 Valid prediction for Augustus_model.g12545.t1 Valid prediction for Augustus_model.g12544.t1 Valid prediction for Augustus_model.g12550.t1 Valid prediction for Augustus_model.g12555.t1 Valid prediction for GlimmerHMM_glimmerT_18629-T1 Valid prediction for GlimmerHMM_glimmerT_18618-T1 Valid prediction for HiQ_model.g12549.t1 Valid prediction for snap_scaffold_7-snap.2920-T1 Valid prediction for snap_scaffold_7-snap.2902-T1 Valid prediction for snap_scaffold_7-snap.2933-T1 Valid prediction for snap_scaffold_7-snap.2930-T1 Valid prediction for snap_scaffold_7-snap.2923-T1 Valid prediction for snap_scaffold_7-snap.2896-T1 Valid prediction for GlimmerHMM_glimmerT_18633-T1 Valid prediction for snap_scaffold_7-snap.2898-T1 Valid prediction for HiQ_model.g12548.t1 Valid prediction for snap_scaffold_7-snap.2893-T1 Valid prediction for GlimmerHMM_glimmerT_18637-T1 Valid prediction for snap_scaffold_7-snap.2909-T1 Valid prediction for snap_scaffold_7-snap.2905-T1 Valid prediction for snap_scaffold_7-snap.2927-T1 Valid prediction for GlimmerHMM_glimmerT_18626-T1 Valid prediction for GlimmerHMM_glimmerT_18627-T1 Couldn't classify 21194, 21257 Sorry, prediction pasa_asmbl_51387.p1 fails validation. (AGT) GC 21194-21257 GT ACG (GTT) AG 21491-21730 GT AGG (GAG) AG 21838-21955 GT AGG (GCT) AG 22048-22135 GT GGG (GTC) AG 22301-22479 GT GGG (ATA) AG 22592-22784 GT CGG (GTG) AG 23000-23128 GT TGG (GCT) AG 23727-23852 GT AGG (GGT) AG 23937-24022 GT AGG (TTC) AG 24098-24207 GT CAG (GTG) AG 24562-24793 GT TGG (GTC) AG 25120-25187 GT GGG (GGG) AG 25410-25618 GT AGG (GAT) AG 25764-25985 TG GAT -recovered pasa_asmbl_51387.p1, terminal, 25764, 25985 -recovered pasa_asmbl_51387.p1, internal, 21491, 21730 -recovered pasa_asmbl_51387.p1, internal, 21838, 21955 -recovered pasa_asmbl_51387.p1, internal, 22048, 22135 -recovered pasa_asmbl_51387.p1, internal, 22301, 22479 -recovered pasa_asmbl_51387.p1, internal, 22592, 22784 -recovered pasa_asmbl_51387.p1, internal, 23000, 23128 -recovered pasa_asmbl_51387.p1, internal, 23727, 23852 -recovered pasa_asmbl_51387.p1, internal, 23937, 24022 -recovered pasa_asmbl_51387.p1, internal, 24098, 24207 -recovered pasa_asmbl_51387.p1, internal, 24562, 24793 -recovered pasa_asmbl_51387.p1, internal, 25120, 25187 -recovered pasa_asmbl_51387.p1, internal, 25410, 25618 Valid prediction for Augustus_model.g12551.t1 Valid prediction for snap_scaffold_7-snap.2906-T1 Valid prediction for GlimmerHMM_glimmerT_18631-T1 Valid prediction for snap_scaffold_7-snap.2922-T1 Valid prediction for snap_scaffold_7-snap.2918-T1 Valid prediction for GlimmerHMM_glimmerT_18613-T1 Valid prediction for HiQ_model.g12553.t1 Valid prediction for GlimmerHMM_glimmerT_18616-T1 Valid prediction for snap_scaffold_7-snap.2910-T1 Valid prediction for GlimmerHMM_glimmerT_18625-T1 Valid prediction for snap_scaffold_7-snap.2932-T1 Valid prediction for GlimmerHMM_glimmerT_18641-T1 Valid prediction for GlimmerHMM_glimmerT_18620-T1 Valid prediction for snap_scaffold_7-snap.2912-T1 Valid prediction for Augustus_model.g12543.t1 Valid prediction for Augustus_model.g12546.t1 Valid prediction for snap_scaffold_7-snap.2934-T1 Couldn't classify 59021, 59079 Sorry, prediction pasa_asmbl_51380.p1 fails validation. (ATG) CA 51910-52038 GT AGG (ACC) AG 54685-54799 GT AGG (GAG) AG 54956-55075 GT GGG (AGA) AG 55405-55491 GT