-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_11183131-11367663 -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_20087-T1 Valid prediction for snap_scaffold_16-snap.2085-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_16-snap.2107-T1 Valid prediction for snap_scaffold_16-snap.2112-T1 Valid prediction for Augustus_model.g26080.t1 Valid prediction for snap_scaffold_16-snap.2080-T1 Valid prediction for snap_scaffold_16-snap.2110-T1 Valid prediction for snap_scaffold_16-snap.2113-T1 Valid prediction for Augustus_model.g26078.t1 Valid prediction for GlimmerHMM_glimmerT_39038-T1 Valid prediction for GlimmerHMM_glimmerT_39052-T1 Valid prediction for GlimmerHMM_glimmerT_39035-T1 Valid prediction for Augustus_model.g26077.t1 Valid prediction for GlimmerHMM_glimmerT_39051-T1 Valid prediction for Augustus_model.g26086.t1 Valid prediction for Augustus_model.g26084.t1 Valid prediction for snap_scaffold_16-snap.2089-T1 Valid prediction for snap_scaffold_16-snap.2097-T1 Valid prediction for Augustus_model.g26089.t1 Valid prediction for snap_scaffold_16-snap.2105-T1 Valid prediction for snap_scaffold_16-snap.2099-T1 Valid prediction for GlimmerHMM_glimmerT_39043-T1 Valid prediction for GlimmerHMM_glimmerT_39040-T1 Valid prediction for GlimmerHMM_glimmerT_39055-T1 Valid prediction for snap_scaffold_16-snap.2095-T1 Couldn't classify 99453, 99686 Couldn't classify 103972, 103993 Sorry, prediction pasa_asmbl_16569.p1 fails validation. (TCC) GG 99453-99686 GT AGG (GTG) AG 100263-100362 GT AGG (ATG) AG 100469-100608 GT AGG (GAG) AG 100984-101092 GT TGG (GTC) AG 103583-103784 GT CTG (GTT) AG 103972-103993 GG GGG add_exon() Sorry, pasa_asmbl_16569.p1 100469-100608-initial-1 is invalid. -recovered pasa_asmbl_16569.p1, initial, 100469, 100608 -recovered pasa_asmbl_16569.p1, internal, 100263, 100362 -recovered pasa_asmbl_16569.p1, internal, 100469, 100608 -recovered pasa_asmbl_16569.p1, internal, 100984, 101092 -recovered pasa_asmbl_16569.p1, internal, 103583, 103784 Valid prediction for snap_scaffold_16-snap.2115-T1 Couldn't classify 119366, 119389 Sorry, prediction pasa_asmbl_16573.p1 fails validation. (GTG) AG 119366-119389 GT GGG (TTC) AG 119491-119796 GA AGG -recovered pasa_asmbl_16573.p1, terminal, 119491, 119796 -recovered pasa_asmbl_16573.p1, internal, 119366, 119389 Valid prediction for snap_scaffold_16-snap.2102-T1 Valid prediction for pasa_asmbl_16575.p1 Valid prediction for GlimmerHMM_glimmerT_39045-T1 Valid prediction for snap_scaffold_16-snap.2084-T1 Valid prediction for snap_scaffold_16-snap.2119-T1 Valid prediction for GlimmerHMM_glimmerT_39048-T1 Couldn't classify 64770, 64871 Couldn't classify 68136, 68215 Sorry, prediction pasa_asmbl_16567.p1 fails validation. (GGA) TA 64770-64871 GT AGG (GCC) AG 66055-66165 GT CAG (GAC) AG 66429-66519 GT TGG (AAG) AG 68136-68215 GT TGG -recovered pasa_asmbl_16567.p1, internal, 66055, 66165 -recovered pasa_asmbl_16567.p1, internal, 66429, 66519 -recovered pasa_asmbl_16567.p1, internal, 68136, 68215 Valid prediction for snap_scaffold_16-snap.2083-T1 Valid prediction for snap_scaffold_16-snap.2101-T1 Couldn't classify 106533, 106610 Couldn't classify 114255, 114394 Sorry, prediction pasa_asmbl_16570.p1 fails validation. (CTG) CT 106533-106610 GT AGG (CTG) AG 107023-107151 GT AGG (CTG) AG 107517-107675 GT AGG (ATC) AG 108131-108275 