-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_12608113-12801988 -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 HiQ_model.g12308.t1 Valid prediction for CodingQuarry_transcript_57675-T1 Couldn't classify 140058, 140244 Sorry, prediction pasa_asmbl_50298.p1 fails validation. (ACC) TG 140058-140244 GT AGG (TGC) AG 141118-141192 GT AGG (ACG) AG 141547-141696 GT AGG (TCA) AG 143851-144418 GT AGG (ACC) AG 144551-144729 GT TAG (GCT) AG 145051-145207 GT AGG (GAG) AG 145568-145623 GT ACG (AGA) AG 146567-146628 GT AGG (TTA) AG 146932-147069 GT AGG (GCT) AG 147279-147355 GT AGG (GTT) AG 147547-147562 GG GAG -recovered pasa_asmbl_50298.p1, terminal, 147547, 147562 -recovered pasa_asmbl_50298.p1, internal, 141118, 141192 -recovered pasa_asmbl_50298.p1, internal, 141547, 141696 -recovered pasa_asmbl_50298.p1, internal, 143851, 144418 -recovered pasa_asmbl_50298.p1, internal, 144551, 144729 -recovered pasa_asmbl_50298.p1, internal, 145051, 145207 -recovered pasa_asmbl_50298.p1, internal, 145568, 145623 -recovered pasa_asmbl_50298.p1, internal, 146567, 146628 -recovered pasa_asmbl_50298.p1, internal, 146932, 147069 -recovered pasa_asmbl_50298.p1, internal, 147279, 147355 Valid prediction for snap_scaffold_7-snap.2368-T1 Valid prediction for pasa_asmbl_50282.p1 Valid prediction for snap_scaffold_7-snap.2358-T1 Valid prediction for GlimmerHMM_glimmerT_18266-T1 Valid prediction for snap_scaffold_7-snap.2370-T1 Valid prediction for pasa_asmbl_50278.p1 Valid prediction for GlimmerHMM_glimmerT_18284-T1 Couldn't classify 95857, 96189 Sorry, prediction pasa_asmbl_50293.p2 fails validation. (ACA) AC 95857-96189 AA GAA Valid prediction for snap_scaffold_7-snap.2367-T1 Valid prediction for Augustus_model.g12319.t1 Valid prediction for snap_scaffold_7-snap.2350-T1 Valid prediction for Augustus_model.g12326.t1 Valid prediction for GlimmerHMM_glimmerT_18270-T1 Valid prediction for snap_scaffold_7-snap.2376-T1 Couldn't classify 32561, 32663 Sorry, prediction pasa_asmbl_50284.p1 fails validation. (TTT) GT 32561-32663 GT ATG (TCA) AG 32787-32901 GT AGG (ATC) AG 33676-33738 GT AGG (CCG) AG 33971-34125 GT CGG (AGC) AG 34366-34461 GT AGG (GAG) AG 34632-34747 TG AGT -recovered pasa_asmbl_50284.p1, terminal, 34632, 34747 -recovered pasa_asmbl_50284.p1, internal, 32787, 32901 -recovered pasa_asmbl_50284.p1, internal, 33676, 33738 -recovered pasa_asmbl_50284.p1, internal, 33971, 34125 -recovered pasa_asmbl_50284.p1, internal, 34366, 34461 Valid prediction for GlimmerHMM_glimmerT_18272-T1 Valid prediction for snap_scaffold_7-snap.2373-T1 Valid prediction for snap_scaffold_7-snap.2378-T1 Valid prediction for GlimmerHMM_glimmerT_18281-T1 Couldn't classify 53767, 54090 Sorry, prediction pasa_asmbl_50287.p1 fails validation. (AGG) CC 53767-54090 AG TCA Couldn't classify 117283, 117384 Sorry, prediction pasa_asmbl_50294.p1 fails validation. (ATG) CC 115269-115325 GT TGG (GTT) AG 115457-115522 GT TGG (AGT) AG 115601-115681 GT AGG (ATA) AG 115852-115955 GT AGG (TCC) AG 116051-116159 GT CTG (CGT) AG 116267-116446 GT AGG (GTG) AG 116757-116881 GT AGG (TGA) AG 117058-117184 GT AGG (CGG) AG 117283-117384 CA