-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_88 -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_88-snap.2-T1 Valid prediction for Augustus_model.g40749.t1 Valid prediction for GeneMark_model.106497_t Valid prediction for GlimmerHMM_glimmerT_61254-T1 Valid prediction for Augustus_model.g40748.t1 Couldn't classify 1815, 1899 Sorry, prediction GeneMark_model.106495_t fails validation. (GCA) AG 1815-1899 GT GGG (AAC) AG 1948-2043 GT GAG (TCA) AG 2163-2386 GT GAG (CCA) AG 2410-2641 GT GAG (GAC) AG 2735-2756 GC GAG -recovered GeneMark_model.106495_t, terminal, 2735, 2756 -recovered GeneMark_model.106495_t, internal, 1815, 1899 -recovered GeneMark_model.106495_t, internal, 1948, 2043 -recovered GeneMark_model.106495_t, internal, 2163, 2386 -recovered GeneMark_model.106495_t, internal, 2410, 2641 -recovered GeneMark_model.106495_t, internal, 2735, 2756 Valid prediction for snap_scaffold_88-snap.3-T1 Couldn't classify 17615, 17748 Sorry, prediction Augustus_model.g40750.t1 fails validation. (ATG) GA 16124-16147 GT CAG (GTC) AG 16476-16691 GT AGG (GCT) AG 17204-17324 GT AGG (ATC) AG 17615-17748 GT AGG -recovered Augustus_model.g40750.t1, initial, 16124, 16147 -recovered Augustus_model.g40750.t1, internal, 16476, 16691 -recovered Augustus_model.g40750.t1, internal, 17204, 17324 -recovered Augustus_model.g40750.t1, internal, 17615, 17748 Valid prediction for snap_scaffold_88-snap.4-T1 Couldn't classify 17615, 17762 Sorry, prediction snap_scaffold_88-snap.5-T1 fails validation. (ATG) TA 9500-9507 GT TCG (AGG) AG 11699-11848 GT AGG (ACT) AG 12213-12536 GT CCG (GGG) AG 12620-12683 GT AAG (GTC) AG 16476-16691 GT AGG (GCT) AG 17204-17324 GT AGG (ATC) AG 17615-17762 GT AGG -recovered snap_scaffold_88-snap.5-T1, initial, 9500, 9507 -recovered snap_scaffold_88-snap.5-T1, internal, 11699, 11848 -recovered snap_scaffold_88-snap.5-T1, internal, 12213, 12536 -recovered snap_scaffold_88-snap.5-T1, internal, 12620, 12683 -recovered snap_scaffold_88-snap.5-T1, internal, 16476, 16691 -recovered snap_scaffold_88-snap.5-T1, internal, 17204, 17324 -recovered snap_scaffold_88-snap.5-T1, internal, 17615, 17762 Couldn't classify 17615, 17748 Sorry, prediction GlimmerHMM_glimmerT_61255-T1 fails validation. (ATG) AG 13233-13262 GT AGG (GTC) AG 16476-16691 GT AGG (GCT) AG 17204-17324 GT AGG (ATC) AG 17615-17748 GT AGG -recovered GlimmerHMM_glimmerT_61255-T1, initial, 13233, 13262 -recovered GlimmerHMM_glimmerT_61255-T1, internal, 13233, 13262 -recovered GlimmerHMM_glimmerT_61255-T1, internal, 16476, 16691 -recovered GlimmerHMM_glimmerT_61255-T1, internal, 17204, 17324 -recovered GlimmerHMM_glimmerT_61255-T1, internal, 17615, 17748 Couldn't classify 17749, 17812 Sorry, prediction GeneMark_model.106498_t fails validation. (ATG) GA 16124-16147 GT CAG (GTC) AG 16476-16691 GT AGG (AGG) AG 16764-16784 GT AGG (GCT) AG 17204-17324 GT AGG (GTG) AG 17749-17812 GT AGG -recovered GeneMark_model.106498_t, initial, 16124, 16147 -recovered GeneMark_model.106498_t, internal, 16476, 16691 -recovered GeneMark_model.106498_t, internal, 16764, 16784 -recovered GeneMark_model.106498_t, internal, 17204, 17324 -recovered GeneMark_model.106498_t, internal, 17749, 17812 -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 17328, 17479 Sorry, prediction snap_scaffold_88-snap.1-T1 fails validation. (ATG) AA 10341-10361 GT CAG (ATA) AG 14400-14511 GT GGG (GAG) AG 14966-15189 GT AGG (GGA) AG 17042-17048 GT AAG (ATG) AG 17328-17479 GT TCG -recovered snap_scaffold_88-snap.1-T1, initial, 10341, 10361 add_exon() Sorry, snap_scaffold_88-snap.1-T1 17328-17479-initial-1 is invalid. -recovered snap_scaffold_88-snap.1-T1, initial, 17328, 17479 -recovered snap_scaffold_88-snap.1-T1, terminal, 17042, 17048 -recovered snap_scaffold_88-snap.1-T1, internal, 14400, 14511 -recovered snap_scaffold_88-snap.1-T1, internal, 14966, 15189 -recovered snap_scaffold_88-snap.1-T1, internal, 17042, 17048 -recovered snap_scaffold_88-snap.1-T1, internal, 17328, 17479 Valid prediction for GeneMark_model.106496_t Couldn't classify 17328, 17479 Sorry, prediction Augustus_model.g40747.t1 fails validation. (ATG) CG 16048-16123 GT GGG (ATG) AG 17328-17479 GT TCG -recovered Augustus_model.g40747.t1, initial, 16048, 16123 add_exon() Sorry, Augustus_model.g40747.t1 17328-17479-initial-1 is invalid. -recovered Augustus_model.g40747.t1, initial, 17328, 17479 -recovered Augustus_model.g40747.t1, internal, 17328, 17479 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7601, rend_intergenic: 2167 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 17941 -exon list size: 83 building trellis 1.2 2.4 3.5 4.7 5.9 7.1 8.2 9.4 10.6 11.8 12.9 14.1 15.3 16.5 17.6 18.8 20.0 21.2 22.4 23.5 24.7 25.9 27.1 28.2 29.4 30.6 31.8 32.9 34.1 35.3 36.5 37.6 38.8 40.0 41.2 42.4 43.5 44.7 45.9 47.1 48.2 49.4 50.6 51.8 52.9 54.1 55.3 56.5 57.6 58.8 60.0 61.2 62.4 63.5 64.7 65.9 67.1 68.2 69.4 70.6 71.8 72.9 74.1 75.3 76.5 77.6 78.8 80.0 81.2 82.4 83.5 84.7 85.9 87.1 88.2 89.4 90.6 91.8 92.9 94.1 95.3 96.5 97.6 98.8 -found 6 predictions from path traversal Error with prediction: snap lend_intergenic: 7601, rend_intergenic: 2167 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 4 predictions persist after filtering for low support