-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_537 -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: +)Couldn't classify 5896, 5990 Sorry, prediction snap_scaffold_537-snap.2-T1 fails validation. (ATG) GG 1373-1605 GT AAG (CAC) AG 2122-2590 GT TGG (GGA) AG 2613-2955 GT AGG (AAG) AG 2997-3061 GT TCG (GGT) AG 3131-3202 GT AGG (AGA) AG 3223-3251 GT AGG (GAA) AG 3821-3957 GT CGG (GCG) AG 4981-5205 GT GGG (TAG) AG 5537-5611 GT AGG (GCG) AG 5896-5990 GT AGG -recovered snap_scaffold_537-snap.2-T1, initial, 1373, 1605 add_exon() Sorry, snap_scaffold_537-snap.2-T1 2613-2955-terminal-3 is invalid. -recovered snap_scaffold_537-snap.2-T1, terminal, 2613, 2955 -recovered snap_scaffold_537-snap.2-T1, internal, 2122, 2590 -recovered snap_scaffold_537-snap.2-T1, internal, 2613, 2955 -recovered snap_scaffold_537-snap.2-T1, internal, 2997, 3061 -recovered snap_scaffold_537-snap.2-T1, internal, 3131, 3202 -recovered snap_scaffold_537-snap.2-T1, internal, 3223, 3251 -recovered snap_scaffold_537-snap.2-T1, internal, 3821, 3957 -recovered snap_scaffold_537-snap.2-T1, internal, 4981, 5205 -recovered snap_scaffold_537-snap.2-T1, internal, 5537, 5611 -recovered snap_scaffold_537-snap.2-T1, internal, 5896, 5990 -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 15, 174 Couldn't classify 5829, 5983 Sorry, prediction pasa_asmbl_46546.p1 fails validation. (CTG) AG 15-174 GT TGG (GGT) AG 393-491 GT AGG (TGT) AG 604-710 GT AGG (GGT) AG 951-1101 GT GGG (ACT) AG 1424-1507 GT GGG (TGC) AG 2075-2248 GT AGG (GTG) AG 2852-3004 GT CAG (AAA) AG 3320-3452 GT GGG (GTT) AG 4372-4434 GT AGG (TGC) AG 5256-5368 GT TGG (ACT) AG 5829-5983 GG TGG -recovered pasa_asmbl_46546.p1, internal, 15, 174 -recovered pasa_asmbl_46546.p1, internal, 393, 491 -recovered pasa_asmbl_46546.p1, internal, 604, 710 -recovered pasa_asmbl_46546.p1, internal, 951, 1101 -recovered pasa_asmbl_46546.p1, internal, 1424, 1507 -recovered pasa_asmbl_46546.p1, internal, 2075, 2248 -recovered pasa_asmbl_46546.p1, internal, 2852, 3004 -recovered pasa_asmbl_46546.p1, internal, 3320, 3452 -recovered pasa_asmbl_46546.p1, internal, 4372, 4434 -recovered pasa_asmbl_46546.p1, internal, 5256, 5368 Valid prediction for CodingQuarry_transcript_52512-T1 Couldn't classify 393, 491 Sorry, prediction GlimmerHMM_glimmerT_60464-T1 fails validation. (GGT) AG 393-491 GT AGG (TGT) AG 604-710 GT AGG (GGT) AG 951-1101 GT GGG (ACT) AG 1424-1507 GT GGG (TGC) AG 2075-2248 GT AGG (GTG) AG 2852-3015 GT AGG (GTA) AG 3316-3452 GT GGG (TGC) AG 5256-5397 AC AAA -recovered GlimmerHMM_glimmerT_60464-T1, terminal, 5256, 5397 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 393, 491 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 604, 710 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 951, 1101 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 1424, 1507 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 2075, 2248 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 2852, 3015 -recovered