TCC -recovered pasa_asmbl_50294.p1, initial, 115269, 115325 -recovered pasa_asmbl_50294.p1, internal, 115457, 115522 -recovered pasa_asmbl_50294.p1, internal, 115601, 115681 -recovered pasa_asmbl_50294.p1, internal, 115852, 115955 -recovered pasa_asmbl_50294.p1, internal, 116051, 116159 -recovered pasa_asmbl_50294.p1, internal, 116267, 116446 -recovered pasa_asmbl_50294.p1, internal, 116757, 116881 -recovered pasa_asmbl_50294.p1, internal, 117058, 117184 Valid prediction for snap_scaffold_7-snap.2362-T1 Valid prediction for snap_scaffold_7-snap.2355-T1 Valid prediction for Augustus_model.g12311.t1 Valid prediction for snap_scaffold_7-snap.2389-T1 Valid prediction for Augustus_model.g12318.t1 Valid prediction for GlimmerHMM_glimmerT_18289-T1 Valid prediction for Augustus_model.g12327.t1 Couldn't classify 118297, 118354 Sorry, prediction pasa_asmbl_50295.p1 fails validation. (AGG) AC 118297-118354 GT AGG (TGG) AG 118466-118617 GT AGG (GTG) AG 118748-118933 GT AGG (ATC) AG 119186-119258 GT AGG (AGG) AG 119365-119507 GT AGG (GAA) AG 119704-119843 GT AAG (GTA) AG 119932-120112 GT AGG (ATC) AG 120222-120329 AC AAA -recovered pasa_asmbl_50295.p1, terminal, 120222, 120329 -recovered pasa_asmbl_50295.p1, internal, 118466, 118617 -recovered pasa_asmbl_50295.p1, internal, 118748, 118933 -recovered pasa_asmbl_50295.p1, internal, 119186, 119258 -recovered pasa_asmbl_50295.p1, internal, 119365, 119507 -recovered pasa_asmbl_50295.p1, internal, 119704, 119843 -recovered pasa_asmbl_50295.p1, internal, 119932, 120112 Valid prediction for CodingQuarry_transcript_57681-T1 Valid prediction for Augustus_model.g12323.t1 Valid prediction for pasa_asmbl_50280.p1 Couldn't classify 90466, 90526 Sorry, prediction pasa_asmbl_50290.p1 fails validation. (GAC) AG 90466-90526 GT AGG (GGC) AG 91340-91461 GT AGG (GAC) AG 92389-92476 GT AGG (GGT) AG 92954-93041 GT AAG (GAC) AG 93875-93978 GT TGG (AGA) AG 94106-94236 AT AAA -recovered pasa_asmbl_50290.p1, terminal, 94106, 94236 -recovered pasa_asmbl_50290.p1, internal, 90466, 90526 -recovered pasa_asmbl_50290.p1, internal, 91340, 91461 -recovered pasa_asmbl_50290.p1, internal, 92389, 92476 -recovered pasa_asmbl_50290.p1, internal, 92954, 93041 -recovered pasa_asmbl_50290.p1, internal, 93875, 93978 Valid prediction for GlimmerHMM_glimmerT_18286-T1 Couldn't classify 54841, 55027 Couldn't classify 56253, 56423 Sorry, prediction pasa_asmbl_50288.p1 fails validation. (CCC) TG 54841-55027 GT TGG (CCT) AG 55140-55300 GT GGG (GAG) AG 55493-55603 GT TGG (TTC) AG 56253-56423 CT CCC -recovered pasa_asmbl_50288.p1, internal, 55140, 55300 -recovered pasa_asmbl_50288.p1, internal, 55493, 55603 Valid prediction for snap_scaffold_7-snap.2381-T1 Valid prediction for HiQ_model.g12306.t1 Valid prediction for HiQ_model.g12310.t1 Valid prediction for GlimmerHMM_glimmerT_18292-T1 Valid prediction for CodingQuarry_transcript_57674-T1 Valid prediction for snap_scaffold_7-snap.2387-T1 Valid prediction for CodingQuarry_transcript_57677-T1 Valid prediction for Augustus_model.g12321.t1 Valid prediction for GlimmerHMM_glimmerT_18278-T1 Valid prediction for CodingQuarry_transcript_57676-T1 