-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_1-239293 -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 Augustus_model.g38353.t1 Valid prediction for Augustus_model.g38352.t1 Valid prediction for snap_scaffold_28-snap.11-T1 Valid prediction for GlimmerHMM_glimmerT_57952-T1 Valid prediction for GlimmerHMM_glimmerT_57932-T1 Valid prediction for GlimmerHMM_glimmerT_57933-T1 Valid prediction for snap_scaffold_28-snap.37-T1 Couldn't classify 26792, 26899 Couldn't classify 28121, 28233 Sorry, prediction pasa_asmbl_37849.p1 fails validation. (GAC) AG 26792-26899 GT ATG (GAC) AG 27192-27351 GT TGG (GTC) AG 28121-28233 AA CCA -recovered pasa_asmbl_37849.p1, internal, 26792, 26899 -recovered pasa_asmbl_37849.p1, internal, 27192, 27351 Valid prediction for snap_scaffold_28-snap.28-T1 Valid prediction for GlimmerHMM_glimmerT_57941-T1 Valid prediction for GlimmerHMM_glimmerT_57929-T1 Valid prediction for GlimmerHMM_glimmerT_57951-T1 Couldn't classify 2214, 2264 Sorry, prediction snap_scaffold_28-snap.2-T1 fails validation. (AAA) AG 2214-2264 GT TGG (GAT) AG 3958-4051 GT CAG (GCC) AG 4383-4439 GT GGG (GGG) AG 7293-7534 GT GGG (GGG) AG 7922-8020 GT TGG (GGC) AG 8728-8827 GT TGG (TCC) AG 10057-10074 CT AGC -recovered snap_scaffold_28-snap.2-T1, terminal, 10057, 10074 -recovered snap_scaffold_28-snap.2-T1, internal, 2214, 2264 -recovered snap_scaffold_28-snap.2-T1, internal, 3958, 4051 -recovered snap_scaffold_28-snap.2-T1, internal, 4383, 4439 -recovered snap_scaffold_28-snap.2-T1, internal, 7293, 7534 -recovered snap_scaffold_28-snap.2-T1, internal, 7922, 8020 -recovered snap_scaffold_28-snap.2-T1, internal, 8728, 8827 Valid prediction for Augustus_model.g38354.t1 Couldn't classify 31463, 31518 Sorry, prediction pasa_asmbl_37249.p1 fails validation. (CAG) TG 31463-31518 GT AGG (CGA) AG 31627-31711 GT AGG (GGA) AG 32701-32797 GT ACG (AAG) AG 33124-33305 GT AGG (GGC) AG 35614-35662 GT AGG (GTT) AG 36084-36280 GT AGG (GCA) AG 36596-36768 GT CGG (GGC) AG 36904-37043 GT CGG (ACA) AG 37306-37361 AC GAA add_exon() Sorry, pasa_asmbl_37249.p1 35614-35662-terminal-3 is invalid. -recovered pasa_asmbl_37249.p1, terminal, 35614, 35662 -recovered pasa_asmbl_37249.p1, terminal, 37306, 37361 -recovered pasa_asmbl_37249.p1, internal, 31627, 31711 -recovered pasa_asmbl_37249.p1, internal, 32701, 32797 -recovered pasa_asmbl_37249.p1, internal, 33124, 33305 -recovered pasa_asmbl_37249.p1, internal, 35614, 35662 -recovered pasa_asmbl_37249.p1, internal, 36084, 36280 -recovered pasa_asmbl_37249.p1, internal, 36596, 36768 -recovered pasa_asmbl_37249.p1, internal, 36904, 37043 Valid prediction for GlimmerHMM_glimmerT_57948-T1 Valid prediction for CodingQuarry_transcript_43506-T1 Valid prediction for snap_scaffold_28-snap.10-T1 Valid prediction for snap_scaffold_28-snap.22-T1 Valid prediction for snap_scaffold_28-snap.38-T1 Valid prediction for HiQ_model.g38356.t1 Couldn't classify 227102, 227130 Sorry, prediction pasa_asmbl_37255.p1 fails validation. (GAC) GA 227102-227130 GT CGG (TGT) AG 228789-228830 GT AAG (TTA) AG 228913-229003 GT CTG (GTT) AG 230266-230414 GT CGG (GGC) AG 230519-230627 GT TGG (CCT) AG 230711-230838 GT AGG (GCT) AG 231066-231165 GT AGG (GTG) AG 231758-231833 GT TGG (CGG) AG 231943-232028 GT AGG (GGA) AG 232186-232290 GT AGG (GTC) AG 232408-232483 GT AGG (ACT) AG 232562-232680 GT AGG (GCG) AG 232758-232841 GT CTG (ATC) AG 233586-233643 GT AGG (CTG) AG 233733-233914 GT AGG (TAT) AG 233982-234116 CA GAC -recovered pasa_asmbl_37255.p1, terminal, 233982, 234116 -recovered pasa_asmbl_37255.p1, internal, 228789, 228830 -recovered