-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_10924259-11151353 -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 CodingQuarry_transcript_46274-T1 Valid prediction for snap_scaffold_3-snap.2211-T1 Valid prediction for GlimmerHMM_glimmerT_7307-T1 Valid prediction for HiQ_model.g4749.t1 Valid prediction for GlimmerHMM_glimmerT_7295-T1 Valid prediction for GlimmerHMM_glimmerT_7303-T1 Valid prediction for snap_scaffold_3-snap.2197-T1 Valid prediction for GlimmerHMM_glimmerT_7306-T1 Valid prediction for snap_scaffold_3-snap.2203-T1 Valid prediction for snap_scaffold_3-snap.2195-T1 Valid prediction for GlimmerHMM_glimmerT_7309-T1 Valid prediction for HiQ_model.g4752.t1 Valid prediction for snap_scaffold_3-snap.2199-T1 Valid prediction for snap_scaffold_3-snap.2192-T1 Valid prediction for snap_scaffold_3-snap.2181-T1 Valid prediction for GlimmerHMM_glimmerT_7315-T1 Valid prediction for snap_scaffold_3-snap.2207-T1 Couldn't classify 109495, 112746 Sorry, prediction pasa_asmbl_40332.p1 fails validation. (ATG) GA 109495-112746 AC AGA Valid prediction for snap_scaffold_3-snap.2196-T1 Valid prediction for snap_scaffold_3-snap.2190-T1 Valid prediction for snap_scaffold_3-snap.2169-T1 Valid prediction for GlimmerHMM_glimmerT_7299-T1 Valid prediction for snap_scaffold_3-snap.2206-T1 Valid prediction for snap_scaffold_3-snap.2182-T1 Valid prediction for snap_scaffold_3-snap.2178-T1 Valid prediction for snap_scaffold_3-snap.2202-T1 Valid prediction for snap_scaffold_3-snap.2189-T1 Valid prediction for snap_scaffold_3-snap.2183-T1 Valid prediction for snap_scaffold_3-snap.2210-T1 Valid prediction for pasa_asmbl_40320.p1 Couldn't classify 72945, 73001 Sorry, prediction pasa_asmbl_40328.p1 fails validation. (GGG) AG 72945-73001 GT AGG (GGT) AG 74355-74444 GT AGG (GGA) AG 74728-74772 GT GTG (GGC) AG 74886-74930 GT CGG (GGT) AG 75021-75083 GT AGG (GGA) AG 75175-75228 GT CGG (GGT) AG 75423-75449 GT AGG (GGA) AG 75569-75634 GT AAG (GGA) AG 75721-75783 GT GAG (GGT) AG 75995-76030 GT AGG (GGT) AG 76157-76195 GT AGG (GGT) AG 76403-76501 GT CAG (GGA) AG 76840-76875 GT AAG (GGA) AG 77058-77117 GT GGG (GGC) AG 77237-77272 GT AGG (GGA) AG 77490-77534 GT CGG (GGC) AG 77661-77693 GT CTG (GGT) AG 78148-78208 GT AGG (GTT) AG 78333-78368 GT TGG (GAA) AG 78457-78603 GT GGG (GCG) AG 78737-78823 GT AGG (GTG) AG 78914-78997 GT AGG (GTT) AG 79203-79273 GT CCG (GGT) AG 79369-79560 GT CCG (GCC) AG 79721-79889 GT AGG (GTG) AG 80089-80181 GT AGG (GTG) AG 80339-80443 GT AGG (GAT) AG 80515-80612 GT AGG (GGA) AG 80818-80968 GT AGG (GTG) AG 81145-81258 GT CGG (GTC) AG 81376-81543 GT AGG (GCC) AG 81693-81782 GT AGG (GCG) AG 82086-82238 GT AGG (GTG) AG 82432-82530 GT AGG (GTG) AG 82627-82716 GT AGG (GTT) AG 82857-82996 GT AGG (GGC) AG 83214-83340 GT AGG (GTC) AG 83465-83545 GT AGG (GTG) AG 83751-83849 GT AGG (GGT) AG 84050-84100 GT AGG (GTA) AG 84267-84452 GT AGG (GAT) AG 84546-84679 GT CTG (GGA) AG 84810-84882 GT TGG (GAA) AG 85403-85474 GT AGG (GTG) AG 85600-85728 GT AGG (GTG) AG 85814-85912 GT AGG (GAC) AG 85987-86199 GT TGG (GTA) AG 86273-86450 GT AGG (GTG) AG 86533-86647 GT TGG (AAC) AG 86813-86985 GT AGG (GAA) AG 87368-87449 AC AAA add_exon() Sorry, pasa_asmbl_40328.p1 85814-85912-terminal-1 is invalid. -recovered pasa_asmbl_40328.p1, terminal, 85814, 85912 add_exon() Sorry, pasa_asmbl_40328.p1 86813-86985-terminal-2 is invalid. -recovered pasa_asmbl_40328.p1, terminal, 86813, 86985 -recovered pasa_asmbl_40328.p1, terminal, 87368, 87449 -recovered pasa_asmbl_40328.p1, internal, 72945, 73001 -recovered pasa_asmbl_40328.p1, internal, 74355, 74444 -recovered pasa_asmbl_40328.p1, internal, 74728, 74772 -recovered pasa_asmbl_40328.p1, internal, 74886, 74930 -recovered pasa_asmbl_40328.p1, internal, 75021, 75083 -recovered pasa_asmbl_40328.p1, internal, 75175, 75228 -recovered pasa_asmbl_40328.p1, internal, 75423, 75449 -recovered pasa_asmbl_40328.p1, internal, 75569, 75634 -recovered pasa_asmbl_40328.p1, internal, 75721, 75783 -recovered pasa_asmbl_40328.p1, internal, 75995, 76030 -recovered pasa_asmbl_40328.p1, internal, 76157, 76195 -recovered pasa_asmbl_40328.p1, internal, 76403, 76501 -recovered pasa_asmbl_40328.p1, internal, 76840, 76875 -recovered pasa_asmbl_40328.p1, internal, 77058, 77117 -recovered pasa_asmbl_40328.p1, internal, 77237, 77272 -recovered pasa_asmbl_40328.p1, internal, 77490, 77534 -recovered pasa_asmbl_40328.p1, internal, 77661, 77693 -recovered pasa_asmbl_40328.p1, internal, 78148, 78208 -recovered pasa_asmbl_40328.p1, internal, 78333, 78368 -recovered pasa_asmbl_40328.p1, internal, 78457, 78603 -recovered pasa_asmbl_40328.p1, internal, 78737, 78823 -recovered