-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_11616973-11893747 -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.2300-T1 Valid prediction for snap_scaffold_3-snap.2323-T1 Valid prediction for GlimmerHMM_glimmerT_7379-T1 Valid prediction for snap_scaffold_3-snap.2309-T1 Valid prediction for GlimmerHMM_glimmerT_7380-T1 Valid prediction for Augustus_model.g4811.t1 Valid prediction for snap_scaffold_3-snap.2304-T1 Valid prediction for snap_scaffold_3-snap.2332-T1 Valid prediction for snap_scaffold_3-snap.2299-T1 Valid prediction for pasa_asmbl_40372.p1 Valid prediction for snap_scaffold_3-snap.2306-T1 Valid prediction for GlimmerHMM_glimmerT_7399-T1 Valid prediction for snap_scaffold_3-snap.2315-T1 Valid prediction for GlimmerHMM_glimmerT_7382-T1 Couldn't classify 25677, 25766 Sorry, prediction pasa_asmbl_40363.p1 fails validation. (ATG) AG 17990-18085 GT GGG (AGC) AG 18188-18334 GT GGG (GAC) AG 18449-18595 GT AGG (GAG) AG 18725-18932 GT AGG (GCT) AG 19370-19590 GT AGG (ACC) AG 19693-19883 GT AGG (GTT) AG 19976-20149 GT AGG (GTA) AG 20578-20719 GT AGG (GTG) AG 20906-21650 GT TGG (GCC) AG 22060-22183 GT TGG (GTA) AG 22281-22506 GT AGG (GTG) AG 24262-24391 GT GGG (GCC) AG 24509-24694 GT CGG (GTA) AG 25161-25381 GT AGG (GTG) AG 25677-25766 TC GGT -recovered pasa_asmbl_40363.p1, initial, 17990, 18085 -recovered pasa_asmbl_40363.p1, internal, 17990, 18085 -recovered pasa_asmbl_40363.p1, internal, 18188, 18334 -recovered pasa_asmbl_40363.p1, internal, 18449, 18595 -recovered pasa_asmbl_40363.p1, internal, 18725, 18932 -recovered pasa_asmbl_40363.p1, internal, 19370, 19590 -recovered pasa_asmbl_40363.p1, internal, 19693, 19883 -recovered pasa_asmbl_40363.p1, internal, 19976, 20149 -recovered pasa_asmbl_40363.p1, internal, 20578, 20719 -recovered pasa_asmbl_40363.p1, internal, 20906, 21650 -recovered pasa_asmbl_40363.p1, internal, 22060, 22183 -recovered pasa_asmbl_40363.p1, internal, 22281, 22506 -recovered pasa_asmbl_40363.p1, internal, 24262, 24391 -recovered pasa_asmbl_40363.p1, internal, 24509, 24694 -recovered pasa_asmbl_40363.p1, internal, 25161, 25381 Valid prediction for GlimmerHMM_glimmerT_7378-T1 Valid prediction for snap_scaffold_3-snap.2333-T1 Valid prediction for GlimmerHMM_glimmerT_7394-T1 Valid prediction for CodingQuarry_transcript_46289-T1 Couldn't classify 14805, 14986 Couldn't classify 15424, 15549 Sorry, prediction pasa_asmbl_40362.p1 fails validation. (TGT) CC 14805-14986 GT AGG (GGC) AG 15067-15307 GT CGG (TTG) AG 15424-15549 GT AGG -recovered pasa_asmbl_40362.p1, internal, 15067, 15307 -recovered pasa_asmbl_40362.p1, internal, 15424, 15549 Valid prediction for snap_scaffold_3-snap.2328-T1 Valid prediction for snap_scaffold_3-snap.2305-T1 Valid prediction for Augustus_model.g4808.t1 Valid prediction for GlimmerHMM_glimmerT_7383-T1 Valid prediction for GlimmerHMM_glimmerT_7396-T1 