GT GGG (GAG) AG 108454-108541 GT AGG (GAT) AG 108635-108675 GT CGG (TGG) AG 108855-109024 GT AGG (GTC) AG 109430-109581 GT AGG (GTC) AG 110750-110922 GT CAG (CGA) AG 111254-111414 GT AGG (GCC) AG 111788-111918 GT AGG (GGG) AG 112114-112243 GT AGG (AAA) AG 112473-112608 GT AGG (ACA) AG 113101-113239 GT ACG (GCT) AG 113702-113771 GT AGG (GAC) AG 113867-114026 GT GAG (AGG) AG 114255-114394 GT AGG add_exon() Sorry, pasa_asmbl_16570.p1 108454-108541-terminal-3 is invalid. -recovered pasa_asmbl_16570.p1, terminal, 108454, 108541 -recovered pasa_asmbl_16570.p1, internal, 107023, 107151 -recovered pasa_asmbl_16570.p1, internal, 107517, 107675 -recovered pasa_asmbl_16570.p1, internal, 108131, 108275 -recovered pasa_asmbl_16570.p1, internal, 108454, 108541 -recovered pasa_asmbl_16570.p1, internal, 108635, 108675 -recovered pasa_asmbl_16570.p1, internal, 108855, 109024 -recovered pasa_asmbl_16570.p1, internal, 109430, 109581 -recovered pasa_asmbl_16570.p1, internal, 110750, 110922 -recovered pasa_asmbl_16570.p1, internal, 111254, 111414 -recovered pasa_asmbl_16570.p1, internal, 111788, 111918 -recovered pasa_asmbl_16570.p1, internal, 112114, 112243 -recovered pasa_asmbl_16570.p1, internal, 112473, 112608 -recovered pasa_asmbl_16570.p1, internal, 113101, 113239 -recovered pasa_asmbl_16570.p1, internal, 113702, 113771 -recovered pasa_asmbl_16570.p1, internal, 113867, 114026 -recovered pasa_asmbl_16570.p1, internal, 114255, 114394 Valid prediction for GlimmerHMM_glimmerT_39050-T1 Valid prediction for HiQ_model.g26083.t1 Valid prediction for snap_scaffold_16-snap.2120-T1 Valid prediction for snap_scaffold_16-snap.2094-T1 Valid prediction for snap_scaffold_16-snap.2091-T1 Valid prediction for snap_scaffold_16-snap.2087-T1 Valid prediction for GlimmerHMM_glimmerT_39041-T1 Valid prediction for snap_scaffold_16-snap.2114-T1 Valid prediction for GlimmerHMM_glimmerT_39046-T1 Valid prediction for HiQ_model.g26081.t1 Valid prediction for GlimmerHMM_glimmerT_39047-T1 Valid prediction for Augustus_model.g26079.t1 Valid prediction for GlimmerHMM_glimmerT_39042-T1 Valid prediction for snap_scaffold_16-snap.2121-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: -)Couldn't classify 178244, 178346 Couldn't classify 182735, 182810 Sorry, prediction pasa_asmbl_17597.p1 fails validation. (AGT) TC 178244-178346 GT CGG (TCA) AG 179399-179502 GT AGG (GGG) AG 179873-179922 GT AGG (GGA) AG 182735-182810 GT AGG -recovered pasa_asmbl_17597.p1, internal, 179399, 179502 -recovered pasa_asmbl_17597.p1, internal, 179873, 179922 -recovered pasa_asmbl_17597.p1, internal, 182735, 182810 Valid prediction for Augustus_model.g26087.t1 Valid prediction for snap_scaffold_16-snap.2118-T1 Valid prediction for GlimmerHMM_glimmerT_39053-T1 Couldn't classify 17141, 17155 Sorry, prediction pasa_asmbl_17337.p1 fails validation. (AAA) AC 17141-17155 GT CGG (TTG) AG 17391-17463 GT AGG (AGT) AG 17566-17641 GT CAG (CCC) AG 17915-17990 GT AGG (AAC) AG 18106-18155 GT CAG (TGC) AG 18279-18336 GT AGG (GTT) AG 18643-18726 GT AGG (CAA) AG 18801-18932 GT AAG (CTT) AG 19833-19945 GT AGG (GGA) AG 20452-20488 GT AAG (GGA) AG 20891-20977 GT AGG (TAT) AG 21264-21359 GT TGG (CCG) AG 21582-21737 GT TTG (ACT) AG 22297-22386 GT TGG (AAT) AG 22577-22747 AA GAA -recovered pasa_asmbl_17337.p1, terminal, 22577, 22747 -recovered pasa_asmbl_17337.p1, internal, 