-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_2748512-2978626 -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_12-snap.572-T1 Valid prediction for snap_scaffold_12-snap.563-T1 Valid prediction for HiQ_model.g19147.t1 Valid prediction for snap_scaffold_12-snap.562-T1 Valid prediction for snap_scaffold_12-snap.584-T1 Valid prediction for GlimmerHMM_glimmerT_29006-T1 Valid prediction for Augustus_model.g19136.t1 Valid prediction for CodingQuarry_transcript_10142-T1 Valid prediction for snap_scaffold_12-snap.588-T1 Valid prediction for pasa_asmbl_8237.p1 Valid prediction for snap_scaffold_12-snap.591-T1 Valid prediction for GlimmerHMM_glimmerT_29014-T1 Valid prediction for GlimmerHMM_glimmerT_29001-T1 Valid prediction for snap_scaffold_12-snap.561-T1 Valid prediction for snap_scaffold_12-snap.580-T1 Valid prediction for snap_scaffold_12-snap.575-T1 Valid prediction for snap_scaffold_12-snap.586-T1 Valid prediction for GlimmerHMM_glimmerT_29009-T1 Valid prediction for snap_scaffold_12-snap.585-T1 Valid prediction for Augustus_model.g19146.t1 Couldn't classify 207205, 207673 Sorry, prediction pasa_asmbl_7532.p1 fails validation. (AGA) CG 207205-207673 GT AGG (CAC) AG 209691-209800 GT AGG (ATC) AG 212316-212420 GT TGG (ATC) AG 213231-213357 GT AGG (TGA) AG 214359-214381 GC GAG -recovered pasa_asmbl_7532.p1, terminal, 214359, 214381 -recovered pasa_asmbl_7532.p1, internal, 209691, 209800 -recovered pasa_asmbl_7532.p1, internal, 212316, 212420 -recovered pasa_asmbl_7532.p1, internal, 213231, 213357 -recovered pasa_asmbl_7532.p1, internal, 214359, 214381 Valid prediction for HiQ_model.g19134.t1 Valid prediction for GlimmerHMM_glimmerT_29002-T1 Valid prediction for HiQ_model.g19144.t1 Valid prediction for snap_scaffold_12-snap.577-T1 Valid prediction for GlimmerHMM_glimmerT_28991-T1 Valid prediction for snap_scaffold_12-snap.566-T1 Valid prediction for snap_scaffold_12-snap.587-T1 Valid prediction for snap_scaffold_12-snap.590-T1 Couldn't classify 13754, 13761 Sorry, prediction pasa_asmbl_7525.p1 fails validation. (TGT) TA 13754-13761 GT GTG (CGC) AG 13850-14006 GT TGG (GTG) AG 14260-14367 GT AGG (GTG) AG 14545-14666 GT AAG (GAG) AG 14788-14857 GT AGG (TAT) AG 15067-15282 GT AGG (GGC) AG 16024-16121 GT TGG (TGC) AG 16220-16283 GT AGG (GTG) AG 16411-16521 GT TGG (CTG) AG 16955-17019 GT AGG (ACT) AG 17109-17171 GT TGG (GGC) AG 17402-17476 GT AGG (ACT) AG 17698-17801 GT CAG (GTG) AG 17928-18050 GT TGG (ACG) AG 18234-18336 GT AAG (GTT) AG 18546-18639 GT AGG (ATG) AG 18985-19088 GT AGG (GTT) AG 19536-19653 GT AGG (AAG) AG 19963-20103 GT AGG (CGC) AG 20272-20385 GT TGG (CAT) AG 20726-20839 GC GAG -recovered pasa_asmbl_7525.p1, initial, 18985, 19088 -recovered pasa_asmbl_7525.p1, terminal, 20726, 20839 -recovered pasa_asmbl_7525.p1, internal, 13850, 14006 -recovered pasa_asmbl_7525.p1, internal, 14260, 14367 -recovered pasa_asmbl_7525.p1, internal, 14545, 14666 -recovered pasa_asmbl_7525.p1, internal, 