-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_2401878-2556294 -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 82432, 82743 Sorry, prediction pasa_asmbl_53835.p1 fails validation. (GCT) AT 82432-82743 AA AGA Valid prediction for snap_scaffold_9-snap.531-T1 Valid prediction for GlimmerHMM_glimmerT_21747-T1 Valid prediction for Augustus_model.g14466.t1 Valid prediction for GlimmerHMM_glimmerT_21755-T1 Valid prediction for snap_scaffold_9-snap.520-T1 Valid prediction for snap_scaffold_9-snap.519-T1 Couldn't classify 86860, 86970 Sorry, prediction pasa_asmbl_53839.p1 fails validation. (TAC) AG 86860-86970 GT TGG (GGT) AG 89185-89352 GT GGG (GGA) AG 89795-89926 GT AGG (GAT) AG 91559-91639 GT CAG (ATC) AG 91954-92070 GT AGG (AAA) AG 93415-93476 GT GGG (GTC) AG 95342-95441 GT CGG (GGG) AG 95564-95707 TA GAT -recovered pasa_asmbl_53839.p1, terminal, 95564, 95707 -recovered pasa_asmbl_53839.p1, internal, 86860, 86970 -recovered pasa_asmbl_53839.p1, internal, 89185, 89352 -recovered pasa_asmbl_53839.p1, internal, 89795, 89926 -recovered pasa_asmbl_53839.p1, internal, 91559, 91639 -recovered pasa_asmbl_53839.p1, internal, 91954, 92070 -recovered pasa_asmbl_53839.p1, internal, 93415, 93476 -recovered pasa_asmbl_53839.p1, internal, 95342, 95441 Valid prediction for snap_scaffold_9-snap.532-T1 Valid prediction for HiQ_model.g14463.t1 Valid prediction for snap_scaffold_9-snap.510-T1 Couldn't classify 82876, 83367 Sorry, prediction pasa_asmbl_53836.p1 fails validation. (CTC) CA 82876-83367 GT AGG (AAA) AG 83467-83547 CG GAC -recovered pasa_asmbl_53836.p1, terminal, 83467, 83547 Valid prediction for snap_scaffold_9-snap.535-T1 Valid prediction for HiQ_model.g14465.t1 Valid prediction for GlimmerHMM_glimmerT_21750-T1 Valid prediction for snap_scaffold_9-snap.524-T1 Valid prediction for GlimmerHMM_glimmerT_21741-T1 Valid prediction for GlimmerHMM_glimmerT_21744-T1 Valid prediction for pasa_asmbl_53841.p1 Valid prediction for GlimmerHMM_glimmerT_21743-T1 Valid prediction for snap_scaffold_9-snap.540-T1 Valid prediction for snap_scaffold_9-snap.541-T1 Valid prediction for snap_scaffold_9-snap.515-T1 Sorry, intron length (8) is less than minimum required (10) Couldn't classify 120460, 120573 Sorry, prediction pasa_asmbl_53844.p1 fails validation. (GTG) GT 120460-120573 GT AGG (CTG) AG 122307-122479 GT AGG (GGC) AG 123023-123137 GT AGG (ATG) AG 123282-123379 GT AGG (AGG) AG 124072-124175 GT TGG (GTA) AG 124513-124706 GT TGG (GTG) AG 125192-125357 GT AGG (TGG) AG 125757-125908 GT AGG (GTG) AG 126207-126380 GT AGG (GGG) AG 126555-126660 GT TGG (GTC) AG 126767-126882 GT AGG (CCC) AG 127290-127415 GT AGG (GGC) AG 128588-128703 GT AGG (GGT) AG 130311-130441 GT TGG (GCT) AG 131061-131233 GT AGG (GTG) AG 131698-131799 AA AGA -recovered pasa_asmbl_53844.p1, initial, 123282, 123379 -recovered pasa_asmbl_53844.p1, terminal, 131698, 131799 -recovered pasa_asmbl_53844.p1, internal, 122307, 122479 -recovered pasa_asmbl_53844.p1, internal, 123023, 123137 -recovered pasa_asmbl_53844.p1, internal, 123282, 123379 -recovered pasa_asmbl_53844.p1, internal, 124072, 124175 -recovered pasa_asmbl_53844.p1, internal, 124513, 124706 -recovered pasa_asmbl_53844.p1, internal, 125192, 125357 -recovered pasa_asmbl_53844.p1, internal, 125757, 125908 -recovered pasa_asmbl_53844.p1, internal, 126207, 126380 -recovered pasa_asmbl_53844.p1, internal, 126555, 126660 -recovered pasa_asmbl_53844.p1, internal, 