-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_7768871-8023535 -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_27457-T1 Valid prediction for GlimmerHMM_glimmerT_27429-T1 Couldn't classify 181705, 181827 Couldn't classify 184123, 184322 Sorry, prediction pasa_asmbl_5701.p1 fails validation. (ATA) AG 181705-181827 GT GGG (GTG) AG 181913-182074 GT AGG (AGA) AG 182808-182937 GT TGG (GCT) AG 184123-184322 AA ACA -recovered pasa_asmbl_5701.p1, internal, 181705, 181827 -recovered pasa_asmbl_5701.p1, internal, 181913, 182074 -recovered pasa_asmbl_5701.p1, internal, 182808, 182937 Valid prediction for HiQ_model.g18155.t1 Valid prediction for GlimmerHMM_glimmerT_27453-T1 Valid prediction for Augustus_model.g18144.t1 Valid prediction for GlimmerHMM_glimmerT_27448-T1 Valid prediction for pasa_asmbl_5698.p1 Valid prediction for snap_scaffold_11-snap.1803-T1 Valid prediction for snap_scaffold_11-snap.1788-T1 Valid prediction for Augustus_model.g18150.t1 Valid prediction for GlimmerHMM_glimmerT_27428-T1 Valid prediction for snap_scaffold_11-snap.1812-T1 Couldn't classify 50526, 50594 Sorry, prediction pasa_asmbl_5681.p1 fails validation. (AGA) AT 50526-50594 GT AGG (GCA) AG 50691-50835 GT AGG (GTC) AG 52524-52617 GT TCG (CAT) AG 52844-52982 GT AGG (TGT) AG 53094-53262 GT GGG (TGG) AG 53423-53460 AG GAA -recovered pasa_asmbl_5681.p1, terminal, 53423, 53460 -recovered pasa_asmbl_5681.p1, internal, 50691, 50835 -recovered pasa_asmbl_5681.p1, internal, 52524, 52617 -recovered pasa_asmbl_5681.p1, internal, 52844, 52982 -recovered pasa_asmbl_5681.p1, internal, 53094, 53262 Valid prediction for CodingQuarry_transcript_8132-T1 Valid prediction for CodingQuarry_transcript_8131-T1 Valid prediction for GlimmerHMM_glimmerT_27450-T1 Valid prediction for GlimmerHMM_glimmerT_27445-T1 Couldn't classify 140004, 140186 Sorry, prediction pasa_asmbl_5694.p1 fails validation. (ACA) GC 140004-140186 GT GGG (TCT) AG 140315-140469 GT TAG (CTA) AG 142154-142282 GT AGG (AAT) AG 144068-144197 GT AGG (AAC) AG 144314-144467 GT TGG (GTC) AG 144863-145053 GA GAG -recovered pasa_asmbl_5694.p1, terminal, 144863, 145053 -recovered pasa_asmbl_5694.p1, internal, 140315, 140469 -recovered pasa_asmbl_5694.p1, internal, 142154, 142282 -recovered pasa_asmbl_5694.p1, internal, 144068, 144197 -recovered pasa_asmbl_5694.p1, internal, 144314, 144467 Valid prediction for GlimmerHMM_glimmerT_27447-T1 Valid prediction for Augustus_model.g18167.t1 Couldn't classify 5929, 6094 Sorry, prediction pasa_asmbl_5680.p1 fails validation. (AGC) AC 5929-6094 GT AGG (GAG) AG 6186-6292 GT CTG (GGC) AG 6383-6530 GT AGG (ACA) AG 6665-6681 GT CGG (CCA) AG 6800-6916 GT CAG (GTG) AG 7056-7176 GT CAG (GAA) AG 7382-7445 GT GGG (GGC) AG 7542-7590 GT AGG (GTG) AG 7675-7787 GT AGG (CTT) AG 7928-8045 GT AGG (TGT) AG 8132-8231 GT CAG (CTG) AG 8448-8644 GT GGG (GCT) AG 8905-9042 GT AGG (CAC) AG 9483-9569 AC AAA -recovered pasa_asmbl_5680.p1, terminal, 9483, 9569 -recovered pasa_asmbl_5680.p1, internal, 6186, 6292 -recovered pasa_asmbl_5680.p1, internal, 6383, 6530 -recovered pasa_asmbl_5680.p1, internal, 6665, 6681 -recovered pasa_asmbl_5680.p1, internal, 6800, 6916 -recovered pasa_asmbl_5680.p1, internal, 7056, 7176 -recovered pasa_asmbl_5680.p1, internal, 7382, 7445 -recovered pasa_asmbl_5680.p1, internal, 