Valid prediction for snap_scaffold_7-snap.2352-T1 Couldn't classify 25555, 26004 Sorry, prediction pasa_asmbl_51256.p1 fails validation. (CAT) AA 25555-26004 AT GAA Valid prediction for snap_scaffold_7-snap.2365-T1 Valid prediction for Augustus_model.g12316.t1 Valid prediction for snap_scaffold_7-snap.2380-T1 Valid prediction for GlimmerHMM_glimmerT_18282-T1 Valid prediction for GlimmerHMM_glimmerT_18268-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_18290-T1 Valid prediction for GlimmerHMM_glimmerT_18285-T1 Valid prediction for snap_scaffold_7-snap.2357-T1 Valid prediction for GlimmerHMM_glimmerT_18276-T1 Valid prediction for snap_scaffold_7-snap.2359-T1 Valid prediction for snap_scaffold_7-snap.2354-T1 Valid prediction for snap_scaffold_7-snap.2385-T1 Valid prediction for GlimmerHMM_glimmerT_18274-T1 Valid prediction for snap_scaffold_7-snap.2371-T1 Valid prediction for pasa_asmbl_51259.p1 Couldn't classify 189054, 189128 Couldn't classify 190632, 190778 Sorry, prediction pasa_asmbl_51253.p1 fails validation. (CTA) AG 189054-189128 GT AGG (GAT) AG 189616-189722 GT GGG (ATC) AG 189924-190054 GT AGG (ACT) AG 190144-190227 GT TGG (GTC) AG 190331-190455 GT CCG (CAA) AG 190632-190778 CA CAC -recovered pasa_asmbl_51253.p1, internal, 189054, 189128 -recovered pasa_asmbl_51253.p1, internal, 189616, 189722 -recovered pasa_asmbl_51253.p1, internal, 189924, 190054 -recovered pasa_asmbl_51253.p1, internal, 190144, 190227 -recovered pasa_asmbl_51253.p1, internal, 190331, 190455 Couldn't classify 146089, 146199 Couldn't classify 146760, 146876 Sorry, prediction pasa_asmbl_51264.p1 fails validation. (GCG) CA 146089-146199 GT AGG (CTG) AG 146321-146467 GT TGG (ACG) AG 146760-146876 GT GGG -recovered pasa_asmbl_51264.p1, internal, 146321, 146467 -recovered pasa_asmbl_51264.p1, internal, 146760, 146876 Valid prediction for Augustus_model.g12309.t1 Valid prediction for Augustus_model.g12325.t1 Valid prediction for snap_scaffold_7-snap.2383-T1 Valid prediction for snap_scaffold_7-snap.2360-T1 Valid prediction for GlimmerHMM_glimmerT_18277-T1 Valid prediction for pasa_asmbl_51258.p1 Valid prediction for snap_scaffold_7-snap.2351-T1 Couldn't classify 69931, 70138 Sorry, prediction pasa_asmbl_51265.p1 fails validation. (GTC) AC 69931-70138 GT AGG (GGA) AG 70677-70950 GT GGG (ACT) AG 71208-71364 GT AGG (GTG) AG 71654-71830 AA AAA -recovered pasa_asmbl_51265.p1, terminal, 71654, 71830 -recovered pasa_asmbl_51265.p1, internal, 70677, 70950 -recovered pasa_asmbl_51265.p1, internal, 71208, 71364 Valid prediction for snap_scaffold_7-snap.2374-T1 Valid prediction for GlimmerHMM_glimmerT_18279-T1 Valid prediction for Augustus_model.g12315.t1 Valid prediction for GlimmerHMM_glimmerT_18269-T1 Valid prediction for snap_scaffold_7-snap.2379-T1 Valid prediction for Augustus_model.g12324.t1 Couldn't classify 180560, 180733 Sorry, prediction pasa_asmbl_51255.p1 fails validation. (ATG) AA 179128-179437 GT AGG (TCT) AG 179532-179771 GT AGG (CGC) AG 179896-180036 GT CTG (CTT) AG 180185-180282 GT AGG (GTT) AG 180362-180475 GT AGG (GTG) AG 180560-180733 TA AGT -recovered pasa_asmbl_51255.p1, initial, 