Valid prediction for snap_scaffold_3-snap.2335-T1 Valid prediction for GlimmerHMM_glimmerT_7398-T1 Couldn't classify 8345, 8394 Couldn't classify 8969, 9026 Sorry, prediction pasa_asmbl_40826.p1 fails validation. (TTC) GC 8345-8394 GT AAG (GCC) AG 8565-8816 GT AGG (GTT) AG 8969-9026 GT AGG add_exon() Sorry, pasa_asmbl_40826.p1 8565-8816-terminal-1 is invalid. -recovered pasa_asmbl_40826.p1, terminal, 8565, 8816 -recovered pasa_asmbl_40826.p1, internal, 8565, 8816 -recovered pasa_asmbl_40826.p1, internal, 8969, 9026 Valid prediction for GlimmerHMM_glimmerT_7400-T1 Valid prediction for GlimmerHMM_glimmerT_7402-T1 Couldn't classify 26489, 26590 Sorry, prediction pasa_asmbl_40367.p1 fails validation. (ATT) CC 26489-26590 GT AGG (AGC) AG 27457-27669 GT AGG (TGT) AG 28080-28190 GT CTG (GTG) AG 28944-29012 GT AGG (CAG) AG 29780-30229 CA GAC -recovered pasa_asmbl_40367.p1, terminal, 29780, 30229 -recovered pasa_asmbl_40367.p1, internal, 27457, 27669 -recovered pasa_asmbl_40367.p1, internal, 28080, 28190 -recovered pasa_asmbl_40367.p1, internal, 28944, 29012 Valid prediction for GlimmerHMM_glimmerT_7386-T1 Valid prediction for CodingQuarry_transcript_46288-T1 Valid prediction for CodingQuarry_transcript_46290-T1 Valid prediction for HiQ_model.g4810.t1 Valid prediction for CodingQuarry_transcript_46286-T1 Valid prediction for GlimmerHMM_glimmerT_7403-T1 Valid prediction for snap_scaffold_3-snap.2326-T1 Couldn't classify 11428, 11560 Couldn't classify 12856, 13045 Sorry, prediction pasa_asmbl_40361.p1 fails validation. (CAG) GT 11428-11560 GT AGG (CGG) AG 11848-11938 GT AGG (GTT) AG 12641-12754 GT TGG (GTA) AG 12856-13045 GA TGG -recovered pasa_asmbl_40361.p1, internal, 11848, 11938 -recovered pasa_asmbl_40361.p1, internal, 12641, 12754 Valid prediction for GlimmerHMM_glimmerT_7391-T1 Valid prediction for CodingQuarry_transcript_46287-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_3-snap.2312-T1 Couldn't classify 82556, 82773 Couldn't classify 83926, 84034 Sorry, prediction pasa_asmbl_39754.p1 fails validation. (GGC) TA 82556-82773 GT AGG (TGC) AG 83926-84034 AG AAA Valid prediction for snap_scaffold_3-snap.2319-T1 Valid prediction for GlimmerHMM_glimmerT_7384-T1 Valid prediction for snap_scaffold_3-snap.2303-T1 Valid prediction for GlimmerHMM_glimmerT_7385-T1 Valid prediction for Augustus_model.g4818.t1 Valid prediction for GlimmerHMM_glimmerT_7389-T1 Valid prediction for Augustus_model.g4815.t1 Valid prediction for Augustus_model.g4819.t1 Valid prediction for snap_scaffold_3-snap.2311-T1 Valid prediction for snap_scaffold_3-snap.2317-T1 Valid prediction for Augustus_model.g4816.t1 Couldn't classify 95443, 95589 Couldn't classify 97413, 97455 Sorry, prediction pasa_asmbl_39193.p1 fails validation. (CAG) TC 95443-95589 GT AGG (GAC) AG 96160-96303 GT AGG (GGC) AG 96721-96866 GT AGG (GGA) AG 97413-97455 GC CGG -recovered pasa_asmbl_39193.p1, internal, 96160, 96303 -recovered pasa_asmbl_39193.p1, internal, 96721, 96866 -recovered pasa_asmbl_39193.p1, internal, 97413, 97455 Couldn't classify 98089, 98227 Sorry, prediction pasa_asmbl_39192.p1 fails validation. (TGC) GG 98089-98227 GT CGG (GCC) AG 98625-98755 GT CGG (GGT) AG 99370-99564 CT GAC -recovered pasa_asmbl_39192.p1, terminal, 99370, 99564 -recovered pasa_asmbl_39192.p1, internal, 98625, 98755 Valid prediction for Augustus_model.g4820.t1 Valid prediction for HiQ_model.g4809.t1 Valid prediction for snap_scaffold_3-snap.2313-T1 Valid prediction for GlimmerHMM_glimmerT_7381-T1 Valid prediction for snap_scaffold_3-snap.2308-T1 Valid prediction for snap_scaffold_3-snap.2325-T1 Couldn't classify 197521, 197595 Couldn't classify 198799, 198813 Sorry, prediction pasa_asmbl_39181.p1 fails validation. (AGT) GC 197521-197595 GT AGG (CCT) AG 197994-198096 GT AGG (GTC) AG 198457-198632 GT AGG (ATG) AG 198799-198813 TG AGT -recovered pasa_asmbl_39181.p1, internal, 197994, 198096 -recovered pasa_asmbl_39181.p1, internal, 198457, 198632 Couldn't classify 199037, 199123 Sorry, prediction pasa_asmbl_39179.p1 fails validation. (GAG) CT 199037-199123 GT AGG (GGT) AG 200269-200368 GT AGG (GGG) AG 201049-201170 GT ACG (CTG) AG 203490-203567 GT AGG (GTA) AG 205427-205507 GT TGG (GCC) AG 206232-206402 GT TGG (GGT) AG 206655-206733 GT AGG (GAA) AG 207037-207122 GT TGG (AAG) AG 207297-207365 GT AGG (AGG) AG 208178-208240 GT TGG (GAC) AG 208662-208697 GT AGG (ATC) AG 209203-209399 GT TGG (GCG) AG 209574-209683 GT AGG (TAT) AG 210836-210916 GT AGG (GAG) AG 211024-211104 GT ACG (ACA) AG 211326-211528 GC AGG (GCC) AG 211679-211762 GT AGG (GAT) AG 213842-214018 GA AGG add_exon() Sorry, pasa_asmbl_39179.p1 210836-210916-terminal-1 is invalid. -recovered pasa_asmbl_39179.p1, terminal, 210836, 210916 -recovered pasa_asmbl_39179.p1, terminal, 213842, 214018 -recovered pasa_asmbl_39179.p1, internal, 200269, 200368 -recovered pasa_asmbl_39179.p1, internal, 201049, 201170 -recovered pasa_asmbl_39179.p1, internal, 203490, 203567 -recovered pasa_asmbl_39179.p1, internal, 205427, 205507 -recovered pasa_asmbl_39179.p1, internal, 206232, 206402 -recovered pasa_asmbl_39179.p1, internal, 206655, 206733 -recovered pasa_asmbl_39179.p1, internal, 207037, 207122 -recovered pasa_asmbl_39179.p1, internal, 207297, 207365 -recovered pasa_asmbl_39179.p1, internal, 208178, 208240 -recovered pasa_asmbl_39179.p1, internal, 208662, 208697 -recovered pasa_asmbl_39179.p1, internal, 209203, 209399 -recovered pasa_asmbl_39179.p1, internal, 209574, 209683 -recovered pasa_asmbl_39179.p1, internal, 210836, 210916 -recovered pasa_asmbl_39179.p1, internal, 211024, 211104 -recovered pasa_asmbl_39179.p1, internal, 211326, 211528 -recovered pasa_asmbl_39179.p1, internal, 211679, 211762 Valid prediction for GlimmerHMM_glimmerT_7387-T1 