7542, 7590 -recovered pasa_asmbl_5680.p1, internal, 7675, 7787 -recovered pasa_asmbl_5680.p1, internal, 7928, 8045 -recovered pasa_asmbl_5680.p1, internal, 8132, 8231 -recovered pasa_asmbl_5680.p1, internal, 8448, 8644 -recovered pasa_asmbl_5680.p1, internal, 8905, 9042 Valid prediction for GlimmerHMM_glimmerT_27438-T1 Valid prediction for snap_scaffold_11-snap.1827-T1 Valid prediction for HiQ_model.g18151.t1 Valid prediction for pasa_asmbl_5689.p1 Valid prediction for GlimmerHMM_glimmerT_27441-T1 Valid prediction for snap_scaffold_11-snap.1802-T1 Valid prediction for snap_scaffold_11-snap.1819-T1 Valid prediction for Augustus_model.g18162.t1 Valid prediction for pasa_asmbl_5686.p1 Valid prediction for GlimmerHMM_glimmerT_27430-T1 Couldn't classify 196470, 197117 Sorry, prediction pasa_asmbl_5704.p1 fails validation. (AGA) AC 196470-197117 GT AAG Valid prediction for GlimmerHMM_glimmerT_27451-T1 Valid prediction for HiQ_model.g18161.t1 Valid prediction for snap_scaffold_11-snap.1817-T1 Valid prediction for snap_scaffold_11-snap.1808-T1 Valid prediction for CodingQuarry_transcript_8134-T1 Valid prediction for GlimmerHMM_glimmerT_27436-T1 Valid prediction for snap_scaffold_11-snap.1814-T1 Valid prediction for CodingQuarry_transcript_8130-T1 Valid prediction for snap_scaffold_11-snap.1794-T1 Valid prediction for Augustus_model.g18147.t1 Valid prediction for snap_scaffold_11-snap.1818-T1 Valid prediction for snap_scaffold_11-snap.1799-T1 Valid prediction for GlimmerHMM_glimmerT_27452-T1 Valid prediction for snap_scaffold_11-snap.1800-T1 Valid prediction for GlimmerHMM_glimmerT_27443-T1 Valid prediction for GlimmerHMM_glimmerT_27433-T1 Valid prediction for snap_scaffold_11-snap.1813-T1 Valid prediction for Augustus_model.g18156.t1 Valid prediction for CodingQuarry_transcript_8129-T1 Couldn't classify 236408, 236615 Couldn't classify 237074, 237190 Sorry, prediction pasa_asmbl_5705.p1 fails validation. (ACG) AA 236408-236615 GT TGG (GTT) AG 236838-236983 GT ATG (GAG) AG 237074-237190 AA CCA -recovered pasa_asmbl_5705.p1, internal, 236838, 236983 Valid prediction for GlimmerHMM_glimmerT_27446-T1 Valid prediction for HiQ_model.g18152.t1 Valid prediction for snap_scaffold_11-snap.1809-T1 Valid prediction for GlimmerHMM_glimmerT_27458-T1 Valid prediction for snap_scaffold_11-snap.1828-T1 Valid prediction for GlimmerHMM_glimmerT_27440-T1 Valid prediction for snap_scaffold_11-snap.1790-T1 Valid prediction for snap_scaffold_11-snap.1795-T1 Valid prediction for CodingQuarry_transcript_8133-T1 Valid prediction for HiQ_model.g18143.t1 Valid prediction for snap_scaffold_11-snap.1804-T1 Valid prediction for CodingQuarry_transcript_8135-T1 Valid prediction for Augustus_model.g18157.t1 Valid prediction for Augustus_model.g18145.t1 Valid prediction for snap_scaffold_11-snap.1792-T1 Valid prediction for CodingQuarry_transcript_8136-T1 Couldn't classify 191004, 191321 Sorry, prediction pasa_asmbl_5703.p1 fails validation. (ATG) TA 191004-191321 CA CCC Valid prediction for GlimmerHMM_glimmerT_27431-T1 Valid prediction for HiQ_model.g18158.t1 Valid prediction for GlimmerHMM_glimmerT_27437-T1 Valid prediction for pasa_asmbl_5684.p1 Valid prediction for snap_scaffold_11-snap.1806-T1 Valid prediction for GlimmerHMM_glimmerT_27439-T1 Valid prediction for snap_scaffold_11-snap.1810-T1 Valid prediction for snap_scaffold_11-snap.1829-T1 Valid prediction for HiQ_model.g18153.t1 Valid prediction for Augustus_model.g18166.