14788, 14857 -recovered pasa_asmbl_7525.p1, internal, 15067, 15282 -recovered pasa_asmbl_7525.p1, internal, 16024, 16121 -recovered pasa_asmbl_7525.p1, internal, 16220, 16283 -recovered pasa_asmbl_7525.p1, internal, 16411, 16521 -recovered pasa_asmbl_7525.p1, internal, 16955, 17019 -recovered pasa_asmbl_7525.p1, internal, 17109, 17171 -recovered pasa_asmbl_7525.p1, internal, 17402, 17476 -recovered pasa_asmbl_7525.p1, internal, 17698, 17801 -recovered pasa_asmbl_7525.p1, internal, 17928, 18050 -recovered pasa_asmbl_7525.p1, internal, 18234, 18336 -recovered pasa_asmbl_7525.p1, internal, 18546, 18639 -recovered pasa_asmbl_7525.p1, internal, 18985, 19088 -recovered pasa_asmbl_7525.p1, internal, 19536, 19653 -recovered pasa_asmbl_7525.p1, internal, 19963, 20103 -recovered pasa_asmbl_7525.p1, internal, 20272, 20385 -recovered pasa_asmbl_7525.p1, internal, 20726, 20839 Valid prediction for GlimmerHMM_glimmerT_29016-T1 Valid prediction for pasa_asmbl_7530.p1 Valid prediction for CodingQuarry_transcript_10143-T1 Valid prediction for GlimmerHMM_glimmerT_29015-T1 Valid prediction for GlimmerHMM_glimmerT_28993-T1 Valid prediction for GlimmerHMM_glimmerT_28990-T1 Valid prediction for GlimmerHMM_glimmerT_28998-T1 Valid prediction for GlimmerHMM_glimmerT_28992-T1 Valid prediction for Augustus_model.g19141.t1 Valid prediction for GlimmerHMM_glimmerT_29013-T1 Valid prediction for GlimmerHMM_glimmerT_28997-T1 Valid prediction for snap_scaffold_12-snap.564-T1 Valid prediction for GlimmerHMM_glimmerT_29008-T1 Valid prediction for Augustus_model.g19145.t1 Valid prediction for Augustus_model.g19138.t1 Valid prediction for GlimmerHMM_glimmerT_29005-T1 Valid prediction for snap_scaffold_12-snap.573-T1 Valid prediction for snap_scaffold_12-snap.571-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 Augustus_model.g19135.t1 Valid prediction for Augustus_model.g19149.t1 Couldn't classify 225592, 225627 Couldn't classify 226711, 226758 Sorry, prediction pasa_asmbl_9193.p1 fails validation. (CGT) AA 225592-225627 GT AGG (GGT) AG 226071-226305 GT TGG (ATT) AG 226464-226570 GC AGG (TTG) AG 226711-226758 AC TCA -recovered pasa_asmbl_9193.p1, internal, 226071, 226305 -recovered pasa_asmbl_9193.p1, internal, 226464, 226570 Valid prediction for snap_scaffold_12-snap.592-T1 Valid prediction for GlimmerHMM_glimmerT_29003-T1 Valid prediction for snap_scaffold_12-snap.578-T1 Valid prediction for snap_scaffold_12-snap.559-T1 Valid prediction for GlimmerHMM_glimmerT_28995-T1 Valid prediction for Augustus_model.g19148.t1 Valid prediction for GlimmerHMM_glimmerT_29017-T1 Valid prediction for snap_scaffold_12-snap.558-T1 Valid prediction for snap_scaffold_12-snap.569-T1 Valid prediction for snap_scaffold_12-snap.582-T1 Valid prediction for snap_scaffold_12-snap.560-T1 Valid prediction for GlimmerHMM_glimmerT_29007-T1 Valid prediction for snap_scaffold_12-snap.568-T1 Valid prediction for GlimmerHMM_glimmerT_28989-T1 