-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_764 -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_764-snap.2-T1 Couldn't classify 4460, 4472 Sorry, prediction GeneMark_model.108335_t fails validation. (ATG) CC 3628-3731 GT AGG (GGG) AG 3759-3776 GT AGG (AGG) AG 3845-3901 GT GGG (AGA) AG 3985-4074 GT AGG (GAG) AG 4380-4436 GT GAG (TCT) AG 4460-4472 GT AGG -recovered GeneMark_model.108335_t, initial, 3628, 3731 -recovered GeneMark_model.108335_t, terminal, 4380, 4436 -recovered GeneMark_model.108335_t, internal, 3759, 3776 -recovered GeneMark_model.108335_t, internal, 3845, 3901 -recovered GeneMark_model.108335_t, internal, 3985, 4074 -recovered GeneMark_model.108335_t, internal, 4380, 4436 -recovered GeneMark_model.108335_t, internal, 4460, 4472 Couldn't classify 967, 1081 Sorry, prediction snap_scaffold_764-snap.1-T1 fails validation. (CGT) AG 967-1081 GT GCG (GGA) AG 2957-3083 GT GTG (GGT) AG 3514-3588 TA GAT -recovered snap_scaffold_764-snap.1-T1, terminal, 3514, 3588 -recovered snap_scaffold_764-snap.1-T1, internal, 967, 1081 -recovered snap_scaffold_764-snap.1-T1, internal, 2957, 3083 -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 3531, 3623 Sorry, prediction GeneMark_model.108334_t fails validation. (ATG) TG 1561-1787 GT GAG (AGA) AG 1813-1824 GT GGG (TAG) AG 1849-1872 GT GGG (AGG) AG 1918-1929 GT AGG (GAG) AG 1952-1963 GT GAG (GGG) AG 1987-2007 GT GGG (AGG) AG 2036-2044 GT ACG (TGG) AG 2066-2077 GT GGG (GGT) AG 2108-2128 GT GAG (GAG) AG 2151-2156 GT GGG (GGG) AG 2181-2201 GT AAG (TGA) AG 2226-2273 GT AGG (GAG) AG 2316-2324 GT GAG (GGT) AG 2354-2401 GT AGG (GCG) AG 2432-2452 GT GAG (GGG) AG 2476-2484 GT GAG (GAG) AG 2507-2527 GT AGG (GAG) AG 2569-2580 GT GAG (AGG) AG 2608-2680 GT GGG (GGG) AG 2710-2720 GT GAG (GAG) AG 2744-2770 GT ACG (GAG) AG 2794-2814 GT CGG (TGA) AG 2854-2865 GT GGG (GAG) AG 2890-2922 GT GGG (GAC) AG 2943-2951 GT GGG (GGG) AG 2981-2995 GT AGG (GAG) AG 3024-3050 GT GGG (GCG) AG 3075-3110 GT GAG (GAG) AG 3133-3156 GT GGG (GAG) AG 3181-3255 GT GAG (GGA) AG 3276-3284 GT GGG (GGG) AG 3309-3317 GT ATG (GAG) AG 3340-3348 GT GAG (GAG) AG 3371-3388 GT GGG (GGT) AG 3418-3474 GT GGG (GAG) AG 3497-3504 GT GGG (TGT) AG 3531-3623 GT AGG -recovered GeneMark_model.108334_t, initial, 1561, 1787 -recovered GeneMark_model.108334_t, terminal, 1952, 1963 add_exon() Sorry, GeneMark_model.108334_t 2108-2128-terminal-1 is invalid. -recovered GeneMark_model.108334_t, terminal, 2108, 2128 -recovered GeneMark_model.108334_t, terminal, 2316, 2324 add_exon() Sorry, GeneMark_model.108334_t 2432-2452-terminal-1 is invalid. -recovered GeneMark_model.108334_t, terminal, 2432, 2452 -recovered GeneMark_model.108334_t, terminal, 2476, 2484 -recovered GeneMark_model.108334_t, terminal, 2569, 2580 -recovered GeneMark_model.108334_t, terminal, 2710, 2720 add_exon() Sorry, GeneMark_model.108334_t 3075-3110-terminal-1 is invalid. -recovered GeneMark_model.108334_t, terminal, 3075, 3110 add_exon() Sorry, GeneMark_model.108334_t 3181-3255-terminal-1 is invalid. -recovered