-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_14935477-15160691 -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 GlimmerHMM_glimmerT_18574-T1 Valid prediction for snap_scaffold_7-snap.2838-T1 Valid prediction for snap_scaffold_7-snap.2832-T1 Valid prediction for snap_scaffold_7-snap.2831-T1 Valid prediction for snap_scaffold_7-snap.2851-T1 Valid prediction for GlimmerHMM_glimmerT_18587-T1 Valid prediction for GlimmerHMM_glimmerT_18577-T1 Couldn't classify 128728, 128893 Sorry, prediction pasa_asmbl_50412.p1 fails validation. (AGG) CC 128728-128893 GT GAG (GCA) AG 129117-129224 GT GAG (GTA) AG 129412-130022 TT GAT add_exon() Sorry, pasa_asmbl_50412.p1 129117-129224-terminal-1 is invalid. -recovered pasa_asmbl_50412.p1, terminal, 129117, 129224 -recovered pasa_asmbl_50412.p1, terminal, 129412, 130022 -recovered pasa_asmbl_50412.p1, internal, 129117, 129224 Valid prediction for GlimmerHMM_glimmerT_18573-T1 Valid prediction for snap_scaffold_7-snap.2828-T1 Valid prediction for GlimmerHMM_glimmerT_18583-T1 Valid prediction for GlimmerHMM_glimmerT_18572-T1 Valid prediction for snap_scaffold_7-snap.2852-T1 Valid prediction for Augustus_model.g12523.t1 Valid prediction for snap_scaffold_7-snap.2844-T1 Valid prediction for snap_scaffold_7-snap.2834-T1 Valid prediction for Augustus_model.g12510.t1 Couldn't classify 30217, 30315 Couldn't classify 37095, 37212 Sorry, prediction pasa_asmbl_50406.p1 fails validation. (GGC) AG 30217-30315 GT AGG (GAA) AG 30643-30736 GT GTG (TGT) AG 31517-31586 GT AAG (GTC) AG 32746-32773 GT AGG (ATC) AG 33288-33342 GT TGG (AGG) AG 34711-34817 GT AGG (GGA) AG 35372-35449 GT AGG (GCT) AG 35808-35870 GT ATG (GAC) AG 35986-36099 GT AGG (AAA) AG 36853-36983 GT ATG (GAG) AG 37095-37212 GG AGG -recovered pasa_asmbl_50406.p1, internal, 30217, 30315 -recovered pasa_asmbl_50406.p1, internal, 30643, 30736 -recovered pasa_asmbl_50406.p1, internal, 31517, 31586 -recovered pasa_asmbl_50406.p1, internal, 32746, 32773 -recovered pasa_asmbl_50406.p1, internal, 33288, 33342 -recovered pasa_asmbl_50406.p1, internal, 34711, 34817 -recovered pasa_asmbl_50406.p1, internal, 35372, 35449 -recovered pasa_asmbl_50406.p1, internal, 35808, 35870 -recovered pasa_asmbl_50406.p1, internal, 35986, 36099 -recovered pasa_asmbl_50406.p1, internal, 36853, 36983 Valid prediction for snap_scaffold_7-snap.2835-T1 Valid prediction for snap_scaffold_7-snap.2817-T1 Valid prediction for snap_scaffold_7-snap.2846-T1 Valid prediction for Augustus_model.g12519.t1 Valid prediction for GlimmerHMM_glimmerT_18571-T1 Couldn't classify 51280, 51348 Sorry, prediction pasa_asmbl_50409.p1 fails validation. (ACT) AG 51280-51348 GT AGG (ATG) AG 51479-51569 GT CAG (AGG) AG 52187-52329 GT AGG (GTG) AG 53266-53446 GT AGG (AGG) AG 53780-53910 GC AGG -recovered pasa_asmbl_50409.p1, initial, 51479, 51569 -recovered pasa_asmbl_50409.p1, terminal, 53780, 53910 -recovered pasa_asmbl_50409.p1, internal, 51280, 51348 -recovered pasa_asmbl_50409.p1, internal, 51479, 51569 -recovered pasa_asmbl_50409.p1, internal, 52187, 52329 -recovered pasa_asmbl_50409.p1, internal, 53266, 53446 -recovered pasa_asmbl_50409.p1, internal, 53780, 53910 Valid prediction for GlimmerHMM_glimmerT_18580-T1 Valid prediction for Augustus_model.g12511.t1 Valid prediction for CodingQuarry_transcript_57720-T1 Valid prediction for snap_scaffold_7-snap.2821-T1 Valid prediction for Augustus_model.g12513.t1 Valid prediction for Augustus_model.g12517.t1 Valid prediction for snap_scaffold_7-snap.2826-T1 Couldn't classify 21884, 22116 Couldn't classify 25702, 25811 Sorry, prediction pasa_asmbl_50405.p1 fails validation. (TTT) AC 21884-22116 GT AGG (GTG) AG 22894-23102 GT AGG (GCT) AG 