pasa_asmbl_37255.p1, internal, 228913, 229003 -recovered pasa_asmbl_37255.p1, internal, 230266, 230414 -recovered pasa_asmbl_37255.p1, internal, 230519, 230627 -recovered pasa_asmbl_37255.p1, internal, 230711, 230838 -recovered pasa_asmbl_37255.p1, internal, 231066, 231165 -recovered pasa_asmbl_37255.p1, internal, 231758, 231833 -recovered pasa_asmbl_37255.p1, internal, 231943, 232028 -recovered pasa_asmbl_37255.p1, internal, 232186, 232290 -recovered pasa_asmbl_37255.p1, internal, 232408, 232483 -recovered pasa_asmbl_37255.p1, internal, 232562, 232680 -recovered pasa_asmbl_37255.p1, internal, 232758, 232841 -recovered pasa_asmbl_37255.p1, internal, 233586, 233643 -recovered pasa_asmbl_37255.p1, internal, 233733, 233914 Valid prediction for snap_scaffold_28-snap.7-T1 Valid prediction for snap_scaffold_28-snap.41-T1 Valid prediction for snap_scaffold_28-snap.5-T1 Valid prediction for CodingQuarry_transcript_43505-T1 Couldn't classify 81831, 82406 Sorry, prediction pasa_asmbl_37251.p1 fails validation. (GGG) AG 81831-82406 CC TGC Valid prediction for snap_scaffold_28-snap.3-T1 Valid prediction for GlimmerHMM_glimmerT_57953-T1 Valid prediction for snap_scaffold_28-snap.32-T1 Valid prediction for Augustus_model.g38342.t1 Valid prediction for GlimmerHMM_glimmerT_57950-T1 Valid prediction for GlimmerHMM_glimmerT_57930-T1 Valid prediction for GlimmerHMM_glimmerT_57942-T1 Valid prediction for CodingQuarry_transcript_43498-T1 Valid prediction for snap_scaffold_28-snap.43-T1 Valid prediction for snap_scaffold_28-snap.16-T1 Valid prediction for snap_scaffold_28-snap.39-T1 Valid prediction for Augustus_model.g38338.t1 Valid prediction for GlimmerHMM_glimmerT_57956-T1 Valid prediction for snap_scaffold_28-snap.19-T1 Valid prediction for snap_scaffold_28-snap.18-T1 Valid prediction for snap_scaffold_28-snap.8-T1 Valid prediction for GlimmerHMM_glimmerT_57935-T1 Valid prediction for Augustus_model.g38343.t1 Valid prediction for Augustus_model.g38344.t1 Valid prediction for snap_scaffold_28-snap.36-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_28-snap.23-T1 Valid prediction for snap_scaffold_28-snap.24-T1 Valid prediction for snap_scaffold_28-snap.14-T1 Valid prediction for Augustus_model.g38336.t1 Valid prediction for GlimmerHMM_glimmerT_57940-T1 Valid prediction for snap_scaffold_28-snap.31-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_57949-T1 Couldn't classify 239138, 239220 Sorry, prediction snap_scaffold_28-snap.1-T1 fails validation. (ATG) GC 230129-230344 GT GAG (ATG) AG 235157-235384 GT GGG (GAG) AG 236519-237133 GT AGG (TAC) AG 238241-238465 GT GGG (GCT) AG 239138-239220 GT AGG -recovered snap_scaffold_28-snap.1-T1, initial, 230129, 230344 -recovered snap_scaffold_28-snap.1-T1, initial, 235157, 235384 -recovered snap_scaffold_28-snap.1-T1, internal, 235157, 235384 -recovered snap_scaffold_28-snap.1-T1, internal, 236519, 237133 -recovered snap_scaffold_28-snap.1-T1, internal, 238241, 238465 -recovered snap_scaffold_28-snap.1-T1, internal, 239138, 239220 Valid prediction for CodingQuarry_transcript_43502-T1 Valid prediction for GlimmerHMM_glimmerT_57939-T1 Valid prediction for GlimmerHMM_glimmerT_57945-T1 Valid prediction for GlimmerHMM_glimmerT_57947-T1 Valid prediction for GlimmerHMM_glimmerT_57944-T1 Valid prediction for snap_scaffold_28-snap.26-T1 Valid prediction for Augustus_model.g38345.t1 Valid prediction for HiQ_model.g38341.t1 Valid prediction for GlimmerHMM_glimmerT_57937-T1 Valid prediction for snap_scaffold_28-snap.30-T1 Valid prediction for Augustus_model.g38339.t1 Valid prediction for Augustus_model.g38337.t1 