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_11-snap.1824-T1 Couldn't classify 22382, 22496 Sorry, prediction pasa_asmbl_6814.p1 fails validation. (ACG) CG 22382-22496 GT AGG (GTT) AG 22856-23055 GT AGG (TTC) AG 23134-23185 GT AGG (GTA) AG 23318-23419 GT TAG (GAA) AG 23594-23724 GT AAG (GTC) AG 23840-23939 GT AGG (ATT) AG 24054-24112 GT AGG (TCA) AG 24263-24345 GT CTG (CAC) AG 24473-24543 GT CAG (TCA) AG 24742-24842 GT GGG (CCC) AG 25089-25229 GT AGG (GTG) AG 25375-25485 GT GGG (GAT) AG 25654-25782 CA AAC -recovered pasa_asmbl_6814.p1, terminal, 23134, 23185 -recovered pasa_asmbl_6814.p1, terminal, 25654, 25782 -recovered pasa_asmbl_6814.p1, internal, 22856, 23055 -recovered pasa_asmbl_6814.p1, internal, 23134, 23185 -recovered pasa_asmbl_6814.p1, internal, 23318, 23419 -recovered pasa_asmbl_6814.p1, internal, 23594, 23724 -recovered pasa_asmbl_6814.p1, internal, 23840, 23939 -recovered pasa_asmbl_6814.p1, internal, 24054, 24112 -recovered pasa_asmbl_6814.p1, internal, 24263, 24345 -recovered pasa_asmbl_6814.p1, internal, 24473, 24543 -recovered pasa_asmbl_6814.p1, internal, 24742, 24842 -recovered pasa_asmbl_6814.p1, internal, 25089, 25229 -recovered pasa_asmbl_6814.p1, internal, 25375, 25485 Valid prediction for GlimmerHMM_glimmerT_27449-T1 Valid prediction for snap_scaffold_11-snap.1823-T1 Valid prediction for HiQ_model.g18148.t1 Valid prediction for Augustus_model.g18164.t1 Valid prediction for Augustus_model.g18146.t1 Valid prediction for CodingQuarry_transcript_8128-T1 Valid prediction for CodingQuarry_transcript_8140-T1 Valid prediction for snap_scaffold_11-snap.1805-T1 Couldn't classify 231851, 232210 Sorry, prediction pasa_asmbl_6294.p1 fails validation. (GAT) TG 231851-232210 CG ACC Valid prediction for GlimmerHMM_glimmerT_27454-T1 Couldn't classify 3210, 3230 Sorry, prediction pasa_asmbl_6816.p1 fails validation. (AGT) AA 3210-3230 GT AGG (TTC) AG 3312-3413 GT AGG (TGT) AG 3561-3680 GT TGG (GTC) AG 3865-3960 GT AGG (GAA) AG 4283-4429 GT AGG (GTG) AG 4565-4653 GT ATG (AGG) AG 4761-4931 GT AGG (ACT) AG 5161-5339 GT AGG (GGG) AG 5420-5621 GT CGG (TGG) AG 5813-5927 GT AAG (GAG) AG 6047-6207 GT CGG (CAT) AG 6294-6429 GT TGG (GCT) AG 6604-6684 GT TGG (GAA) AG 6780-6950 GT AGG (GAA) AG 7190-7327 GT AGG (GAA) AG 7444-7589 GT AGG (GGA) AG 8404-8529 GT AGG (GTC) AG 8628-8733 GT CGG (GTT) AG 9054-9206 GT TGG (GAT) AG 9390-9487 GT AGG (TAA) AG 9699-9789 CT AAC add_exon() Sorry, pasa_asmbl_6816.p1 5161-5339-terminal-2 is invalid. -recovered pasa_asmbl_6816.p1, terminal, 5161, 5339 -recovered pasa_asmbl_6816.p1, terminal, 9699, 9789 -recovered pasa_asmbl_6816.p1, internal, 3312, 3413 -recovered pasa_asmbl_6816.p1, internal, 3561, 3680 -recovered pasa_asmbl_6816.p1, internal, 3865, 3960 -recovered pasa_asmbl_6816.p1, internal, 4283, 4429 -recovered pasa_asmbl_6816.p1, internal, 4565, 4653 -recovered pasa_asmbl_6816.p1, internal, 4761, 4931 -recovered pasa_asmbl_6816.p1, internal, 5161, 5339 -recovered pasa_asmbl_6816.p1, internal, 5420, 5621 -recovered pasa_asmbl_6816.p1, internal, 5813, 5927 -recovered pasa_asmbl_6816.p1, internal, 6047, 6207 -recovered pasa_asmbl_6816.p1, internal, 