126767, 126882 -recovered pasa_asmbl_53844.p1, internal, 127290, 127415 -recovered pasa_asmbl_53844.p1, internal, 128588, 128703 -recovered pasa_asmbl_53844.p1, internal, 130311, 130441 -recovered pasa_asmbl_53844.p1, internal, 131061, 131233 Valid prediction for CodingQuarry_transcript_62115-T1 Valid prediction for HiQ_model.g14460.t1 Valid prediction for snap_scaffold_9-snap.526-T1 Valid prediction for snap_scaffold_9-snap.529-T1 Valid prediction for snap_scaffold_9-snap.521-T1 Valid prediction for HiQ_model.g14459.t1 Valid prediction for snap_scaffold_9-snap.512-T1 Valid prediction for snap_scaffold_9-snap.537-T1 Valid prediction for snap_scaffold_9-snap.518-T1 Valid prediction for Augustus_model.g14458.t1 Valid prediction for GlimmerHMM_glimmerT_21754-T1 Valid prediction for snap_scaffold_9-snap.525-T1 Valid prediction for snap_scaffold_9-snap.544-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_9-snap.514-T1 Valid prediction for snap_scaffold_9-snap.538-T1 Valid prediction for snap_scaffold_9-snap.528-T1 Valid prediction for GlimmerHMM_glimmerT_21751-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_21745-T1 Valid prediction for GlimmerHMM_glimmerT_21749-T1 Valid prediction for HiQ_model.g14457.t1 Valid prediction for snap_scaffold_9-snap.545-T1 Valid prediction for snap_scaffold_9-snap.522-T1 Valid prediction for GlimmerHMM_glimmerT_21739-T1 Valid prediction for snap_scaffold_9-snap.530-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_9-snap.511-T1 Valid prediction for GlimmerHMM_glimmerT_21752-T1 Valid prediction for Augustus_model.g14453.t1 Couldn't classify 39807, 39875 Couldn't classify 42030, 42122 Sorry, prediction pasa_asmbl_54881.p1 fails validation. (AAG) AC 39807-39875 GT AGG (ATT) AG 40261-40445 GT AGG (GCT) AG 41157-41274 GT AGG (GTG) AG 41478-41693 GT GGG (CTG) AG 42030-42122 GT GGG -recovered pasa_asmbl_54881.p1, internal, 40261, 40445 -recovered pasa_asmbl_54881.p1, internal, 41157, 41274 -recovered pasa_asmbl_54881.p1, internal, 41478, 41693 -recovered pasa_asmbl_54881.p1, internal, 42030, 42122 Valid prediction for GlimmerHMM_glimmerT_21736-T1 Valid prediction for Augustus_model.g14455.t1 Valid prediction for snap_scaffold_9-snap.546-T1 Valid prediction for GlimmerHMM_glimmerT_21738-T1 Valid prediction for GlimmerHMM_glimmerT_21746-T1 Valid prediction for Augustus_model.g14461.t1 Valid prediction for Augustus_model.g14462.t1 Valid prediction for Augustus_model.g14464.t1 Valid prediction for pasa_asmbl_54875.p1 Valid prediction for GlimmerHMM_glimmerT_21737-T1 Valid prediction for Augustus_model.g14454.t1 Valid prediction for snap_scaffold_9-snap.513-T1 Valid prediction for snap_scaffold_9-snap.539-T1 Valid prediction for GlimmerHMM_glimmerT_21742-T1 Valid prediction for snap_scaffold_9-snap.533-T1 Couldn't classify 107373, 108039 Sorry, prediction pasa_asmbl_54871.p1 fails validation. (CCC) CC 107373-108039 GT AGG (CTG) AG 108399-108487 GT AGG (GAT) AG 108586-108802 GT AGG (AGC) AG 109103-109236 GT AGG (GCT) AG 109333-109491 GT CGG (CCG) AG 109679-110077 GT GGG (CTC) AG 110426-110572 GT CGG (GAA) AG 110797-111030 GT AAG (CCT) AG 111357-111461 GT AGG (AAC) AG 113117-113455 GT AGG (CCT) AG 113673-113787 GT AGG (CGC) AG 113960-114065 GT AGG (GAA) AG 114357-114610 GT CGG (TGA) AG 114887-115008 GT AGG (GAG) AG 115237-115409 GT GGG (GCT) AG 115629-115754 GT AGG (GGA) AG 115906-115987 GT TGG (AGC) AG 116197-116295 GT TGG (GAC) AG 116465-116599 