Valid prediction for GlimmerHMM_glimmerT_29011-T1 Valid prediction for GlimmerHMM_glimmerT_28999-T1 Valid prediction for GlimmerHMM_glimmerT_28996-T1 Couldn't classify 5685, 5837 Sorry, prediction pasa_asmbl_8339.p1 fails validation. (ATG) CA 365-383 GT GGG (ATA) AG 883-955 GT AGG (CTC) AG 1062-1212 GT CGG (CCT) AG 1461-1573 GT ACG (GTA) AG 1880-2099 GT AGG (GTT) AG 2319-2477 GT AGG (GGA) AG 2780-2944 GT TGG (GTG) AG 3165-3361 GT GGG (GTA) AG 3591-3710 GT GGG (AAT) AG 3865-4051 GT AGG (GTG) AG 4413-4556 GT AGG (GGT) AG 4693-4832 GT GAG (TGC) AG 5251-5362 GT AGG (GTG) AG 5685-5837 AG ACA -recovered pasa_asmbl_8339.p1, initial, 365, 383 -recovered pasa_asmbl_8339.p1, internal, 883, 955 -recovered pasa_asmbl_8339.p1, internal, 1062, 1212 -recovered pasa_asmbl_8339.p1, internal, 1461, 1573 -recovered pasa_asmbl_8339.p1, internal, 1880, 2099 -recovered pasa_asmbl_8339.p1, internal, 2319, 2477 -recovered pasa_asmbl_8339.p1, internal, 2780, 2944 -recovered pasa_asmbl_8339.p1, internal, 3165, 3361 -recovered pasa_asmbl_8339.p1, internal, 3591, 3710 -recovered pasa_asmbl_8339.p1, internal, 3865, 4051 -recovered pasa_asmbl_8339.p1, internal, 4413, 4556 -recovered pasa_asmbl_8339.p1, internal, 4693, 4832 -recovered pasa_asmbl_8339.p1, internal, 5251, 5362 Valid prediction for GlimmerHMM_glimmerT_29004-T1 Valid prediction for snap_scaffold_12-snap.579-T1 Valid prediction for GlimmerHMM_glimmerT_29018-T1 Valid prediction for Augustus_model.g19133.t1 Couldn't classify 57954, 58198 Sorry, prediction pasa_asmbl_8332.p1 fails validation. (ATG) AC 52870-52906 GT AAG (TTG) AG 53167-54940 GT CTG (GCT) AG 55083-55244 GT AGG (GCT) AG 55748-55918 GT AGG (GTT) AG 56275-56448 GT AGG (GCT) AG 56826-56999 GT AGG (GCT) AG 57244-57417 GT AAG (TGT) AG 57580-57626 GT ATG (ATG) AG 57954-58198 GC GAG -recovered pasa_asmbl_8332.p1, initial, 52870, 52906 add_exon() Sorry, pasa_asmbl_8332.p1 57954-58198-initial-1 is invalid. -recovered pasa_asmbl_8332.p1, initial, 57954, 58198 add_exon() Sorry, pasa_asmbl_8332.p1 56275-56448-terminal-1 is invalid. -recovered pasa_asmbl_8332.p1, terminal, 56275, 56448 add_exon() Sorry, pasa_asmbl_8332.p1 56826-56999-terminal-1 is invalid. -recovered pasa_asmbl_8332.p1, terminal, 56826, 56999 -recovered pasa_asmbl_8332.p1, internal, 53167, 54940 -recovered pasa_asmbl_8332.p1, internal, 55083, 55244 -recovered pasa_asmbl_8332.p1, internal, 55748, 55918 -recovered pasa_asmbl_8332.p1, internal, 56275, 56448 -recovered pasa_asmbl_8332.p1, internal, 56826, 56999 -recovered pasa_asmbl_8332.p1, internal, 57244, 57417 -recovered pasa_asmbl_8332.p1, internal, 57580, 57626 -recovered pasa_asmbl_8332.p1, internal, 57954, 58198 Valid prediction for Augustus_model.g19139.t1 Valid prediction for snap_scaffold_12-snap.583-T1 Valid prediction for GlimmerHMM_glimmerT_29019-T1 Valid prediction for snap_scaffold_12-snap.570-T1 Valid prediction for snap_scaffold_12-snap.576-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for