6294, 6429 -recovered pasa_asmbl_6816.p1, internal, 6604, 6684 -recovered pasa_asmbl_6816.p1, internal, 6780, 6950 -recovered pasa_asmbl_6816.p1, internal, 7190, 7327 -recovered pasa_asmbl_6816.p1, internal, 7444, 7589 -recovered pasa_asmbl_6816.p1, internal, 8404, 8529 -recovered pasa_asmbl_6816.p1, internal, 8628, 8733 -recovered pasa_asmbl_6816.p1, internal, 9054, 9206 -recovered pasa_asmbl_6816.p1, internal, 9390, 9487 Valid prediction for snap_scaffold_11-snap.1798-T1 Valid prediction for snap_scaffold_11-snap.1801-T1 Valid prediction for GlimmerHMM_glimmerT_27434-T1 Valid prediction for snap_scaffold_11-snap.1831-T1 Valid prediction for snap_scaffold_11-snap.1797-T1 Couldn't classify 152283, 152360 Couldn't classify 152688, 152771 Sorry, prediction pasa_asmbl_7351.p1 fails validation. (AGG) AG 152283-152360 GT AGG (GTG) AG 152451-152588 GT AGG (TTT) AG 152688-152771 AA GGA -recovered pasa_asmbl_7351.p1, internal, 152283, 152360 -recovered pasa_asmbl_7351.p1, internal, 152451, 152588 Valid prediction for GlimmerHMM_glimmerT_27444-T1 Valid prediction for snap_scaffold_11-snap.1820-T1 Valid prediction for pasa_asmbl_6807.p1 Valid prediction for snap_scaffold_11-snap.1825-T1 Valid prediction for snap_scaffold_11-snap.1811-T1 Valid prediction for snap_scaffold_11-snap.1793-T1 Valid prediction for Augustus_model.g18160.t1 Valid prediction for HiQ_model.g18165.t1 Valid prediction for snap_scaffold_11-snap.1832-T1 Valid prediction for snap_scaffold_11-snap.1791-T1 Valid prediction for Augustus_model.g18154.t1 Valid prediction for Augustus_model.g18142.t1 Valid prediction for pasa_asmbl_6808.p1 Valid prediction for snap_scaffold_11-snap.1815-T1 Valid prediction for Augustus_model.g18168.t1 Valid prediction for snap_scaffold_11-snap.1830-T1 Valid prediction for GlimmerHMM_glimmerT_27432-T1 Valid prediction for snap_scaffold_11-snap.1816-T1 Valid prediction for GlimmerHMM_glimmerT_27442-T1 Valid prediction for GlimmerHMM_glimmerT_27435-T1 Valid prediction for Augustus_model.g18159.t1 Valid prediction for CodingQuarry_transcript_8137-T1 Valid prediction for snap_scaffold_11-snap.1787-T1 Valid prediction for snap_scaffold_11-snap.1796-T1 Valid prediction for CodingQuarry_transcript_8127-T1 Valid prediction for Augustus_model.g18163.t1 Valid prediction for snap_scaffold_11-snap.1822-T1 Valid prediction for snap_scaffold_11-snap.1807-T1 Valid prediction for GlimmerHMM_glimmerT_27455-T1 Valid prediction for snap_scaffold_11-snap.1789-T1 Valid prediction for snap_scaffold_11-snap.1826-T1 Valid prediction for Augustus_model.g18149.t1 Valid prediction for snap_scaffold_11-snap.1821-T1 Couldn't classify 51049, 51126 Couldn't classify 51913, 51977 Sorry, prediction pasa_asmbl_7357.p1 fails validation. (GAG) AG 51049-51126 GT AGG (AGC) AG 51357-51566 GT AGG (TTG) AG 51697-51817 GT AGG (GGC) AG 51913-51977 GG CAG -recovered pasa_asmbl_7357.p1, internal, 51049, 51126 -recovered pasa_asmbl_7357.p1, internal, 51357, 51566 -recovered pasa_asmbl_7357.p1, internal, 51697, 51817 Valid prediction for GlimmerHMM_glimmerT_27456-T1 Valid prediction for GlimmerHMM_glimmerT_27459-T1 Valid prediction for pasa_asmbl_6812.