AGG (AAA) AG 55612-55699 GT AGG (CTG) AG 55893-55971 GT AGG (GAC) AG 57337-57418 GT AGG (ACA) AG 59021-59079 TC TCT -recovered pasa_asmbl_51380.p1, initial, 51910, 52038 -recovered pasa_asmbl_51380.p1, internal, 54685, 54799 -recovered pasa_asmbl_51380.p1, internal, 54956, 55075 -recovered pasa_asmbl_51380.p1, internal, 55405, 55491 -recovered pasa_asmbl_51380.p1, internal, 55612, 55699 -recovered pasa_asmbl_51380.p1, internal, 55893, 55971 -recovered pasa_asmbl_51380.p1, internal, 57337, 57418 Valid prediction for snap_scaffold_7-snap.2899-T1 Valid prediction for pasa_asmbl_51377.p1 Valid prediction for Augustus_model.g12547.t1 Valid prediction for GlimmerHMM_glimmerT_18634-T1 Valid prediction for snap_scaffold_7-snap.2907-T1 Valid prediction for snap_scaffold_7-snap.2897-T1 Valid prediction for GlimmerHMM_glimmerT_18638-T1 Valid prediction for GlimmerHMM_glimmerT_18611-T1 Valid prediction for snap_scaffold_7-snap.2925-T1 Couldn't classify 36753, 36950 Sorry, prediction pasa_asmbl_51386.p1 fails validation. (CAT) AG 36753-36950 GT TGG (ACA) AG 37276-37452 GT AGG (CTG) AG 37748-37818 GT AGG (TGC) AG 38563-38662 GT AGG (GTT) AG 38753-38806 GT GGG (AAA) AG 38911-38976 GT ATG (ATG) AG 39074-39142 GT AGG (GGT) AG 39406-39502 GT GAG (TAT) AG 39625-39695 TG GAT -recovered pasa_asmbl_51386.p1, initial, 39074, 39142 -recovered pasa_asmbl_51386.p1, terminal, 39625, 39695 -recovered pasa_asmbl_51386.p1, internal, 36753, 36950 -recovered pasa_asmbl_51386.p1, internal, 37276, 37452 -recovered pasa_asmbl_51386.p1, internal, 37748, 37818 -recovered pasa_asmbl_51386.p1, internal, 38563, 38662 -recovered pasa_asmbl_51386.p1, internal, 38753, 38806 -recovered pasa_asmbl_51386.p1, internal, 38911, 38976 -recovered pasa_asmbl_51386.p1, internal, 39074, 39142 -recovered pasa_asmbl_51386.p1, internal, 39406, 39502 Valid prediction for snap_scaffold_7-snap.2914-T1 Valid prediction for Augustus_model.g12556.t1 Valid prediction for GlimmerHMM_glimmerT_18635-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45253, rend_intergenic: 38534 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53050, rend_intergenic: 48922 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58320, rend_intergenic: 55090 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91411, rend_intergenic: 91070 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 104271, rend_intergenic: 99400 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 144956, rend_intergenic: 116976 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 155869, rend_intergenic: 147473 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 169930, rend_intergenic: 158921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 189025, rend_intergenic: 184680 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 193812, rend_intergenic: 191281 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 210923, rend_intergenic: 204720 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 218051, rend_intergenic: 217888 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 224374 -exon list size: 490 building trellis 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.3 3.5 3.7 3.9 4.1 4.3 4.5 4.7 4.9 5.1 5.3 5.5 5.7 5.9 6.1 6.3 6.5 6.7 6.9 7.1 7.3 7.5 7.7 7.9 8.1 8.3 8.5 8.7 8.9 9.1 9.3 9.6 9.8 10.0 10.2 10.4 10.6 10.8 11.0 11.2 11.4 11.6 11.8 12.0 12.2 12.4 