-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_57 -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_57-snap.2-T1 Couldn't classify 24545, 24637 Sorry, prediction GlimmerHMM_glimmerT_61110-T1 fails validation. (ATG) GC 20527-20562 GT TGG (ATC) AG 23027-23209 GT AGG (GAG) AG 23572-23715 GT GGG (GTG) AG 24545-24637 GT AGG -recovered GlimmerHMM_glimmerT_61110-T1, initial, 20527, 20562 -recovered GlimmerHMM_glimmerT_61110-T1, internal, 23027, 23209 -recovered GlimmerHMM_glimmerT_61110-T1, internal, 23572, 23715 -recovered GlimmerHMM_glimmerT_61110-T1, internal, 24545, 24637 Couldn't classify 25666, 25766 Sorry, prediction snap_scaffold_57-snap.6-T1 fails validation. (ATG) GG 16750-16941 GT AAG (GGT) AG 19672-19796 GT GGG (GTC) AG 23041-23209 GT AGG (GTG) AG 24545-24637 GT AGG (GGG) AG 25666-25766 GT GGG -recovered snap_scaffold_57-snap.6-T1, initial, 16750, 16941 -recovered snap_scaffold_57-snap.6-T1, internal, 19672, 19796 -recovered snap_scaffold_57-snap.6-T1, internal, 23041, 23209 -recovered snap_scaffold_57-snap.6-T1, internal, 24545, 24637 -recovered snap_scaffold_57-snap.6-T1, internal, 25666, 25766 Valid prediction for GlimmerHMM_glimmerT_61105-T1 Valid prediction for Augustus_model.g40649.t1 Valid prediction for GeneMark_model.106316_t Valid prediction for GeneMark_model.106312_t Valid prediction for snap_scaffold_57-snap.4-T1 Valid prediction for Augustus_model.g40650.t1 Valid prediction for Augustus_model.g40651.t1 Valid prediction for snap_scaffold_57-snap.3-T1 Valid prediction for GlimmerHMM_glimmerT_61103-T1 Valid prediction for GeneMark_model.106311_t Couldn't classify 9405, 9519 Sorry, prediction CodingQuarry_transcript_52408-T1 fails validation. (ATG) TG 8557-8640 GT CCG (GGC) AG 9106-9299 GC TGG (GCA) CT 9405-9519 GC AAG -recovered CodingQuarry_transcript_52408-T1, initial, 8557, 8640 -recovered CodingQuarry_transcript_52408-T1, internal, 9106, 9299 Valid prediction for GlimmerHMM_glimmerT_61102-T1 add_exon() Sorry, GlimmerHMM_glimmerT_61102-T1 1808-2336-terminal-1 is invalid. Valid prediction for snap_scaffold_57-snap.1-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_61106-T1 Valid prediction for GlimmerHMM_glimmerT_61109-T1 Valid prediction for GlimmerHMM_glimmerT_61104-T1 Valid prediction for GlimmerHMM_glimmerT_61108-T1 Couldn't classify 11637, 11676 Sorry, prediction pasa_asmbl_46540.p1 fails validation. (ACA) CA 11637-11676 GT AGG (CTA) AG 12394-12495 GT AGG (AAA) AG 12668-12739 GT CGG (GAG) AG 12829-12927 GT AGG (ACT) AG 13172-13273 GT TGG (CCC) AG 13357-13429 GT AAG (GAA) AG 13506-13585 GT CAG (AGC) AG 13715-13914 GT AGG (CAA) AG 14034-14112 GT AGG (GGG) AG 14209-14354 GT CGG (GGG) AG 14630-14686 GT GGG (CTC) AG 14975-15068 GT TGG (ATT) AG 15284-15357 AA GAA add_exon() Sorry, pasa_asmbl_46540.p1 14034-14112-terminal-3 is invalid. -recovered pasa_asmbl_46540.p1, terminal, 14034, 14112 -recovered pasa_asmbl_46540.p1, terminal, 15284, 15357 -recovered pasa_asmbl_46540.p1, internal, 12394, 12495 -recovered pasa_asmbl_46540.p1, internal, 12668, 12739 -recovered pasa_asmbl_46540.p1, internal, 12829, 12927 -recovered pasa_asmbl_46540.p1, internal, 13172, 13273 -recovered pasa_asmbl_46540.p1, internal, 13357, 13429 -recovered pasa_asmbl_46540.p1, internal, 13506, 13585 -recovered pasa_asmbl_46540.p1, internal, 13715, 13914 -recovered pasa_asmbl_46540.p1, internal, 14034, 14112 -recovered pasa_asmbl_46540.p1, internal, 14209, 14354 -recovered pasa_asmbl_46540.p1, internal, 14630, 14686 -recovered pasa_asmbl_46540.p1, internal, 14975, 15068 Couldn't classify 50, 113 Sorry, prediction GeneMark_model.106317_t fails validation. (CAG) AG 50-113 GT GTG (GGG) AG 144-269 GT ATG (AAA) AG 308-362 CA GAC -recovered GeneMark_model.106317_t, terminal, 308, 362 -recovered GeneMark_model.106317_t, internal, 50, 113 -recovered GeneMark_model.106317_t, internal, 144, 269 Valid prediction for GeneMark_model.106314_t Valid prediction for Augustus_model.g40653.t1 Valid prediction for GlimmerHMM_glimmerT_61107-T1 Valid prediction for GeneMark_model.106313_t Valid prediction for HiQ_model.g40652.t1 Valid prediction for GeneMark_model.106315_t Valid prediction for snap_scaffold_57-snap.5-T1 Sorry, intron length (4) is less than minimum required (10) -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -) -building DP trellis -building trellis in range 1 - 25772 -exon list size: 108 building trellis 0.9 1.8 2.7 3.6 4.5 5.5 6.4 7.3 8.2 9.1 10.0 10.9 11.8 12.7 13.6 14.5 15.5 16.4 17.3 18.2 19.1 20.0 20.9 21.8 22.7 23.6 24.5 25.5 26.4 27.3 28.2 29.1 30.0 30.9 31.8 32.7 33.6 34.5 35.5 36.4 37.3 38.2 39.1 40.0 40.9 41.8 42.7 43.6 44.5 45.5 46.4 47.3 48.2 49.1 50.0 50.9 51.8 52.7 53.6 54.5 55.5 56.4 57.3 58.2 59.1 60.0 60.9 61.8 62.7 63.6 64.5 65.5 66.4 67.3 68.2 69.1 70.0 70.9 71.8 72.7 73.6 74.5 75.5 76.4 77.3 78.2 79.1 80.0 80.9 81.8 82.7 83.6 84.5 85.5 86.4 87.3 88.2 89.1 90.0 90.9 91.8 92.7 93.6 94.5 95.5 96.4 97.3 98.2 99.1 -found 8 predictions from path traversal -reporting highest scoring path thru the trellis. -found 6 predictions persist after filtering for low support