pasa_asmbl_40328.p1, internal, 78914, 78997 -recovered pasa_asmbl_40328.p1, internal, 79203, 79273 -recovered pasa_asmbl_40328.p1, internal, 79369, 79560 -recovered pasa_asmbl_40328.p1, internal, 79721, 79889 -recovered pasa_asmbl_40328.p1, internal, 80089, 80181 -recovered pasa_asmbl_40328.p1, internal, 80339, 80443 -recovered pasa_asmbl_40328.p1, internal, 80515, 80612 -recovered pasa_asmbl_40328.p1, internal, 80818, 80968 -recovered pasa_asmbl_40328.p1, internal, 81145, 81258 -recovered pasa_asmbl_40328.p1, internal, 81376, 81543 -recovered pasa_asmbl_40328.p1, internal, 81693, 81782 -recovered pasa_asmbl_40328.p1, internal, 82086, 82238 -recovered pasa_asmbl_40328.p1, internal, 82432, 82530 -recovered pasa_asmbl_40328.p1, internal, 82627, 82716 -recovered pasa_asmbl_40328.p1, internal, 82857, 82996 -recovered pasa_asmbl_40328.p1, internal, 83214, 83340 -recovered pasa_asmbl_40328.p1, internal, 83465, 83545 -recovered pasa_asmbl_40328.p1, internal, 83751, 83849 -recovered pasa_asmbl_40328.p1, internal, 84050, 84100 -recovered pasa_asmbl_40328.p1, internal, 84267, 84452 -recovered pasa_asmbl_40328.p1, internal, 84546, 84679 -recovered pasa_asmbl_40328.p1, internal, 84810, 84882 -recovered pasa_asmbl_40328.p1, internal, 85403, 85474 -recovered pasa_asmbl_40328.p1, internal, 85600, 85728 -recovered pasa_asmbl_40328.p1, internal, 85814, 85912 -recovered pasa_asmbl_40328.p1, internal, 85987, 86199 -recovered pasa_asmbl_40328.p1, internal, 86273, 86450 -recovered pasa_asmbl_40328.p1, internal, 86533, 86647 -recovered pasa_asmbl_40328.p1, internal, 86813, 86985 Valid prediction for snap_scaffold_3-snap.2177-T1 Valid prediction for Augustus_model.g4754.t1 Valid prediction for snap_scaffold_3-snap.2200-T1 Couldn't classify 16198, 16442 Sorry, prediction pasa_asmbl_40323.p1 fails validation. (ATG) CC 13866-14055 GT AGG (GTC) AG 16198-16442 GG AGG -recovered pasa_asmbl_40323.p1, initial, 13866, 14055 Valid prediction for HiQ_model.g4755.t1 Valid prediction for GlimmerHMM_glimmerT_7313-T1 Valid prediction for GlimmerHMM_glimmerT_7293-T1 Valid prediction for GlimmerHMM_glimmerT_7314-T1 Couldn't classify 119976, 120314 Sorry, prediction pasa_asmbl_40333.p1 fails validation. (AGA) AC 119976-120314 CC GAC Valid prediction for snap_scaffold_3-snap.2175-T1 Valid prediction for CodingQuarry_transcript_46271-T1 Valid prediction for GlimmerHMM_glimmerT_7301-T1 Valid prediction for snap_scaffold_3-snap.2172-T1 Valid prediction for snap_scaffold_3-snap.2185-T1 Valid prediction for Augustus_model.g4756.t1 Valid prediction for snap_scaffold_3-snap.2201-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.2180-T1 Valid prediction for GlimmerHMM_glimmerT_7304-T1 Valid prediction for HiQ_model.g4753.t1 Valid prediction for HiQ_model.g4751.t1 Valid prediction for snap_scaffold_3-snap.2191-T1 Valid prediction for snap_scaffold_3-snap.2170-T1 Valid prediction for pasa_asmbl_39125.p1 Valid prediction for GlimmerHMM_glimmerT_7310-T1 Valid prediction for snap_scaffold_3-snap.2186-T1 Valid prediction for Augustus_model.g4757.t1 Valid prediction for snap_scaffold_3-snap.2188-T1 Valid prediction for GlimmerHMM_glimmerT_7305-T1 Valid prediction for GlimmerHMM_glimmerT_7302-T1 Valid prediction for snap_scaffold_3-snap.2204-T1 Valid prediction for GlimmerHMM_glimmerT_7300-T1 Valid prediction for snap_scaffold_3-snap.2193-T1 Valid prediction for snap_scaffold_3-snap.2176-T1 Valid prediction for snap_scaffold_3-snap.2184-T1 Valid prediction for GlimmerHMM_glimmerT_7297-T1 Valid prediction for Augustus_model.g4759.t1 Couldn't classify 217604, 217698 Sorry, prediction pasa_asmbl_39120.p1 fails validation. (ACG) CC 217604-217698 GT AGG (GCA) AG 218234-218397 GT AGG (ACG) AG 218691-218839 GT TGG (GTG) AG 218967-219599 CT AGC -recovered pasa_asmbl_39120.p1, terminal, 218967, 219599 -recovered pasa_asmbl_39120.p1, internal, 218234, 218397 -recovered pasa_asmbl_39120.p1, internal, 218691, 218839 Valid prediction for snap_scaffold_3-snap.2194-T1 Valid prediction for GlimmerHMM_glimmerT_7308-T1 Valid prediction for GlimmerHMM_glimmerT_7296-T1 Valid prediction for Augustus_model.g4761.t1 Valid prediction for snap_scaffold_3-snap.2209-T1 Valid prediction for Augustus_model.g4762.t1 Valid prediction for GlimmerHMM_glimmerT_7294-T1 Valid prediction for HiQ_model.g4750.t1 Valid prediction for snap_scaffold_3-snap.2187-T1 Valid prediction for Augustus_model.g4760.t1 Valid prediction for CodingQuarry_transcript_46273-T1 Valid prediction for snap_scaffold_3-snap.2198-T1 Valid prediction for snap_scaffold_3-snap.2179-T1 Valid prediction for snap_scaffold_3-snap.2171-T1 Valid prediction for snap_scaffold_3-snap.2213-T1 Valid prediction for snap_scaffold_3-snap.2212-T1 Valid prediction for snap_scaffold_3-snap.2205-T1 Valid prediction for snap_scaffold_3-snap.2173-T1 Valid prediction for GlimmerHMM_glimmerT_7298-T1 Valid prediction for CodingQuarry_transcript_46272-T1 Valid prediction for Augustus_model.g4758.t1 Valid prediction for GlimmerHMM_glimmerT_7311-T1 Valid prediction for GlimmerHMM_glimmerT_7312-T1 Valid prediction for snap_scaffold_3-snap.2174-T1 Valid prediction for snap_scaffold_3-snap.2208-T1 Valid prediction for pasa_asmbl_39122.