snap_scaffold_12-snap.581-T1 Valid prediction for snap_scaffold_12-snap.589-T1 Valid prediction for GlimmerHMM_glimmerT_29010-T1 Valid prediction for GlimmerHMM_glimmerT_29012-T1 Couldn't classify 205746, 205898 Couldn't classify 206425, 206568 Sorry, prediction pasa_asmbl_9248.p1 fails validation. (GAT) AG 205746-205898 GT TGG (GTG) AG 206425-206568 AT TTA -recovered pasa_asmbl_9248.p1, internal, 205746, 205898 Couldn't classify 223477, 223507 Couldn't classify 224335, 224462 Sorry, prediction pasa_asmbl_9179.p1 fails validation. (AAG) CG 223477-223507 GT TGG (ATG) AG 223612-223715 GT AAG (GAG) AG 224058-224181 GT TGG (GTA) AG 224335-224462 GT AGG add_exon() Sorry, pasa_asmbl_9179.p1 223612-223715-initial-1 is invalid. -recovered pasa_asmbl_9179.p1, initial, 223612, 223715 -recovered pasa_asmbl_9179.p1, internal, 223612, 223715 -recovered pasa_asmbl_9179.p1, internal, 224058, 224181 -recovered pasa_asmbl_9179.p1, internal, 224335, 224462 Couldn't classify 9781, 9943 Sorry, prediction pasa_asmbl_8337.p1 fails validation. (AGG) CC 9781-9943 GT AGG (GGA) AG 10238-10334 GT AGG (GTC) AG 10451-10545 GT GGG (GGA) AG 10878-11128 GT GGG (GTC) AG 11774-11863 GT AGG (GAC) AG 12129-12236 GT AGG (GTG) AG 12588-12701 GT AGG (GTG) AG 12791-12955 GG GAG -recovered pasa_asmbl_8337.p1, terminal, 12791, 12955 -recovered pasa_asmbl_8337.p1, internal, 10238, 10334 -recovered pasa_asmbl_8337.p1, internal, 10451, 10545 -recovered pasa_asmbl_8337.p1, internal, 10878, 11128 -recovered pasa_asmbl_8337.p1, internal, 11774, 11863 -recovered pasa_asmbl_8337.p1, internal, 12129, 12236 -recovered pasa_asmbl_8337.p1, internal, 12588, 12701 Valid prediction for GlimmerHMM_glimmerT_29000-T1 Couldn't classify 49582, 49676 Couldn't classify 51395, 51512 Sorry, prediction pasa_asmbl_8334.p1 fails validation. (TCA) CC 49582-49676 GT CAG (GAT) AG 50067-50183 GT CAG (GAT) AG 50893-51009 GT CAG (GAT) AG 51395-51512 TA AGT -recovered pasa_asmbl_8334.p1, internal, 50067, 50183 -recovered pasa_asmbl_8334.p1, internal, 50893, 51009 Valid prediction for Augustus_model.g19142.t1 Valid prediction for Augustus_model.g19140.t1 Valid prediction for snap_scaffold_12-snap.567-T1 Valid prediction for Augustus_model.g19137.t1 Valid prediction for GlimmerHMM_glimmerT_28988-T1 Valid prediction for snap_scaffold_12-snap.574-T1 Valid prediction for snap_scaffold_12-snap.565-T1 Couldn't classify 207057, 207150 Sorry, prediction pasa_asmbl_8328.p1 fails validation. (TAC) TC 207057-207150 GT AGG (TTT) AG 207829-208094 GA AGG -recovered pasa_asmbl_8328.p1, terminal, 207829, 208094 Valid prediction for Augustus_model.g19143.t1 Valid prediction for GlimmerHMM_glimmerT_28994-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11984, rend_intergenic: 7551 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27289, rend_intergenic: 22022 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 52719, rend_intergenic: 36889 