GT AGG (GCT) AG 116723-116804 GT CTG (GTG) AG 117008-117148 GT CAG (ACT) AG 117667-117848 GA AGG -recovered pasa_asmbl_54871.p1, terminal, 117667, 117848 -recovered pasa_asmbl_54871.p1, internal, 108399, 108487 -recovered pasa_asmbl_54871.p1, internal, 108586, 108802 -recovered pasa_asmbl_54871.p1, internal, 109103, 109236 -recovered pasa_asmbl_54871.p1, internal, 109333, 109491 -recovered pasa_asmbl_54871.p1, internal, 109679, 110077 -recovered pasa_asmbl_54871.p1, internal, 110426, 110572 -recovered pasa_asmbl_54871.p1, internal, 110797, 111030 -recovered pasa_asmbl_54871.p1, internal, 111357, 111461 -recovered pasa_asmbl_54871.p1, internal, 113117, 113455 -recovered pasa_asmbl_54871.p1, internal, 113673, 113787 -recovered pasa_asmbl_54871.p1, internal, 113960, 114065 -recovered pasa_asmbl_54871.p1, internal, 114357, 114610 -recovered pasa_asmbl_54871.p1, internal, 114887, 115008 -recovered pasa_asmbl_54871.p1, internal, 115237, 115409 -recovered pasa_asmbl_54871.p1, internal, 115629, 115754 -recovered pasa_asmbl_54871.p1, internal, 115906, 115987 -recovered pasa_asmbl_54871.p1, internal, 116197, 116295 -recovered pasa_asmbl_54871.p1, internal, 116465, 116599 -recovered pasa_asmbl_54871.p1, internal, 116723, 116804 -recovered pasa_asmbl_54871.p1, internal, 117008, 117148 Valid prediction for snap_scaffold_9-snap.534-T1 Valid prediction for snap_scaffold_9-snap.527-T1 Valid prediction for snap_scaffold_9-snap.536-T1 Valid prediction for GlimmerHMM_glimmerT_21735-T1 Valid prediction for GlimmerHMM_glimmerT_21753-T1 Valid prediction for snap_scaffold_9-snap.517-T1 Valid prediction for GlimmerHMM_glimmerT_21748-T1 Valid prediction for snap_scaffold_9-snap.542-T1 Valid prediction for GlimmerHMM_glimmerT_21740-T1 Valid prediction for snap_scaffold_9-snap.543-T1 Couldn't classify 53807, 53987 Sorry, prediction pasa_asmbl_54878.p1 fails validation. (ATG) CA 53311-53461 GT AGG (ACC) AG 53556-53703 GT GGG (GTT) AG 53807-53987 CT TCC -recovered pasa_asmbl_54878.p1, initial, 53311, 53461 -recovered pasa_asmbl_54878.p1, internal, 53556, 53703 Valid prediction for Augustus_model.g14456.t1 Valid prediction for snap_scaffold_9-snap.523-T1 Valid prediction for snap_scaffold_9-snap.516-T1 Valid prediction for Augustus_model.g14452.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10951, rend_intergenic: 3758 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 22288, rend_intergenic: 21302 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33841, rend_intergenic: 22361 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38016, rend_intergenic: 36570 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 56510, rend_intergenic: 42445 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 61588, rend_intergenic: 56702 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75711, rend_intergenic: 68955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81358, rend_intergenic: 77106 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 101107, rend_intergenic: 99178 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 108888, rend_intergenic: 104923 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 116445, rend_intergenic: 111425 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131799, rend_intergenic: 122303 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143174, rend_intergenic: 136762 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 154417 -exon list size: 