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9553, rend_intergenic: 5201 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21266, rend_intergenic: 18658 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 23675, rend_intergenic: 22531 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30413, rend_intergenic: 27646 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100746, rend_intergenic: 97451 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143580, rend_intergenic: 139572 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 254665 -exon list size: 447 building trellis 0.2 0.4 0.7 0.9 1.1 1.3 1.6 1.8 2.0 2.2 2.4 2.7 2.9 3.1 3.3 3.6 3.8 4.0 4.2 4.5 4.7 4.9 5.1 5.3 5.6 5.8 6.0 6.2 6.5 6.7 6.9 7.1 7.3 7.6 7.8 8.0 8.2 8.5 8.7 8.9 9.1 9.4 9.6 9.8 10.0 10.2 10.5 10.7 10.9 11.1 11.4 11.6 11.8 12.0 12.2 12.5 12.7 12.9 13.1 13.4 13.6 13.8 14.0 14.3 14.5 14.7 14.9 15.1 15.4 15.6 15.8 16.0 16.3 16.5 16.7 16.9 17.1 17.4 17.6 17.8 18.0 18.3 18.5 18.7 18.9 19.2 19.4 19.6 19.8 20.0 20.3 20.5 20.7 20.9 21.2 21.4 21.6 21.8 22.0 22.3 22.5 22.7 22.9 23.2 23.4 23.6 23.8 24.1 24.3 24.5 24.7 24.9 25.2 25.4 25.6 25.8 26.1 26.3 26.5 26.7 26.9 27.2 27.4 27.6 27.8 28.1 28.3 28.5 28.7 29.0 29.2 29.4 29.6 29.8 30.1 30.3 30.5 30.7 31.0 31.2 31.4 31.6 31.8 32.1 32.3 32.5 32.7 33.0 33.2 33.4 33.6 33.9 34.1 34.3 34.5 34.7 35.0 35.2 35.4 35.6 35.9 36.1 36.3 36.5 36.7 37.0 37.2 37.4 37.6 37.9 38.1 38.3 38.5 38.8 39.0 39.2 39.4 39.6 39.9 40.1 40.3 40.5 40.8 41.0 41.2 41.4 41.6 41.9 42.1 42.3 42.5 42.8 43.0 43.2 43.4 43.7 43.9 44.1 44.3 44.5 44.8 45.0 45.2 45.4 45.7 45.9 46.1 46.3 46.5 46.8 47.0 47.2 47.4 47.7 47.9 48.1 48.3 48.6 48.8 49.0 49.2 49.4 49.7 49.9 50.1 50.3 50.6 50.8 51.0 51.2 51.4 51.7 51.9 52.1 52.3 52.6 52.8 53.0 53.2 53.5 53.7 53.9 54.1 54.3 54.6 54.8 55.0 55.2 55.5 55.7 55.9 56.1 56.3 56.6 56.8 57.0 57.2 57.5 57.7 57.9 58.1 58.4 58.6 58.8 59.0 59.2 59.5 59.7 59.9 60.1 60.4 60.6 60.8 61.0 61.2 61.5 61.7 61.9 62.1 62.4 62.6 62.8 63.0 63.3 63.5 63.7 63.9 64.1 64.4 64.6 64.8 65.0 65.3 65.5 65.7 65.9 66.1 66.4 66.6 66.8 67.0 67.3 67.5 67.7 67.9 68.2 68.4 68.6 68.8 69.0 69.3 69.5 69.7 69.9 70.2 70.4 70.6 70.8 71.0 71.3 71.5 71.7 71.9 72.2 72.4 72.6 72.8 73.1 73.3 73.5 73.7 73.9 74.2 74.4 74.6 74.8 75.1 75.3 75.5 75.7 75.9 76.2 76.4 76.6 76.8 77.1 77.3 77.5 77.7 78.0 78.2 78.4 78.6 78.8 79.1 79.3 79.5 79.7 80.0 80.2 80.4 80.6 80.8 81.1 81.3 81.5 81.7 82.0 82.2 82.4 82.6 82.9 83.1 83.3 83.5 83.7 84.0 84.2 84.4 84.6 84.9 85.1 85.3 85.5 85.7 86.0 86.2 86.4 86.6 86.9 87.1 87.3 87.5 87.8 88.0 88.2 88.4 88.6 88.9 89.1 89.3 89.5 89.8 90.0 90.2 90.4 90.6 90.9 91.1 91.3 91.5 91.8 92.0 92.2 92.4 92.7 92.9 93.1 93.3 93.5 93.8 94.0 94.2 94.4 94.7 94.9 95.1 95.3 95.5 95.8 96.0 96.2 96.4 96.7 96.9 97.1 97.3 97.6 97.8 98.0 98.2 98.4 98.7 98.9 99.1 99.3 99.6 99.8 -found 34 predictions from path traversal Error with prediction: snap lend_intergenic: 9553, rend_intergenic: 5201 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 21266, rend_intergenic: 18658 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 23675, rend_intergenic: 22531 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30413, rend_intergenic: 27646 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100746, rend_intergenic: 97451 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143580, rend_intergenic: 139572 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 33 predictions persist after filtering for low support