-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_385 -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 GeneMark_model.107487_t Couldn't classify 7294, 7383 Sorry, prediction snap_scaffold_385-snap.2-T1 fails validation. (ATG) AC 900-1129 GT GCG (GGC) AG 1391-1483 GT ACG (TGA) AG 2225-2378 GT CTG (CAC) AG 7294-7383 GT GAG -recovered snap_scaffold_385-snap.2-T1, initial, 900, 1129 -recovered snap_scaffold_385-snap.2-T1, internal, 1391, 1483 -recovered snap_scaffold_385-snap.2-T1, internal, 2225, 2378 -recovered snap_scaffold_385-snap.2-T1, internal, 7294, 7383 -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 133, 147 Sorry, prediction GeneMark_model.107488_t fails validation. (GCA) AG 133-147 GT ACG (CGA) AG 2755-2955 GT GAG (GAA) AG 3009-3062 GT ACG (AAA) AG 3087-3137 GT AAG (GGA) AG 3205-3223 GT AGG (GAT) AG 3974-4004 GT TGG (CTG) AG 4722-4800 GT GGG (AAT) AG 5189-5271 GT AGG (CTG) AG 5465-5564 GT GGG (CCT) AG 5593-5661 GT GAG (GGG) AG 5690-5711 TC AAT add_exon() Sorry, GeneMark_model.107488_t 5189-5271-terminal-2 is invalid. -recovered GeneMark_model.107488_t, terminal, 5189, 5271 -recovered GeneMark_model.107488_t, terminal, 5690, 5711 -recovered GeneMark_model.107488_t, internal, 133, 147 -recovered GeneMark_model.107488_t, internal, 2755, 2955 -recovered GeneMark_model.107488_t, internal, 3009, 3062 -recovered GeneMark_model.107488_t, internal, 3087, 3137 -recovered GeneMark_model.107488_t, internal, 3205, 3223 -recovered GeneMark_model.107488_t, internal, 3974, 4004 -recovered GeneMark_model.107488_t, internal, 4722, 4800 -recovered GeneMark_model.107488_t, internal, 5189, 5271 -recovered GeneMark_model.107488_t, internal, 5465, 5564 -recovered GeneMark_model.107488_t, internal, 5593, 5661 Valid prediction for GlimmerHMM_glimmerT_61778-T1 Couldn't classify 5982, 6175 Couldn't classify 7341, 7469 Sorry, prediction pasa_asmbl_41016.p1 fails validation. (CAG) CC 5982-6175 GT TGG (GGA) AG 6443-6672 GT CAG (GTA) AG 6962-7131 GT AGG (AGT) AG 7341-7469 CC CCC -recovered pasa_asmbl_41016.p1, internal, 6443, 6672 -recovered pasa_asmbl_41016.p1, internal, 6962, 7131 Couldn't classify 6440, 6535 Sorry, prediction CodingQuarry_transcript_46469-T1 fails validation. (ATG) AA 6173-6175 GT TGG (CAG) TG 6440-6535 GC GAG -recovered CodingQuarry_transcript_46469-T1, initial, 6173, 6175 Couldn't classify 196, 294 Couldn't classify 7341, 7451 Sorry, prediction Augustus_model.g41058.t1 fails validation. (GTG) AG 196-294 GT AGG (TGT) AG 4367-4400 GT TGG (CTG) AG 4722-4768 GT AGG (TCC) AG 5985-6175 GT TGG (GGA) AG 6443-6672 GT CAG (GTA) AG 6962-7131 GT AGG (AGT) AG 7341-7451 GT AGG -recovered Augustus_model.g41058.t1, internal, 196, 294 -recovered Augustus_model.g41058.t1, internal, 4367, 4400 -recovered Augustus_model.g41058.t1, internal, 4722, 4768 -recovered Augustus_model.g41058.t1, internal, 5985, 6175 -recovered Augustus_model.g41058.t1, internal, 6443, 6672 -recovered Augustus_model.g41058.t1, internal, 6962, 7131 -recovered Augustus_model.g41058.t1, internal, 7341, 7451 Couldn't classify 7341, 7451 Sorry, prediction snap_scaffold_385-snap.1-T1 fails validation. (ATG) CC 3017-3062 GT ACG (CTG) AG 4722-4800 GT GGG (AAT) AG 5189-5271 GT AGG (GGG) AG 5645-5730 GT ACG (TCC) AG 5985-6175 GT TGG (GGA) AG 6443-6672 GT CAG (GTA) AG 6962-7131 GT AGG (AGT) AG 7341-7451 GT AGG -recovered snap_scaffold_385-snap.1-T1, initial, 3017, 3062 add_exon() Sorry, snap_scaffold_385-snap.1-T1 5189-5271-terminal-2 is invalid. -recovered snap_scaffold_385-snap.1-T1, terminal, 5189, 5271 -recovered snap_scaffold_385-snap.1-T1, internal, 4722, 4800 -recovered snap_scaffold_385-snap.1-T1, internal, 5189, 5271 -recovered snap_scaffold_385-snap.1-T1, internal, 5645, 5730 -recovered snap_scaffold_385-snap.1-T1, internal, 5985, 6175 -recovered snap_scaffold_385-snap.1-T1, internal, 6443, 6672 -recovered snap_scaffold_385-snap.1-T1, internal, 6962, 7131 -recovered snap_scaffold_385-snap.1-T1, internal, 7341, 7451 Couldn't classify 115, 147 Sorry, prediction snap_scaffold_385-snap.3-T1 fails validation. (AGG) AG 115-147 GT ACG (GTG) AG 196-294 GT AGG (ACA) AG 2714-2959 AG GAA -recovered snap_scaffold_385-snap.3-T1, terminal, 2714, 2959 -recovered snap_scaffold_385-snap.3-T1, internal, 115, 147 -recovered snap_scaffold_385-snap.3-T1, internal, 196, 294 Valid prediction for CodingQuarry_transcript_46468-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4475, rend_intergenic: 900 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 7383, rend_intergenic: 4533 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 7491 -exon list size: 55 building trellis 1.8 3.5 5.3 7.0 8.8 10.5 12.3 14.0 15.8 17.5 19.3 21.1 22.8 24.6 26.3 28.1 29.8 31.6 33.3 35.1 36.8 38.6 40.4 42.1 43.9 45.6 47.4 49.1 50.9 52.6 54.4 56.1 57.9 59.6 61.4 63.2 64.9 66.7 68.4 70.2 71.9 73.7 75.4 77.2 78.9 80.7 82.5 84.2 86.0 87.7 89.5 91.2 93.0 94.7 96.5 98.2 -found 2 predictions from path traversal Error with prediction: snap lend_intergenic: 4475, rend_intergenic: 900 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 7383, rend_intergenic: 4533 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 1 predictions persist after filtering for low support