179128, 179437 -recovered pasa_asmbl_51255.p1, internal, 179532, 179771 -recovered pasa_asmbl_51255.p1, internal, 179896, 180036 -recovered pasa_asmbl_51255.p1, internal, 180185, 180282 -recovered pasa_asmbl_51255.p1, internal, 180362, 180475 Valid prediction for snap_scaffold_7-snap.2372-T1 Valid prediction for GlimmerHMM_glimmerT_18273-T1 Valid prediction for GlimmerHMM_glimmerT_18291-T1 Valid prediction for snap_scaffold_7-snap.2375-T1 Valid prediction for snap_scaffold_7-snap.2363-T1 Valid prediction for snap_scaffold_7-snap.2364-T1 Valid prediction for Augustus_model.g12307.t1 Valid prediction for snap_scaffold_7-snap.2366-T1 Valid prediction for GlimmerHMM_glimmerT_18293-T1 Valid prediction for snap_scaffold_7-snap.2377-T1 Valid prediction for Augustus_model.g12320.t1 Valid prediction for snap_scaffold_7-snap.2384-T1 Couldn't classify 185426, 186178 Sorry, prediction pasa_asmbl_51254.p1 fails validation. (AAG) TG 185426-186178 CT AAC Valid prediction for snap_scaffold_7-snap.2361-T1 Valid prediction for Augustus_model.g12312.t1 Valid prediction for GlimmerHMM_glimmerT_18283-T1 Valid prediction for Augustus_model.g12322.t1 Valid prediction for Augustus_model.g12314.t1 Valid prediction for snap_scaffold_7-snap.2388-T1 Valid prediction for Augustus_model.g12317.t1 Valid prediction for snap_scaffold_7-snap.2353-T1 Valid prediction for GlimmerHMM_glimmerT_18287-T1 Couldn't classify 147965, 148019 Sorry, prediction pasa_asmbl_51263.p1 fails validation. (TCT) AA 147965-148019 GT AGG (GTG) AG 148214-148257 GT AGG (AAC) AG 148352-148386 GT AGG (TGC) AG 148506-148758 GA GAG -recovered pasa_asmbl_51263.p1, terminal, 148506, 148758 -recovered pasa_asmbl_51263.p1, internal, 148214, 148257 -recovered pasa_asmbl_51263.p1, internal, 148352, 148386 Valid prediction for HiQ_model.g12313.t1 Valid prediction for snap_scaffold_7-snap.2386-T1 Valid prediction for CodingQuarry_transcript_57678-T1 Valid prediction for snap_scaffold_7-snap.2382-T1 Valid prediction for GlimmerHMM_glimmerT_18280-T1 Valid prediction for snap_scaffold_7-snap.2369-T1 Valid prediction for GlimmerHMM_glimmerT_18288-T1 Valid prediction for snap_scaffold_7-snap.2356-T1 Valid prediction for GlimmerHMM_glimmerT_18271-T1 Valid prediction for GlimmerHMM_glimmerT_18275-T1 Valid prediction for CodingQuarry_transcript_57679-T1 Valid prediction for GlimmerHMM_glimmerT_18267-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30093, rend_intergenic: 22576 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59538, rend_intergenic: 56322 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70189, rend_intergenic: 65348 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87075, rend_intergenic: 78168 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95829, rend_intergenic: 89942 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107720, rend_intergenic: 102391 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118948, rend_intergenic: 116781 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120327, rend_intergenic: 119171 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 147789, rend_intergenic: 138306 