Valid prediction for HiQ_model.g38355.t1 Valid prediction for Augustus_model.g38335.t1 Valid prediction for pasa_asmbl_37891.p1 Valid prediction for snap_scaffold_28-snap.42-T1 Valid prediction for Augustus_model.g38351.t1 Valid prediction for GlimmerHMM_glimmerT_57955-T1 Valid prediction for snap_scaffold_28-snap.21-T1 Valid prediction for CodingQuarry_transcript_43499-T1 Couldn't classify 88447, 88500 Sorry, prediction pasa_asmbl_37896.p1 fails validation. (ACC) GC 88447-88500 GT ACG (ACT) AG 91070-91196 GT AGG (ATG) AG 92122-92290 GT AGG (GAG) AG 94201-94282 TT GAT add_exon() Sorry, pasa_asmbl_37896.p1 92122-92290-initial-1 is invalid. -recovered pasa_asmbl_37896.p1, initial, 92122, 92290 -recovered pasa_asmbl_37896.p1, terminal, 94201, 94282 -recovered pasa_asmbl_37896.p1, internal, 91070, 91196 -recovered pasa_asmbl_37896.p1, internal, 92122, 92290 Valid prediction for Augustus_model.g38350.t1 Valid prediction for GlimmerHMM_glimmerT_57938-T1 Valid prediction for snap_scaffold_28-snap.6-T1 Valid prediction for CodingQuarry_transcript_43501-T1 Valid prediction for Augustus_model.g38340.t1 Valid prediction for GlimmerHMM_glimmerT_57946-T1 Valid prediction for pasa_asmbl_37901.p1 Valid prediction for pasa_asmbl_37881.p1 Valid prediction for snap_scaffold_28-snap.20-T1 Valid prediction for HiQ_model.g38346.t1 Valid prediction for snap_scaffold_28-snap.17-T1 Valid prediction for snap_scaffold_28-snap.33-T1 Valid prediction for snap_scaffold_28-snap.27-T1 Valid prediction for Augustus_model.g38349.t1 Valid prediction for GlimmerHMM_glimmerT_57934-T1 Couldn't classify 191399, 191457 Couldn't classify 193050, 193180 Sorry, prediction pasa_asmbl_38616.p1 fails validation. (TTC) TC 191399-191457 GT TGG (GTA) AG 192462-192673 GT ACG (TTA) AG 192851-192943 GT AAG (CGG) AG 193050-193180 TG CCT -recovered pasa_asmbl_38616.p1, internal, 192462, 192673 -recovered pasa_asmbl_38616.p1, internal, 192851, 192943 Valid prediction for snap_scaffold_28-snap.4-T1 Valid prediction for GlimmerHMM_glimmerT_57928-T1 Valid prediction for GlimmerHMM_glimmerT_57954-T1 Valid prediction for GlimmerHMM_glimmerT_57943-T1 Valid prediction for snap_scaffold_28-snap.40-T1 Valid prediction for snap_scaffold_28-snap.13-T1 Couldn't classify 189669, 189836 Couldn't classify 190459, 190522 Sorry, prediction pasa_asmbl_38614.p1 fails validation. (CTG) AG 189669-189836 GT ACG (ATC) AG 190194-190369 GT GGG (GTT) AG 190459-190522 CA AGC -recovered pasa_asmbl_38614.p1, internal, 189669, 189836 -recovered pasa_asmbl_38614.p1, internal, 190194, 190369 Valid prediction for snap_scaffold_28-snap.15-T1 Valid prediction for snap_scaffold_28-snap.9-T1 Valid prediction for snap_scaffold_28-snap.25-T1 Valid prediction for snap_scaffold_28-snap.12-T1 Valid prediction for snap_scaffold_28-snap.29-T1 Valid prediction for Augustus_model.g38347.t1 Valid prediction for CodingQuarry_transcript_43504-T1 Valid prediction for GlimmerHMM_glimmerT_57936-T1 Valid prediction for CodingQuarry_transcript_43503-T1 Valid prediction for snap_scaffold_28-snap.34-T1 Valid prediction for Augustus_model.g38348.t1 Couldn't classify 197319, 197393 Sorry, prediction pasa_asmbl_37879.p2 fails validation. (TGC) TG 197319-197393 GT AGG (AGA) AG 197541-197577 GT AGG (ACG) AG 198893-199043 GT CAG (TTA) AG 199216-199360 GG AGG -recovered pasa_asmbl_37879.p2, terminal, 199216, 199360 -recovered pasa_asmbl_37879.p2, internal, 197541, 197577 -recovered pasa_asmbl_37879.p2, internal, 198893, 199043 Valid prediction for snap_scaffold_28-snap.35-T1 Valid prediction for