-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_529347-677554 -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_9-snap.125-T1 Valid prediction for snap_scaffold_9-snap.143-T1 Valid prediction for snap_scaffold_9-snap.137-T1 Couldn't classify 104975, 105325 Sorry, prediction pasa_asmbl_53777.p1 fails validation. (GGA) TA 104975-105325 TA AGT Valid prediction for GlimmerHMM_glimmerT_21514-T1 Valid prediction for snap_scaffold_9-snap.128-T1 Valid prediction for CodingQuarry_transcript_62097-T1 Valid prediction for HiQ_model.g14306.t1 Valid prediction for snap_scaffold_9-snap.156-T1 Valid prediction for CodingQuarry_transcript_62098-T1 Valid prediction for snap_scaffold_9-snap.142-T1 Valid prediction for snap_scaffold_9-snap.158-T1 Valid prediction for CodingQuarry_transcript_62100-T1 Valid prediction for snap_scaffold_9-snap.141-T1 Valid prediction for Augustus_model.g14312.t1 Valid prediction for Augustus_model.g14311.t1 Valid prediction for pasa_asmbl_53763.p1 Valid prediction for GlimmerHMM_glimmerT_21504-T1 Valid prediction for Augustus_model.g14315.t1 Valid prediction for HiQ_model.g14301.t1 Valid prediction for GlimmerHMM_glimmerT_21517-T1 Valid prediction for GlimmerHMM_glimmerT_21509-T1 Valid prediction for snap_scaffold_9-snap.154-T1 Valid prediction for snap_scaffold_9-snap.124-T1 Valid prediction for GlimmerHMM_glimmerT_21512-T1 Valid prediction for snap_scaffold_9-snap.149-T1 Valid prediction for GlimmerHMM_glimmerT_21500-T1 Valid prediction for GlimmerHMM_glimmerT_21513-T1 Valid prediction for snap_scaffold_9-snap.139-T1 Valid prediction for GlimmerHMM_glimmerT_21502-T1 Valid prediction for GlimmerHMM_glimmerT_21511-T1 Couldn't classify 125410, 125465 Sorry, prediction pasa_asmbl_53789.p1 fails validation. (CTC) GG 125410-125465 GT CGG (GTC) AG 126909-127071 GT AGG (TTC) AG 127329-127553 GT AGG (GTG) AG 127889-128098 GT AGG (GAG) AG 128777-129361 TC GAT -recovered pasa_asmbl_53789.p1, terminal, 128777, 129361 -recovered pasa_asmbl_53789.p1, internal, 126909, 127071 -recovered pasa_asmbl_53789.p1, internal, 127329, 127553 -recovered pasa_asmbl_53789.p1, internal, 127889, 128098 Valid prediction for GlimmerHMM_glimmerT_21499-T1 Valid prediction for pasa_asmbl_53775.p2 Couldn't classify 117580, 117684 Sorry, prediction pasa_asmbl_53784.p1 fails validation. (ATG) AC 109914-109982 GT AGG (ACT) AG 111306-111350 GT AGG (AAC) AG 112471-112560 GT CGG (CAA) AG 112930-112959 GT AGG (AAT) AG 113186-113238 GT AGG (GAA) AG 113559-113654 GT AAG (TCC) AG 114241-114326 GT AAG (ATG) AG 114731-114817 GT AGG (GTG) AG 114945-115114 GT AGG (ATT) AG 116345-116389 GT ACG (ATC) AG 116505-116636 GT AGG (ACT) AG 116911-117039 GT AGG (GAG) AG 117580-117684 GT AGG -recovered pasa_asmbl_53784.p1, initial, 109914, 109982 add_exon() Sorry, pasa_asmbl_53784.p1 114731-114817-initial-1 is invalid. -recovered pasa_asmbl_53784.p1, initial, 114731, 114817 -recovered pasa_asmbl_53784.p1, terminal, 114731, 114817 -recovered pasa_asmbl_53784.p1, internal, 111306, 111350 -recovered pasa_asmbl_53784.p1, internal, 112471, 112560 -recovered pasa_asmbl_53784.p1, internal, 112930, 112959 -recovered pasa_asmbl_53784.p1, internal, 113186, 113238 -recovered pasa_asmbl_53784.p1, internal, 113559, 113654 -recovered pasa_asmbl_53784.p1, internal, 114241, 114326 -recovered pasa_asmbl_53784.p1, internal, 114731, 114817 -recovered pasa_asmbl_53784.p1, internal, 114945, 115114 -recovered pasa_asmbl_53784.p1, internal, 116345, 116389 -recovered pasa_asmbl_53784.p1, internal, 116505, 116636 -recovered pasa_asmbl_53784.p1, internal, 116911, 117039 -recovered pasa_asmbl_53784.p1, internal, 117580, 117684 Valid prediction for snap_scaffold_9-snap.159-T1 Sorry, intron