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 182840, rend_intergenic: 181316 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 185988, rend_intergenic: 185785 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 193876 -exon list size: 373 building trellis 0.3 0.5 0.8 1.1 1.3 1.6 1.9 2.1 2.4 2.7 2.9 3.2 3.5 3.7 4.0 4.3 4.5 4.8 5.1 5.3 5.6 5.9 6.1 6.4 6.7 6.9 7.2 7.5 7.7 8.0 8.3 8.5 8.8 9.1 9.3 9.6 9.9 10.1 10.4 10.7 10.9 11.2 11.5 11.7 12.0 12.3 12.5 12.8 13.1 13.3 13.6 13.9 14.1 14.4 14.7 14.9 15.2 15.5 15.7 16.0 16.3 16.5 16.8 17.1 17.3 17.6 17.9 18.1 18.4 18.7 18.9 19.2 19.5 19.7 20.0 20.3 20.5 20.8 21.1 21.3 21.6 21.9 22.1 22.4 22.7 22.9 23.2 23.5 23.7 24.0 24.3 24.5 24.8 25.1 25.3 25.6 25.9 26.1 26.4 26.7 26.9 27.2 27.5 27.7 28.0 28.3 28.5 28.8 29.1 29.3 29.6 29.9 30.1 30.4 30.7 30.9 31.2 31.5 31.7 32.0 32.3 32.5 32.8 33.1 33.3 33.6 33.9 34.1 34.4 34.7 34.9 35.2 35.5 35.7 36.0 36.3 36.5 36.8 37.1 37.3 37.6 37.9 38.1 38.4 38.7 38.9 39.2 39.5 39.7 40.0 40.3 40.5 40.8 41.1 41.3 41.6 41.9 42.1 42.4 42.7 42.9 43.2 43.5 43.7 44.0 44.3 44.5 44.8 45.1 45.3 45.6 45.9 46.1 46.4 46.7 46.9 47.2 47.5 47.7 48.0 48.3 48.5 48.8 49.1 49.3 49.6 49.9 50.1 50.4 50.7 50.9 51.2 51.5 51.7 52.0 52.3 52.5 52.8 53.1 53.3 53.6 53.9 54.1 54.4 54.7 54.9 55.2 55.5 55.7 56.0 56.3 56.5 56.8 57.1 57.3 57.6 57.9 58.1 58.4 58.7 58.9 59.2 59.5 59.7 60.0 60.3 60.5 60.8 61.1 61.3 61.6 61.9 62.1 62.4 62.7 62.9 63.2 63.5 63.7 64.0 64.3 64.5 64.8 65.1 65.3 65.6 65.9 66.1 66.4 66.7 66.9 67.2 67.5 67.7 68.0 68.3 68.5 68.8 69.1 69.3 69.6 69.9 70.1 70.4 70.7 70.9 71.2 71.5 71.7 72.0 72.3 72.5 72.8 73.1 73.3 73.6 73.9 74.1 74.4 74.7 74.9 75.2 75.5 75.7 76.0 76.3 76.5 76.8 77.1 77.3 77.6 77.9 78.1 78.4 78.7 78.9 79.2 79.5 79.7 80.0 80.3 80.5 80.8 81.1 81.3 81.6 81.9 82.1 82.4 82.7 82.9 83.2 83.5 83.7 84.0 84.3 84.5 84.8 85.1 85.3 85.6 85.9 86.1 86.4 86.7 86.9 87.2 87.5 87.7 88.0 88.3 88.5 88.8 89.1 89.3 89.6 89.9 90.1 90.4 90.7 90.9 91.2 91.5 91.7 92.0 92.3 92.5 92.8 93.1 93.3 93.6 93.9 94.1 94.4 94.7 94.9 95.2 95.5 95.7 96.0 96.3 96.5 96.8 97.1 97.3 97.6 97.9 98.1 98.4 98.7 98.9 99.2 99.5 99.7 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 30093, rend_intergenic: 22576 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59538, rend_intergenic: 56322 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70189, rend_intergenic: 65348 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 87075, rend_intergenic: 78168 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95829, rend_intergenic: 89942 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107720, rend_intergenic: 102391 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118948, rend_intergenic: 116781 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120327, rend_intergenic: 119171 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 147789, rend_intergenic: 138306 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 182840, rend_intergenic: 181316 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 185988, rend_intergenic: 185785 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 22 predictions persist after filtering for low support