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128048, rend_intergenic: 123987 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133973, rend_intergenic: 131174 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 206522, rend_intergenic: 202065 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 230115 -exon list size: 398 building trellis 0.2 0.5 0.8 1.0 1.2 1.5 1.8 2.0 2.2 2.5 2.8 3.0 3.2 3.5 3.8 4.0 4.2 4.5 4.8 5.0 5.2 5.5 5.8 6.0 6.2 6.5 6.8 7.0 7.2 7.5 7.8 8.0 8.2 8.5 8.8 9.0 9.2 9.5 9.8 10.0 10.2 10.5 10.8 11.0 11.2 11.5 11.8 12.0 12.2 12.5 12.8 13.0 13.2 13.5 13.8 14.0 14.2 14.5 14.8 15.0 15.2 15.5 15.8 16.0 16.2 16.5 16.8 17.0 17.2 17.5 17.8 18.0 18.2 18.5 18.8 19.0 19.2 19.5 19.8 20.0 20.2 20.5 20.8 21.0 21.2 21.5 21.8 22.0 22.2 22.5 22.8 23.0 23.2 23.5 23.8 24.0 24.2 24.5 24.8 25.0 25.2 25.5 25.8 26.0 26.2 26.5 26.8 27.0 27.3 27.5 27.8 28.0 28.2 28.5 28.7 29.0 29.2 29.5 29.8 30.0 30.2 30.5 30.8 31.0 31.2 31.5 31.8 32.0 32.2 32.5 32.8 33.0 33.2 33.5 33.8 34.0 34.2 34.5 34.8 35.0 35.2 35.5 35.8 36.0 36.2 36.5 36.8 37.0 37.2 37.5 37.8 38.0 38.2 38.5 38.8 39.0 39.2 39.5 39.8 40.0 40.2 40.5 40.8 41.0 41.2 41.5 41.8 42.0 42.2 42.5 42.8 43.0 43.2 43.5 43.8 44.0 44.2 44.5 44.8 45.0 45.2 45.5 45.8 46.0 46.2 46.5 46.8 47.0 47.2 47.5 47.8 48.0 48.2 48.5 48.8 49.0 49.2 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 52.8 53.0 53.2 53.5 53.8 54.0 54.2 54.5 54.8 55.0 55.2 55.5 55.8 56.0 56.2 56.5 56.8 57.0 57.2 57.5 57.8 58.0 58.2 58.5 58.8 59.0 59.2 59.5 59.8 60.0 60.2 60.5 60.8 61.0 61.3 61.5 61.8 62.0 62.3 62.5 62.7 63.0 63.2 63.5 63.7 64.0 64.2 64.5 64.8 65.0 65.2 65.5 65.8 66.0 66.2 66.5 66.8 67.0 67.2 67.5 67.8 68.0 68.2 68.5 68.8 69.0 69.2 69.5 69.8 70.0 70.2 70.5 70.8 71.0 71.2 71.5 71.8 72.0 72.2 72.5 72.8 73.0 73.2 73.5 73.8 74.0 74.2 74.5 74.8 75.0 75.2 75.5 75.8 76.0 76.2 76.5 76.8 77.0 77.2 77.5 77.8 78.0 78.2 78.5 78.8 79.0 79.2 79.5 79.8 80.0 80.2 80.5 80.8 81.0 81.2 81.5 81.8 82.0 82.2 82.5 82.8 83.0 83.2 83.5 83.8 84.0 84.2 84.5 84.8 85.0 85.2 85.5 85.8 86.0 86.2 86.5 86.8 87.0 87.2 87.5 87.8 88.0 88.2 88.5 88.8 89.0 89.2 89.5 89.8 90.0 90.2 90.5 90.8 91.0 91.2 91.5 91.8 92.0 92.2 92.5 92.8 93.0 93.2 93.5 93.8 94.0 94.2 94.5 94.8 95.0 95.2 95.5 95.8 96.0 96.2 96.5 96.8 97.0 97.2 97.5 97.8 98.0 98.2 98.5 98.8 99.0 99.2 99.5 99.8 -found 26 predictions from path traversal Error with prediction: snap lend_intergenic: 11984, rend_intergenic: 7551 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27289, rend_intergenic: 22022 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 52719, rend_intergenic: 36889 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128048, rend_intergenic: 123987 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133973, rend_intergenic: 131174 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 206522, rend_intergenic: 202065 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 18 predictions persist after filtering for low support