GeneMark_model.108334_t, terminal, 3181, 3255 -recovered GeneMark_model.108334_t, terminal, 3340, 3348 -recovered GeneMark_model.108334_t, internal, 1813, 1824 -recovered GeneMark_model.108334_t, internal, 1849, 1872 -recovered GeneMark_model.108334_t, internal, 1918, 1929 -recovered GeneMark_model.108334_t, internal, 1952, 1963 -recovered GeneMark_model.108334_t, internal, 1987, 2007 -recovered GeneMark_model.108334_t, internal, 2036, 2044 -recovered GeneMark_model.108334_t, internal, 2066, 2077 -recovered GeneMark_model.108334_t, internal, 2108, 2128 -recovered GeneMark_model.108334_t, internal, 2151, 2156 -recovered GeneMark_model.108334_t, internal, 2181, 2201 -recovered GeneMark_model.108334_t, internal, 2226, 2273 -recovered GeneMark_model.108334_t, internal, 2316, 2324 -recovered GeneMark_model.108334_t, internal, 2354, 2401 -recovered GeneMark_model.108334_t, internal, 2432, 2452 -recovered GeneMark_model.108334_t, internal, 2476, 2484 -recovered GeneMark_model.108334_t, internal, 2507, 2527 -recovered GeneMark_model.108334_t, internal, 2569, 2580 -recovered GeneMark_model.108334_t, internal, 2608, 2680 -recovered GeneMark_model.108334_t, internal, 2710, 2720 -recovered GeneMark_model.108334_t, internal, 2744, 2770 -recovered GeneMark_model.108334_t, internal, 2794, 2814 -recovered GeneMark_model.108334_t, internal, 2854, 2865 -recovered GeneMark_model.108334_t, internal, 2890, 2922 -recovered GeneMark_model.108334_t, internal, 2943, 2951 -recovered GeneMark_model.108334_t, internal, 2981, 2995 -recovered GeneMark_model.108334_t, internal, 3024, 3050 -recovered GeneMark_model.108334_t, internal, 3075, 3110 -recovered GeneMark_model.108334_t, internal, 3133, 3156 -recovered GeneMark_model.108334_t, internal, 3181, 3255 -recovered GeneMark_model.108334_t, internal, 3276, 3284 -recovered GeneMark_model.108334_t, internal, 3309, 3317 -recovered GeneMark_model.108334_t, internal, 3340, 3348 -recovered GeneMark_model.108334_t, internal, 3371, 3388 -recovered GeneMark_model.108334_t, internal, 3418, 3474 -recovered GeneMark_model.108334_t, internal, 3497, 3504 -recovered GeneMark_model.108334_t, internal, 3531, 3623 Valid prediction for GlimmerHMM_glimmerT_62211-T1 add_exon() Sorry, GlimmerHMM_glimmerT_62211-T1 1580-1791-terminal-1 is invalid. -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -) -building DP trellis -building trellis in range 1 - 4607 -exon list size: 92 building trellis 1.1 2.1 3.2 4.3 5.3 6.4 7.4 8.5 9.6 10.6 11.7 12.8 13.8 14.9 16.0 17.0 18.1 19.1 20.2 21.3 22.3 23.4 24.5 25.5 26.6 27.7 28.7 29.8 30.9 31.9 33.0 34.0 35.1 36.2 37.2 38.3 39.4 40.4 41.5 42.6 43.6 44.7 45.7 46.8 47.9 48.9 50.0 51.1 52.1 53.2 54.3 55.3 56.4 57.4 58.5 59.6 60.6 61.7 62.8 63.8 64.9 66.0 67.0 68.1 69.1 70.2 71.3 72.3 73.4 74.5 75.5 76.6 77.7 78.7 79.8 80.9 81.9 83.0 84.0 85.1 86.2 87.2 88.3 89.4 90.4 91.5 92.6 93.6 94.7 95.7 96.8 97.9 98.9 -found 2 predictions from path traversal -reporting highest scoring path thru the trellis. -found 1 predictions persist after filtering for low support