17391, 17463 -recovered pasa_asmbl_17337.p1, internal, 17566, 17641 -recovered pasa_asmbl_17337.p1, internal, 17915, 17990 -recovered pasa_asmbl_17337.p1, internal, 18106, 18155 -recovered pasa_asmbl_17337.p1, internal, 18279, 18336 -recovered pasa_asmbl_17337.p1, internal, 18643, 18726 -recovered pasa_asmbl_17337.p1, internal, 18801, 18932 -recovered pasa_asmbl_17337.p1, internal, 19833, 19945 -recovered pasa_asmbl_17337.p1, internal, 20452, 20488 -recovered pasa_asmbl_17337.p1, internal, 20891, 20977 -recovered pasa_asmbl_17337.p1, internal, 21264, 21359 -recovered pasa_asmbl_17337.p1, internal, 21582, 21737 -recovered pasa_asmbl_17337.p1, internal, 22297, 22386 Valid prediction for Augustus_model.g26076.t1 Couldn't classify 171298, 171416 Couldn't classify 174294, 174421 Sorry, prediction pasa_asmbl_17335.p1 fails validation. (GAC) CA 171298-171416 GT AGG (GCG) AG 171954-172057 GT AGG (CCG) AG 173066-173215 GT AAG (GTC) AG 174294-174421 AA CCA -recovered pasa_asmbl_17335.p1, internal, 171954, 172057 -recovered pasa_asmbl_17335.p1, internal, 173066, 173215 Valid prediction for snap_scaffold_16-snap.2090-T1 Valid prediction for snap_scaffold_16-snap.2092-T1 Valid prediction for snap_scaffold_16-snap.2082-T1 Valid prediction for snap_scaffold_16-snap.2081-T1 Valid prediction for snap_scaffold_16-snap.2093-T1 Valid prediction for GlimmerHMM_glimmerT_39037-T1 Valid prediction for snap_scaffold_16-snap.2100-T1 Valid prediction for snap_scaffold_16-snap.2098-T1 Valid prediction for snap_scaffold_16-snap.2106-T1 Valid prediction for snap_scaffold_16-snap.2104-T1 Valid prediction for snap_scaffold_16-snap.2103-T1 Valid prediction for GlimmerHMM_glimmerT_39039-T1 Valid prediction for snap_scaffold_16-snap.2096-T1 Valid prediction for snap_scaffold_16-snap.2109-T1 Valid prediction for GlimmerHMM_glimmerT_39036-T1 Valid prediction for Augustus_model.g26082.t1 Valid prediction for snap_scaffold_16-snap.2086-T1 Valid prediction for Augustus_model.g26074.t1 Valid prediction for GlimmerHMM_glimmerT_39049-T1 Valid prediction for GlimmerHMM_glimmerT_39054-T1 Valid prediction for Augustus_model.g26088.t1 Valid prediction for snap_scaffold_16-snap.2116-T1 Valid prediction for snap_scaffold_16-snap.2111-T1 Valid prediction for snap_scaffold_16-snap.2088-T1 Valid prediction for Augustus_model.g26075.t1 Valid prediction for snap_scaffold_16-snap.2117-T1 Valid prediction for snap_scaffold_16-snap.2108-T1 Valid prediction for GlimmerHMM_glimmerT_39044-T1 Valid prediction for Augustus_model.g26085.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24449, rend_intergenic: 10041 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 37820, rend_intergenic: 35719 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 44365, rend_intergenic: 42801 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 52095, rend_intergenic: 49485 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 69038, rend_intergenic: 59505 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 79654, rend_intergenic: 77848 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 83579, rend_intergenic: 79802 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95928, rend_intergenic: 86248 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 101115, rend_intergenic: 97350 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118215, rend_intergenic: 