12.6 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.7 15.9 16.1 16.3 16.5 16.7 16.9 17.1 17.3 17.5 17.7 17.9 18.1 18.3 18.5 18.7 18.9 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.5 20.7 20.9 21.1 21.3 21.5 21.7 22.0 22.2 22.4 22.6 22.8 23.0 23.2 23.4 23.6 23.8 24.0 24.2 24.4 24.6 24.8 25.0 25.2 25.4 25.6 25.8 26.0 26.2 26.4 26.6 26.8 27.0 27.2 27.4 27.6 27.8 28.0 28.3 28.5 28.7 28.9 29.1 29.3 29.5 29.7 29.9 30.1 30.3 30.5 30.7 30.9 31.1 31.3 31.5 31.7 31.9 32.1 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.6 34.8 35.0 35.2 35.4 35.6 35.8 36.0 36.2 36.4 36.6 36.8 37.0 37.2 37.4 37.6 37.8 38.0 38.2 38.4 38.6 38.8 39.0 39.2 39.4 39.6 39.8 40.0 40.2 40.4 40.7 40.9 41.1 41.3 41.5 41.7 41.9 42.1 42.3 42.5 42.7 42.9 43.1 43.3 43.5 43.7 43.9 44.1 44.3 44.5 44.7 44.9 45.1 45.3 45.5 45.7 45.9 46.1 46.3 46.5 46.7 47.0 47.2 47.4 47.6 47.8 48.0 48.2 48.4 48.6 48.8 49.0 49.2 49.4 49.6 49.8 50.0 50.2 50.4 50.6 50.8 51.0 51.2 51.4 51.6 51.8 52.0 52.2 52.4 52.6 52.8 53.0 53.3 53.5 53.7 53.9 54.1 54.3 54.5 54.7 54.9 55.1 55.3 55.5 55.7 55.9 56.1 56.3 56.5 56.7 56.9 57.1 57.3 57.5 57.7 57.9 58.1 58.3 58.5 58.7 58.9 59.1 59.3 59.6 59.8 60.0 60.2 60.4 60.6 60.8 61.0 61.2 61.4 61.6 61.8 62.0 62.2 62.4 62.6 62.8 63.0 63.2 63.4 63.6 63.8 64.0 64.2 64.4 64.6 64.8 65.0 65.2 65.4 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.1 67.3 67.5 67.7 67.9 68.1 68.3 68.5 68.7 68.9 69.1 69.3 69.5 69.7 69.9 70.1 70.3 70.5 70.7 70.9 71.1 71.3 71.5 71.7 72.0 72.2 72.4 72.6 72.8 73.0 73.2 73.4 73.6 73.8 74.0 74.2 74.4 74.6 74.8 75.0 75.2 75.4 75.6 75.8 76.0 76.2 76.4 76.6 76.8 77.0 77.2 77.4 77.6 77.8 78.0 78.3 78.5 78.7 78.9 79.1 79.3 79.5 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.1 81.3 81.5 81.7 81.9 82.1 82.3 82.5 82.7 82.9 83.1 83.3 83.5 83.7 83.9 84.1 84.3 84.6 84.8 85.0 85.2 85.4 85.6 85.8 86.0 86.2 86.4 86.6 86.8 87.0 87.2 87.4 87.6 87.8 88.0 88.2 88.4 88.6 88.8 89.0 89.2 89.4 89.6 89.8 90.0 90.2 90.4 90.7 90.9 91.1 91.3 91.5 91.7 91.9 92.1 92.3 92.5 92.7 92.9 93.1 93.3 93.5 93.7 93.9 94.1 94.3 94.5 94.7 94.9 95.1 95.3 95.5 95.7 95.9 96.1 96.3 96.5 96.7 97.0 97.2 97.4 97.6 97.8 98.0 98.2 98.4 98.6 98.8 99.0 99.2 99.4 99.6 99.8 -found 28 predictions from path traversal Error with prediction: snap lend_intergenic: 45253, rend_intergenic: 38534 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53050, rend_intergenic: 48922 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58320, rend_intergenic: 55090 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91411, rend_intergenic: 91070 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 104271, rend_intergenic: 99400 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 144956, rend_intergenic: 116976 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 155869, rend_intergenic: 147473 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 169930, rend_intergenic: 158921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 189025, rend_intergenic: 184680 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 193812, rend_intergenic: 191281 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 210923, rend_intergenic: 204720 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 218051, rend_intergenic: 217888 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 22 predictions persist after filtering for low support