23358-23480 GT GGG (GGG) AG 23863-23984 GT GGG (GTA) AG 24138-24196 GT AGG (CAC) AG 24281-24367 GT GGG (GGA) AG 24510-24636 GT AGG (ACC) AG 24813-24957 GT AGG (ATG) AG 25224-25381 GT TGG (CCT) AG 25474-25579 GT AGG (CTA) AG 25702-25811 GG GTG add_exon() Sorry, pasa_asmbl_50405.p1 25224-25381-initial-1 is invalid. -recovered pasa_asmbl_50405.p1, initial, 25224, 25381 -recovered pasa_asmbl_50405.p1, internal, 22894, 23102 -recovered pasa_asmbl_50405.p1, internal, 23358, 23480 -recovered pasa_asmbl_50405.p1, internal, 23863, 23984 -recovered pasa_asmbl_50405.p1, internal, 24138, 24196 -recovered pasa_asmbl_50405.p1, internal, 24281, 24367 -recovered pasa_asmbl_50405.p1, internal, 24510, 24636 -recovered pasa_asmbl_50405.p1, internal, 24813, 24957 -recovered pasa_asmbl_50405.p1, internal, 25224, 25381 -recovered pasa_asmbl_50405.p1, internal, 25474, 25579 Valid prediction for GlimmerHMM_glimmerT_18588-T1 Valid prediction for snap_scaffold_7-snap.2836-T1 Valid prediction for snap_scaffold_7-snap.2848-T1 Valid prediction for GlimmerHMM_glimmerT_18570-T1 Valid prediction for snap_scaffold_7-snap.2839-T1 Valid prediction for Augustus_model.g12509.t1 Valid prediction for snap_scaffold_7-snap.2815-T1 Couldn't classify 61649, 61781 Sorry, prediction pasa_asmbl_50410.p1 fails validation. (AGG) CC 61649-61781 GT ACG (TCA) AG 62149-62264 GT CGG (CGC) AG 64861-64935 GT AGG (GTG) AG 65300-65384 GT CAG (ATA) AG 66024-66166 GT CTG (GAG) AG 67758-67832 CT AAC -recovered pasa_asmbl_50410.p1, terminal, 67758, 67832 -recovered pasa_asmbl_50410.p1, internal, 62149, 62264 -recovered pasa_asmbl_50410.p1, internal, 64861, 64935 -recovered pasa_asmbl_50410.p1, internal, 65300, 65384 -recovered pasa_asmbl_50410.p1, internal, 66024, 66166 Valid prediction for snap_scaffold_7-snap.2825-T1 Valid prediction for GlimmerHMM_glimmerT_18576-T1 Valid prediction for snap_scaffold_7-snap.2810-T1 Valid prediction for HiQ_model.g12508.t1 Valid prediction for snap_scaffold_7-snap.2816-T1 Valid prediction for Augustus_model.g12507.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_18568-T1 Couldn't classify 139606, 139645 Sorry, prediction pasa_asmbl_51351.p1 fails validation. (TTG) CT 139606-139645 GT AGG (GTT) AG 139729-140000 GT AGG (GAA) AG 140836-140898 CA AAC -recovered pasa_asmbl_51351.p1, terminal, 140836, 140898 -recovered pasa_asmbl_51351.p1, internal, 139729, 140000 Valid prediction for GlimmerHMM_glimmerT_18589-T1 Valid prediction for GlimmerHMM_glimmerT_18575-T1 Valid prediction for GlimmerHMM_glimmerT_18584-T1 Valid prediction for snap_scaffold_7-snap.2812-T1 Valid prediction for GlimmerHMM_glimmerT_18578-T1 Valid prediction for Augustus_model.g12520.t1 Valid prediction for snap_scaffold_7-snap.2819-T1 Valid prediction for Augustus_model.g12515.t1 Valid prediction for snap_scaffold_7-snap.2822-T1 Valid prediction for snap_scaffold_7-snap.2849-T1 Valid prediction for Augustus_model.g12522.t1 Valid prediction for snap_scaffold_7-snap.2823-T1 Valid prediction for Augustus_model.g12514.t1 Valid prediction for snap_scaffold_7-snap.2840-T1 Valid prediction for Augustus_model.g12506.t1 Valid prediction for snap_scaffold_7-snap.2827-T1 Sorry, intron length (9) is less than minimum required (10) Sorry, intron length (3) is less than minimum required (10) Valid prediction for Augustus_model.g12521.t1 Valid prediction for snap_scaffold_7-snap.2837-T1 Valid prediction for GlimmerHMM_glimmerT_18585-T1 Valid prediction for snap_scaffold_7-snap.2841-T1 Valid prediction for CodingQuarry_transcript_57722-T1 Valid prediction for snap_scaffold_7-snap.2820-T1 Valid prediction for Augustus_model.g12524.t1 Valid prediction for GlimmerHMM_glimmerT_18579-T1 Couldn't classify 