106947 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127873, rend_intergenic: 124063 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 168958, rend_intergenic: 167524 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 184533 -exon list size: 441 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 8.4 8.6 8.8 9.0 9.3 9.5 9.7 9.9 10.2 10.4 10.6 10.8 11.1 11.3 11.5 11.7 12.0 12.2 12.4 12.6 12.9 13.1 13.3 13.5 13.8 14.0 14.2 14.4 14.7 14.9 15.1 15.3 15.6 15.8 16.0 16.3 16.5 16.7 16.9 17.2 17.4 17.6 17.8 18.1 18.3 18.5 18.7 19.0 19.2 19.4 19.6 19.9 20.1 20.3 20.5 20.8 21.0 21.2 21.4 21.7 21.9 22.1 22.3 22.6 22.8 23.0 23.3 23.5 23.7 23.9 24.2 24.4 24.6 24.8 25.1 25.3 25.5 25.7 26.0 26.2 26.4 26.6 26.9 27.1 27.3 27.5 27.8 28.0 28.2 28.4 28.7 28.9 29.1 29.3 29.6 29.8 30.0 30.2 30.5 30.7 30.9 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 34.8 35.0 35.2 35.4 35.7 35.9 36.1 36.3 36.6 36.8 37.0 37.2 37.5 37.7 37.9 38.1 38.4 38.6 38.8 39.1 39.3 39.5 39.7 40.0 40.2 40.4 40.6 40.9 41.1 41.3 41.5 41.8 42.0 42.2 42.4 42.7 42.9 43.1 43.3 43.6 43.8 44.0 44.2 44.5 44.7 44.9 45.1 45.4 45.6 45.8 46.0 46.3 46.5 46.7 47.0 47.2 47.4 47.6 47.9 48.1 48.3 48.5 48.8 49.0 49.2 49.4 49.7 49.9 50.1 50.3 50.6 50.8 51.0 51.2 51.5 51.7 51.9 52.1 52.4 52.6 52.8 53.0 53.3 53.5 53.7 54.0 54.2 54.4 54.6 54.9 55.1 55.3 55.5 55.8 56.0 56.2 56.4 56.7 56.9 57.1 57.3 57.6 57.8 58.0 58.2 58.5 58.7 58.9 59.1 59.4 59.6 59.8 60.0 60.3 60.5 60.7 60.9 61.2 61.4 61.6 61.9 62.1 62.3 62.5 62.8 63.0 63.2 63.4 63.7 63.9 64.1 64.3 64.6 64.8 65.0 65.2 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 69.1 69.3 69.5 69.8 70.0 70.2 70.4 70.7 70.9 71.1 71.3 71.6 71.8 72.0 72.2 72.5 72.7 72.9 73.1 73.4 73.6 73.8 74.0 74.3 74.5 74.7 74.9 75.2 75.4 75.6 75.8 76.1 76.3 76.5 76.7 77.0 77.2 77.4 77.7 77.9 78.1 78.3 78.6 78.8 79.0 79.2 79.5 79.7 79.9 80.1 80.4 80.6 80.8 81.0 81.3 81.5 81.7 81.9 82.2 82.4 82.6 82.8 83.1 83.3 83.5 83.7 84.0 84.2 84.4 84.7 84.9 85.1 85.3 85.6 85.8 86.0 86.2 86.5 86.7 86.9 87.1 87.4 87.6 87.8 88.0 88.3 88.5 88.7 88.9 89.2 89.4 89.6 89.8 90.1 90.3 90.5 90.7 91.0 91.2 91.4 91.6 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 29 predictions from path traversal Error with prediction: snap lend_intergenic: 24449, rend_intergenic: 10041 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 37820, rend_intergenic: 35719 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 44365, rend_intergenic: 42801 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 52095, rend_intergenic: 49485 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 69038, rend_intergenic: 59505 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 79654, rend_intergenic: 77848 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 83579, rend_intergenic: 79802 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95928, rend_intergenic: 86248 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 101115, rend_intergenic: 97350 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118215, rend_intergenic: 106947 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127873, rend_intergenic: 124063 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 168958, rend_intergenic: 167524 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 21 predictions persist after filtering for low support