442 building trellis 0.2 0.5 0.7 0.9 1.1 1.4 1.6 1.8 2.0 2.3 2.5 2.7 2.9 3.2 3.4 3.6 3.8 4.1 4.3 4.5 4.7 5.0 5.2 5.4 5.6 5.9 6.1 6.3 6.5 6.8 7.0 7.2 7.4 7.7 7.9 8.1 8.3 8.6 8.8 9.0 9.2 9.5 9.7 9.9 10.1 10.4 10.6 10.8 11.0 11.3 11.5 11.7 11.9 12.2 12.4 12.6 12.8 13.1 13.3 13.5 13.7 14.0 14.2 14.4 14.6 14.9 15.1 15.3 15.5 15.8 16.0 16.2 16.4 16.7 16.9 17.1 17.3 17.6 17.8 18.0 18.2 18.5 18.7 18.9 19.1 19.4 19.6 19.8 20.0 20.3 20.5 20.7 20.9 21.2 21.4 21.6 21.8 22.1 22.3 22.5 22.7 23.0 23.2 23.4 23.6 23.9 24.1 24.3 24.5 24.8 25.0 25.2 25.5 25.7 25.9 26.1 26.4 26.6 26.8 27.0 27.3 27.5 27.7 27.9 28.2 28.4 28.6 28.8 29.1 29.3 29.5 29.7 30.0 30.2 30.4 30.6 30.9 31.1 31.3 31.5 31.8 32.0 32.2 32.4 32.7 32.9 33.1 33.3 33.6 33.8 34.0 34.2 34.5 34.7 34.9 35.1 35.4 35.6 35.8 36.0 36.3 36.5 36.7 36.9 37.2 37.4 37.6 37.8 38.1 38.3 38.5 38.7 39.0 39.2 39.4 39.6 39.9 40.1 40.3 40.5 40.8 41.0 41.2 41.4 41.7 41.9 42.1 42.3 42.6 42.8 43.0 43.2 43.5 43.7 43.9 44.1 44.4 44.6 44.8 45.0 45.3 45.5 45.7 45.9 46.2 46.4 46.6 46.8 47.1 47.3 47.5 47.7 48.0 48.2 48.4 48.6 48.9 49.1 49.3 49.5 49.8 50.0 50.2 50.5 50.7 50.9 51.1 51.4 51.6 51.8 52.0 52.3 52.5 52.7 52.9 53.2 53.4 53.6 53.8 54.1 54.3 54.5 54.7 55.0 55.2 55.4 55.6 55.9 56.1 56.3 56.5 56.8 57.0 57.2 57.4 57.7 57.9 58.1 58.3 58.6 58.8 59.0 59.2 59.5 59.7 59.9 60.1 60.4 60.6 60.8 61.0 61.3 61.5 61.7 61.9 62.2 62.4 62.6 62.8 63.1 63.3 63.5 63.7 64.0 64.2 64.4 64.6 64.9 65.1 65.3 65.5 65.8 66.0 66.2 66.4 66.7 66.9 67.1 67.3 67.6 67.8 68.0 68.2 68.5 68.7 68.9 69.1 69.4 69.6 69.8 70.0 70.3 70.5 70.7 70.9 71.2 71.4 71.6 71.8 72.1 72.3 72.5 72.7 73.0 73.2 73.4 73.6 73.9 74.1 74.3 74.5 74.8 75.0 75.2 75.5 75.7 75.9 76.1 76.4 76.6 76.8 77.0 77.3 77.5 77.7 77.9 78.2 78.4 78.6 78.8 79.1 79.3 79.5 79.7 80.0 80.2 80.4 80.6 80.9 81.1 81.3 81.5 81.8 82.0 82.2 82.4 82.7 82.9 83.1 83.3 83.6 83.8 84.0 84.2 84.5 84.7 84.9 85.1 85.4 85.6 85.8 86.0 86.3 86.5 86.7 86.9 87.2 87.4 87.6 87.8 88.1 88.3 88.5 88.7 89.0 89.2 89.4 89.6 89.9 90.1 90.3 90.5 90.8 91.0 91.2 91.4 91.7 91.9 92.1 92.3 92.6 92.8 93.0 93.2 93.5 93.7 93.9 94.1 94.4 94.6 94.8 95.0 95.3 95.5 95.7 95.9 96.2 96.4 96.6 96.8 97.1 97.3 97.5 97.7 98.0 98.2 98.4 98.6 98.9 99.1 99.3 99.5 99.8 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 10951, rend_intergenic: 3758 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 22288, rend_intergenic: 21302 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33841, rend_intergenic: 22361 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38016, rend_intergenic: 36570 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 56510, rend_intergenic: 42445 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 61588, rend_intergenic: 56702 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75711, rend_intergenic: 68955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81358, rend_intergenic: 77106 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 101107, rend_intergenic: 99178 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 108888, rend_intergenic: 104923 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 116445, rend_intergenic: 111425 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131799, rend_intergenic: 122303 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143174, rend_intergenic: 136762 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 24 predictions persist after filtering for low support -no exons in range 143175 - 154417