134005, 134805 Sorry, prediction pasa_asmbl_51352.p1 fails validation. (CCT) TA 134005-134805 AG AAA Valid prediction for snap_scaffold_7-snap.2845-T1 Valid prediction for Augustus_model.g12518.t1 Valid prediction for pasa_asmbl_51353.p2 Valid prediction for snap_scaffold_7-snap.2814-T1 Valid prediction for snap_scaffold_7-snap.2818-T1 Couldn't classify 36382, 36474 Sorry, prediction pasa_asmbl_51364.p1 fails validation. (ATG) CA 34055-34091 GT GGG (GTA) AG 34239-34395 GT AGG (GCT) AG 34565-34688 GT AAG (AGC) AG 34868-35038 GT AGG (GTG) AG 35353-35516 GT AGG (AAC) AG 35881-36022 GT CTG (AAA) AG 36382-36474 GC CTG -recovered pasa_asmbl_51364.p1, initial, 34055, 34091 -recovered pasa_asmbl_51364.p1, internal, 34239, 34395 -recovered pasa_asmbl_51364.p1, internal, 34565, 34688 -recovered pasa_asmbl_51364.p1, internal, 34868, 35038 -recovered pasa_asmbl_51364.p1, internal, 35353, 35516 -recovered pasa_asmbl_51364.p1, internal, 35881, 36022 -recovered pasa_asmbl_51364.p1, internal, 36382, 36474 Couldn't classify 88796, 89014 Couldn't classify 89653, 90150 Sorry, prediction pasa_asmbl_51362.p1 fails validation. (AGA) CC 88796-89014 GT AGG (GTG) AG 89653-90150 AC CCA Couldn't classify 77292, 77318 Couldn't classify 77593, 77868 Sorry, prediction pasa_asmbl_51363.p1 fails validation. (AGC) CT 77292-77318 GT AGG (CAG) AG 77593-77868 AG AGA Valid prediction for Augustus_model.g12516.t1 Valid prediction for HiQ_model.g12525.t1 Valid prediction for GlimmerHMM_glimmerT_18582-T1 Valid prediction for snap_scaffold_7-snap.2842-T1 Valid prediction for snap_scaffold_7-snap.2824-T1 Valid prediction for snap_scaffold_7-snap.2833-T1 Couldn't classify 90439, 91698 Sorry, prediction pasa_asmbl_51361.p1 fails validation. (CCA) GC 90439-91698 GT TGG Valid prediction for Augustus_model.g12512.t1 Valid prediction for CodingQuarry_transcript_57721-T1 Valid prediction for snap_scaffold_7-snap.2850-T1 Valid prediction for GlimmerHMM_glimmerT_18581-T1 Couldn't classify 116928, 117500 Sorry, prediction pasa_asmbl_51357.p1 fails validation. (GAC) CA 116928-117500 CT CTC Valid prediction for GlimmerHMM_glimmerT_18586-T1 Valid prediction for snap_scaffold_7-snap.2843-T1 Valid prediction for snap_scaffold_7-snap.2847-T1 Valid prediction for CodingQuarry_transcript_57723-T1 Valid prediction for snap_scaffold_7-snap.2813-T1 Valid prediction for GlimmerHMM_glimmerT_18569-T1 Couldn't classify 107098, 107161 Sorry, prediction pasa_asmbl_51358.p1 fails validation. (CTA) CA 107098-107161 GT AAG (GAT) AG 107419-107567 GT AGG (TCT) AG 109916-110005 GT GGG (ACG) AG 110908-111084 AA GAA -recovered pasa_asmbl_51358.p1, terminal, 110908, 111084 -recovered pasa_asmbl_51358.p1, internal, 107419, 107567 -recovered pasa_asmbl_51358.p1, internal, 109916, 110005 Valid prediction for snap_scaffold_7-snap.2811-T1 Valid prediction for snap_scaffold_7-snap.2830-T1 Valid prediction for snap_scaffold_7-snap.2829-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4880, rend_intergenic: 2520 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20852, rend_intergenic: 13410 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55136, rend_intergenic: 33246 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67832, rend_intergenic: 57282 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75960, rend_intergenic: 73440 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 82458, rend_intergenic: 76531 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 113869, rend_intergenic: 99475 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134940, rend_intergenic: 133374 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137706, rend_intergenic: 135055 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 