GlimmerHMM_glimmerT_57931-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9165, rend_intergenic: 2214 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50281, rend_intergenic: 47833 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 78632, rend_intergenic: 76310 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 80919, rend_intergenic: 79617 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90043, rend_intergenic: 83408 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 113957, rend_intergenic: 112120 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 135860, rend_intergenic: 133163 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143093, rend_intergenic: 136542 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 157485, rend_intergenic: 146499 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 216944, rend_intergenic: 213176 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 239293 -exon list size: 404 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 3.4 3.7 3.9 4.2 4.4 4.7 4.9 5.2 5.4 5.7 5.9 6.2 6.4 6.7 6.9 7.1 7.4 7.6 7.9 8.1 8.4 8.6 8.9 9.1 9.4 9.6 9.9 10.1 10.3 10.6 10.8 11.1 11.3 11.6 11.8 12.1 12.3 12.6 12.8 13.1 13.3 13.5 13.8 14.0 14.3 14.5 14.8 15.0 15.3 15.5 15.8 16.0 16.3 16.5 16.7 17.0 17.2 17.5 17.7 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 22.2 22.4 22.7 22.9 23.2 23.4 23.6 23.9 24.1 24.4 24.6 24.9 25.1 25.4 25.6 25.9 26.1 26.4 26.6 26.8 27.1 27.3 27.6 27.8 28.1 28.3 28.6 28.8 29.1 29.3 29.6 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 36.9 37.2 37.4 37.7 37.9 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 41.9 42.1 42.4 42.6 42.9 43.1 43.3 43.6 43.8 44.1 44.3 44.6 44.8 45.1 45.3 45.6 45.8 46.1 46.3 46.6 46.8 47.0 47.3 47.5 47.8 48.0 48.3 48.5 48.8 49.0 49.3 49.5 49.8 50.0 50.2 50.5 50.7 51.0 51.2 51.5 51.7 52.0 52.2 52.5 52.7 53.0 53.2 53.4 53.7 53.9 54.2 54.4 54.7 54.9 55.2 55.4 55.7 55.9 56.2 56.4 56.7 56.9 57.1 57.4 57.6 57.9 58.1 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 62.1 62.3 62.6 62.8 63.1 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 70.4 70.7 70.9 71.2 71.4 71.7 71.9 72.2 72.4 72.7 72.9 73.2 73.4 73.6 73.9 74.1 74.4 74.6 74.9 75.1 75.4 75.6 75.9 76.1 76.4 76.6 76.8 77.1 77.3 77.6 77.8 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 82.3 82.5 82.8 83.0 83.3 83.5 83.7 84.0 84.2 84.5 84.7 85.0 85.2 85.5 85.7 86.0 86.2 86.5 86.7 86.9 87.2 87.4 87.7 87.9 88.2 88.4 88.7 88.9 89.2 89.4 89.7 89.9 90.1 90.4 90.6 90.9 91.1 91.4 91.6 91.9 92.1 92.4 92.6 92.9 93.1 93.3 93.6 93.8 94.1 94.3 94.6 94.8 95.1 95.3 95.6 95.8 96.1 96.3 96.6 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 23 predictions from path traversal Error with prediction: snap lend_intergenic: 9165, rend_intergenic: 2214 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50281, rend_intergenic: 47833 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 78632, rend_intergenic: 76310 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 80919, rend_intergenic: 79617 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90043, rend_intergenic: 83408 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 113957, rend_intergenic: 112120 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 135860, rend_intergenic: 133163 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143093, rend_intergenic: 136542 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 157485, rend_intergenic: 146499 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 216944, rend_intergenic: 213176 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 23 predictions persist after filtering for low support