GlimmerHMM_glimmerT_60464-T1, internal, 3316, 3452 Couldn't classify 1, 174 Couldn't classify 5829, 6019 Sorry, prediction HiQ_model.g40025.t1 fails validation. (TGA) AG 1-174 GT TGG (GGT) AG 393-491 GT AGG (TGT) AG 604-710 GT AGG (GGT) AG 951-1101 GT GGG (ACT) AG 1424-1507 GT GGG (TGC) AG 2075-2248 GT AGG (GTG) AG 2852-3015 GT AGG (GTA) AG 3316-3452 GT GGG (GTT) AG 4372-4434 GT AGG (TGC) AG 5256-5368 GT TGG (ACT) AG 5829-6019 AG -recovered HiQ_model.g40025.t1, internal, 393, 491 -recovered HiQ_model.g40025.t1, internal, 604, 710 -recovered HiQ_model.g40025.t1, internal, 951, 1101 -recovered HiQ_model.g40025.t1, internal, 1424, 1507 -recovered HiQ_model.g40025.t1, internal, 2075, 2248 -recovered HiQ_model.g40025.t1, internal, 2852, 3015 -recovered HiQ_model.g40025.t1, internal, 3316, 3452 -recovered HiQ_model.g40025.t1, internal, 4372, 4434 -recovered HiQ_model.g40025.t1, internal, 5256, 5368 Couldn't classify 5829, 5984 Sorry, prediction snap_scaffold_537-snap.1-T1 fails validation. (ATG) TG 3644-3912 GT TGG (GTT) AG 4372-4434 GT AGG (TGC) AG 5256-5368 GT TGG (ACT) AG 5829-5984 GT GGG -recovered snap_scaffold_537-snap.1-T1, initial, 3644, 3912 -recovered snap_scaffold_537-snap.1-T1, internal, 4372, 4434 -recovered snap_scaffold_537-snap.1-T1, internal, 5256, 5368 -recovered snap_scaffold_537-snap.1-T1, internal, 5829, 5984 Valid prediction for GlimmerHMM_glimmerT_60463-T1 Couldn't classify 87, 174 Sorry, prediction snap_scaffold_537-snap.3-T1 fails validation. (CAG) AG 87-174 GT TGG (GGT) AG 393-491 GT AGG (TGT) AG 604-710 GT AGG (GGT) AG 951-1101 GT GGG (ACT) AG 1424-1507 GT GGG (TGC) AG 2075-2248 GT AGG (GTG) AG 2852-3015 GT AGG (GTA) AG 3316-3452 GT GGG (TGT) AG 3484-3610 TG GAT -recovered snap_scaffold_537-snap.3-T1, terminal, 3484, 3610 -recovered snap_scaffold_537-snap.3-T1, internal, 87, 174 -recovered snap_scaffold_537-snap.3-T1, internal, 393, 491 -recovered snap_scaffold_537-snap.3-T1, internal, 604, 710 -recovered snap_scaffold_537-snap.3-T1, internal, 951, 1101 -recovered snap_scaffold_537-snap.3-T1, internal, 1424, 1507 -recovered snap_scaffold_537-snap.3-T1, internal, 2075, 2248 -recovered snap_scaffold_537-snap.3-T1, internal, 2852, 3015 -recovered snap_scaffold_537-snap.3-T1, internal, 3316, 3452 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2376, rend_intergenic: 1373 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 5990, rend_intergenic: 2410 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 6019 -exon list size: 45 building trellis 2.1 4.3 6.4 8.5 10.6 12.8 14.9 17.0 19.1 21.3 23.4 25.5 27.7 29.8 31.9 34.0 36.2 38.3 40.4 42.6 44.7 46.8 48.9 51.1 53.2 55.3 57.4 59.6 61.7 63.8 66.0 68.1 70.2 72.3 74.5 76.6 78.7 80.9 83.0 85.1 87.2 89.4 91.5 93.6 95.7 97.9 -found 1 predictions from path traversal Error with prediction: snap lend_intergenic: 2376, rend_intergenic: 1373 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 5990, rend_intergenic: 2410 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