199011, rend_intergenic: 194224 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 208049, rend_intergenic: 203074 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 213110, rend_intergenic: 210563 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 225215 -exon list size: 401 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 2.0 2.2 2.5 2.7 3.0 3.2 3.5 3.7 4.0 4.2 4.5 4.7 5.0 5.2 5.5 5.7 6.0 6.2 6.5 6.7 6.9 7.2 7.4 7.7 7.9 8.2 8.4 8.7 8.9 9.2 9.4 9.7 9.9 10.2 10.4 10.7 10.9 11.2 11.4 11.7 11.9 12.2 12.4 12.7 12.9 13.2 13.4 13.6 13.9 14.1 14.4 14.6 14.9 15.1 15.4 15.6 15.9 16.1 16.4 16.6 16.9 17.1 17.4 17.6 17.9 18.1 18.4 18.6 18.9 19.1 19.4 19.6 19.9 20.1 20.3 20.6 20.8 21.1 21.3 21.6 21.8 22.1 22.3 22.6 22.8 23.1 23.3 23.6 23.8 24.1 24.3 24.6 24.8 25.1 25.3 25.6 25.8 26.1 26.3 26.6 26.8 27.0 27.3 27.5 27.8 28.0 28.3 28.5 28.8 29.0 29.3 29.5 29.8 30.0 30.3 30.5 30.8 31.0 31.3 31.5 31.8 32.0 32.3 32.5 32.8 33.0 33.3 33.5 33.7 34.0 34.2 34.5 34.7 35.0 35.2 35.5 35.7 36.0 36.2 36.5 36.7 37.0 37.2 37.5 37.7 38.0 38.2 38.5 38.7 39.0 39.2 39.5 39.7 40.0 40.2 40.4 40.7 40.9 41.2 41.4 41.7 41.9 42.2 42.4 42.7 42.9 43.2 43.4 43.7 43.9 44.2 44.4 44.7 44.9 45.2 45.4 45.7 45.9 46.2 46.4 46.7 46.9 47.1 47.4 47.6 47.9 48.1 48.4 48.6 48.9 49.1 49.4 49.6 49.9 50.1 50.4 50.6 50.9 51.1 51.4 51.6 51.9 52.1 52.4 52.6 52.9 53.1 53.3 53.6 53.8 54.1 54.3 54.6 54.8 55.1 55.3 55.6 55.8 56.1 56.3 56.6 56.8 57.1 57.3 57.6 57.8 58.1 58.3 58.6 58.8 59.1 59.3 59.6 59.8 60.0 60.3 60.5 60.8 61.0 61.3 61.5 61.8 62.0 62.3 62.5 62.8 63.0 63.3 63.5 63.8 64.0 64.3 64.5 64.8 65.0 65.3 65.5 65.8 66.0 66.3 66.5 66.7 67.0 67.2 67.5 67.7 68.0 68.2 68.5 68.7 69.0 69.2 69.5 69.7 70.0 70.2 70.5 70.7 71.0 71.2 71.5 71.7 72.0 72.2 72.5 72.7 73.0 73.2 73.4 73.7 73.9 74.2 74.4 74.7 74.9 75.2 75.4 75.7 75.9 76.2 76.4 76.7 76.9 77.2 77.4 77.7 77.9 78.2 78.4 78.7 78.9 79.2 79.4 79.7 79.9 80.1 80.4 80.6 80.9 81.1 81.4 81.6 81.9 82.1 82.4 82.6 82.9 83.1 83.4 83.6 83.9 84.1 84.4 84.6 84.9 85.1 85.4 85.6 85.9 86.1 86.4 86.6 86.8 87.1 87.3 87.6 87.8 88.1 88.3 88.6 88.8 89.1 89.3 89.6 89.8 90.1 90.3 90.6 90.8 91.1 91.3 91.6 91.8 92.1 92.3 92.6 92.8 93.1 93.3 93.5 93.8 94.0 94.3 94.5 94.8 95.0 95.3 95.5 95.8 96.0 96.3 96.5 96.8 97.0 97.3 97.5 97.8 98.0 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 29 predictions from path traversal Error with prediction: snap lend_intergenic: 4880, rend_intergenic: 2520 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20852, rend_intergenic: 13410 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55136, rend_intergenic: 33246 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67832, rend_intergenic: 57282 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75960, rend_intergenic: 73440 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 82458, rend_intergenic: 76531 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 113869, rend_intergenic: 99475 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134940, rend_intergenic: 133374 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137706, rend_intergenic: 135055 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 199011, rend_intergenic: 194224 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 208049, rend_intergenic: 203074 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 213110, rend_intergenic: 210563 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 20 predictions persist after filtering for low support -building DP trellis -building trellis in range 212606 - 225215 -exon list size: 9 building trellis 9.1 18.2 27.3 36.4 45.5 54.5 63.6 72.7 81.8 90.9 -found 2 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support