Valid prediction for GlimmerHMM_glimmerT_7390-T1 Valid prediction for snap_scaffold_3-snap.2330-T1 Valid prediction for pasa_asmbl_39177.p1 Valid prediction for GlimmerHMM_glimmerT_7397-T1 Valid prediction for snap_scaffold_3-snap.2316-T1 Valid prediction for GlimmerHMM_glimmerT_7395-T1 Valid prediction for GlimmerHMM_glimmerT_7393-T1 Valid prediction for GlimmerHMM_glimmerT_7392-T1 Valid prediction for snap_scaffold_3-snap.2302-T1 Valid prediction for GlimmerHMM_glimmerT_7401-T1 Valid prediction for snap_scaffold_3-snap.2307-T1 Valid prediction for snap_scaffold_3-snap.2301-T1 Sorry, intron length (8) is less than minimum required (10) Valid prediction for snap_scaffold_3-snap.2334-T1 Couldn't classify 114442, 115011 Sorry, prediction pasa_asmbl_39188.p1 fails validation. (GCT) AG 114442-115011 GT AGG (GTT) AG 116144-116217 GT AAG (TGG) AG 116333-116408 GT ATG (TTG) AG 119390-119452 CA GAC -recovered pasa_asmbl_39188.p1, terminal, 119390, 119452 -recovered pasa_asmbl_39188.p1, internal, 114442, 115011 -recovered pasa_asmbl_39188.p1, internal, 116144, 116217 -recovered pasa_asmbl_39188.p1, internal, 116333, 116408 Couldn't classify 124218, 124376 Sorry, prediction pasa_asmbl_39185.p2 fails validation. (ATG) CA 123205-123357 GT CGG (GAG) AG 124218-124376 TG AGT -recovered pasa_asmbl_39185.p2, initial, 123205, 123357 Valid prediction for Augustus_model.g4813.t1 Valid prediction for snap_scaffold_3-snap.2329-T1 Valid prediction for snap_scaffold_3-snap.2327-T1 Valid prediction for snap_scaffold_3-snap.2314-T1 Valid prediction for snap_scaffold_3-snap.2318-T1 Valid prediction for snap_scaffold_3-snap.2324-T1 Valid prediction for Augustus_model.g4812.t1 Valid prediction for GlimmerHMM_glimmerT_7388-T1 Valid prediction for snap_scaffold_3-snap.2310-T1 Valid prediction for HiQ_model.g4817.t1 Valid prediction for pasa_asmbl_39183.p1 Valid prediction for snap_scaffold_3-snap.2321-T1 Valid prediction for snap_scaffold_3-snap.2331-T1 Valid prediction for snap_scaffold_3-snap.2298-T1 Valid prediction for HiQ_model.g4814.t1 Valid prediction for snap_scaffold_3-snap.2320-T1 Valid prediction for snap_scaffold_3-snap.2322-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7388, rend_intergenic: 4569 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30535, rend_intergenic: 14076 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 73231, rend_intergenic: 66636 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140896, rend_intergenic: 134085 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 190189, rend_intergenic: 183353 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 276775 -exon list size: 442 building trellis 0.2 0.5 0.7 0.9 1.1 1.4 1.6 1.8 2.0 2.3 2.5 2.7 2.9 3.2 3.4 3.6 3.8 4.1 4.3 4.5 4.7 5.0 5.2 5.4 5.6 5.9 6.1 6.3 6.5 6.8 7.0 7.2 7.4 7.7 7.9 8.1 8.3 8.6 8.8 9.0 9.2 9.5 9.7 9.9 10.1 10.4 10.6 10.8 