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25009, rend_intergenic: 23281 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27221, rend_intergenic: 25212 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40969, rend_intergenic: 27321 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48037, rend_intergenic: 42578 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59264, rend_intergenic: 50466 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68012, rend_intergenic: 63628 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75244, rend_intergenic: 68675 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87271, rend_intergenic: 76363 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 98786, rend_intergenic: 95631 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103892, rend_intergenic: 99375 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 121225, rend_intergenic: 115412 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146337, rend_intergenic: 127378 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 181317, rend_intergenic: 150552 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192293, rend_intergenic: 188980 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 204109, rend_intergenic: 196875 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 212854, rend_intergenic: 204765 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 224230, rend_intergenic: 214570 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 227095 -exon list size: 506 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 3.1 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 9.4 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 15.6 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 21.9 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 28.1 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 34.4 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 40.6 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 46.9 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 53.1 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 59.4 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 65.6 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 71.9 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 78.1 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 84.4 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 90.6 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 96.9 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 24 predictions from path traversal Error with prediction: snap lend_intergenic: 25009, rend_intergenic: 23281 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27221, rend_intergenic: 25212 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40969, rend_intergenic: 27321 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48037, rend_intergenic: 42578 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59264, rend_intergenic: 50466 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68012, rend_intergenic: 63628 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75244, rend_intergenic: 68675 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87271, rend_intergenic: 76363 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 98786, rend_intergenic: 95631 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103892, rend_intergenic: 99375 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 121225, rend_intergenic: 115412 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146337, rend_intergenic: 127378 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 181317, rend_intergenic: 150552 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192293, rend_intergenic: 188980 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 204109, rend_intergenic: 196875 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 212854, rend_intergenic: 204765 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 224230, rend_intergenic: 214570 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 13 predictions persist after filtering for low support