11.0 11.3 11.5 11.7 11.9 12.2 12.4 12.6 12.8 13.1 13.3 13.5 13.7 14.0 14.2 14.4 14.6 14.9 15.1 15.3 15.5 15.8 16.0 16.2 16.4 16.7 16.9 17.1 17.3 17.6 17.8 18.0 18.2 18.5 18.7 18.9 19.1 19.4 19.6 19.8 20.0 20.3 20.5 20.7 20.9 21.2 21.4 21.6 21.8 22.1 22.3 22.5 22.7 23.0 23.2 23.4 23.6 23.9 24.1 24.3 24.5 24.8 25.0 25.2 25.5 25.7 25.9 26.1 26.4 26.6 26.8 27.0 27.3 27.5 27.7 27.9 28.2 28.4 28.6 28.8 29.1 29.3 29.5 29.7 30.0 30.2 30.4 30.6 30.9 31.1 31.3 31.5 31.8 32.0 32.2 32.4 32.7 32.9 33.1 33.3 33.6 33.8 34.0 34.2 34.5 34.7 34.9 35.1 35.4 35.6 35.8 36.0 36.3 36.5 36.7 36.9 37.2 37.4 37.6 37.8 38.1 38.3 38.5 38.7 39.0 39.2 39.4 39.6 39.9 40.1 40.3 40.5 40.8 41.0 41.2 41.4 41.7 41.9 42.1 42.3 42.6 42.8 43.0 43.2 43.5 43.7 43.9 44.1 44.4 44.6 44.8 45.0 45.3 45.5 45.7 45.9 46.2 46.4 46.6 46.8 47.1 47.3 47.5 47.7 48.0 48.2 48.4 48.6 48.9 49.1 49.3 49.5 49.8 50.0 50.2 50.5 50.7 50.9 51.1 51.4 51.6 51.8 52.0 52.3 52.5 52.7 52.9 53.2 53.4 53.6 53.8 54.1 54.3 54.5 54.7 55.0 55.2 55.4 55.6 55.9 56.1 56.3 56.5 56.8 57.0 57.2 57.4 57.7 57.9 58.1 58.3 58.6 58.8 59.0 59.2 59.5 59.7 59.9 60.1 60.4 60.6 60.8 61.0 61.3 61.5 61.7 61.9 62.2 62.4 62.6 62.8 63.1 63.3 63.5 63.7 64.0 64.2 64.4 64.6 64.9 65.1 65.3 65.5 65.8 66.0 66.2 66.4 66.7 66.9 67.1 67.3 67.6 67.8 68.0 68.2 68.5 68.7 68.9 69.1 69.4 69.6 69.8 70.0 70.3 70.5 70.7 70.9 71.2 71.4 71.6 71.8 72.1 72.3 72.5 72.7 73.0 73.2 73.4 73.6 73.9 74.1 74.3 74.5 74.8 75.0 75.2 75.5 75.7 75.9 76.1 76.4 76.6 76.8 77.0 77.3 77.5 77.7 77.9 78.2 78.4 78.6 78.8 79.1 79.3 79.5 79.7 80.0 80.2 80.4 80.6 80.9 81.1 81.3 81.5 81.8 82.0 82.2 82.4 82.7 82.9 83.1 83.3 83.6 83.8 84.0 84.2 84.5 84.7 84.9 85.1 85.4 85.6 85.8 86.0 86.3 86.5 86.7 86.9 87.2 87.4 87.6 87.8 88.1 88.3 88.5 88.7 89.0 89.2 89.4 89.6 89.9 90.1 90.3 90.5 90.8 91.0 91.2 91.4 91.7 91.9 92.1 92.3 92.6 92.8 93.0 93.2 93.5 93.7 93.9 94.1 94.4 94.6 94.8 95.0 95.3 95.5 95.7 95.9 96.2 96.4 96.6 96.8 97.1 97.3 97.5 97.7 98.0 98.2 98.4 98.6 98.9 99.1 99.3 99.5 99.8 -found 25 predictions from path traversal Error with prediction: snap lend_intergenic: 7388, rend_intergenic: 4569 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30535, rend_intergenic: 14076 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 73231, rend_intergenic: 66636 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140896, rend_intergenic: 134085 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 190189, rend_intergenic: 183353 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 19 predictions persist after filtering for low support -building DP trellis -building trellis in range 259757 - 276775 -exon list size: 13 building trellis 6.7 13.3 20.0 26.7 33.3 40.0 46.7 53.3 60.0 66.7 73.3 80.0 86.7 93.3 -found 3 predictions from path traversal -reporting highest scoring path thru the trellis. -found 2 predictions persist after filtering for low support