length (3) is less than minimum required (10) Couldn't classify 35761, 36075 Sorry, prediction pasa_asmbl_53764.p1 fails validation. (ATG) AG 30903-31081 GT CGG (GCT) AG 32023-32204 GT GGG (AGC) AG 32953-33128 GT GGG (GAC) AG 33226-33307 GT AGG (GCT) AG 33667-33799 GT AGG (GTC) AG 34193-34284 GT AGG (CCG) AG 34569-34825 GT TGG (TGC) AG 35761-36075 AC CCA -recovered pasa_asmbl_53764.p1, initial, 30903, 31081 -recovered pasa_asmbl_53764.p1, internal, 30903, 31081 -recovered pasa_asmbl_53764.p1, internal, 32023, 32204 -recovered pasa_asmbl_53764.p1, internal, 32953, 33128 -recovered pasa_asmbl_53764.p1, internal, 33226, 33307 -recovered pasa_asmbl_53764.p1, internal, 33667, 33799 -recovered pasa_asmbl_53764.p1, internal, 34193, 34284 -recovered pasa_asmbl_53764.p1, internal, 34569, 34825 Valid prediction for Augustus_model.g14302.t1 Valid prediction for snap_scaffold_9-snap.145-T1 Couldn't classify 119302, 119467 Sorry, prediction pasa_asmbl_53786.p1 fails validation. (CAG) CC 119302-119467 GT AGG (GTT) AG 121205-121299 GT ATG (GTG) AG 121632-121727 AG AGA -recovered pasa_asmbl_53786.p1, terminal, 121632, 121727 -recovered pasa_asmbl_53786.p1, internal, 121205, 121299 Valid prediction for snap_scaffold_9-snap.153-T1 Couldn't classify 38825, 38864 Sorry, prediction pasa_asmbl_53774.p1 fails validation. (GAC) GA 38825-38864 GT GTG (TTA) AG 38983-39018 GT AGG (TTC) AG 39107-39358 GT TGG (AGG) AG 40987-41241 GT GGG (AGG) AG 41338-41417 GT AGG (GTG) AG 44142-44327 TG AGT -recovered pasa_asmbl_53774.p1, terminal, 44142, 44327 -recovered pasa_asmbl_53774.p1, internal, 38983, 39018 -recovered pasa_asmbl_53774.p1, internal, 39107, 39358 -recovered pasa_asmbl_53774.p1, internal, 40987, 41241 -recovered pasa_asmbl_53774.p1, internal, 41338, 41417 Valid prediction for snap_scaffold_9-snap.147-T1 Valid prediction for GlimmerHMM_glimmerT_21503-T1 Valid prediction for snap_scaffold_9-snap.129-T1 Valid prediction for snap_scaffold_9-snap.131-T1 Sorry, intron length (3) is less than minimum required (10) Sorry, intron length (3) is less than minimum required (10) Valid prediction for HiQ_model.g14313.t1 Valid prediction for Augustus_model.g14314.t1 Valid prediction for HiQ_model.g14304.t1 Couldn't classify 38825, 38864 Sorry, prediction pasa_asmbl_53770.p1 fails validation. (GAC) GA 38825-38864 GT GTG (TTA) AG 38983-39018 GT AGG (TTC) AG 39107-39358 GT TGG (AGG) AG 40987-41241 GT GGG (AGG) AG 41338-41603 TG AGT -recovered pasa_asmbl_53770.p1, terminal, 41338, 41603 -recovered pasa_asmbl_53770.p1, internal, 38983, 39018 -recovered pasa_asmbl_53770.p1, internal, 39107, 39358 -recovered pasa_asmbl_53770.p1, internal, 40987, 41241 Valid prediction for HiQ_model.g14305.t1 Valid prediction for GlimmerHMM_glimmerT_21518-T1 Valid prediction for GlimmerHMM_glimmerT_21519-T1 Valid prediction for snap_scaffold_9-snap.151-T1 Valid prediction for CodingQuarry_transcript_62095-T1 Valid prediction for GlimmerHMM_glimmerT_21516-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: -)Couldn't classify 121725, 121902 Couldn't classify 122385, 122416 Sorry, prediction pasa_asmbl_54802.p3 fails validation. (TTC) CC 121725-121902 GT AGG (ACA) AG 122112-122267 GT AGG (ATA) AG 122385-122416 TC GCT -recovered pasa_asmbl_54802.p3, internal, 122112, 122267 Valid prediction for Augustus_model.g14309.t1 Valid prediction for snap_scaffold_9-snap.135-T1 Valid prediction for GlimmerHMM_glimmerT_21510-T1 Valid prediction for snap_scaffold_9-snap.127-T1 Valid prediction for GlimmerHMM_glimmerT_21507-T1 Valid prediction for GlimmerHMM_glimmerT_21515-T1 Valid prediction for snap_scaffold_9-snap.144-T1 Valid prediction for Augustus_model.g14308.t1 Valid prediction for pasa_asmbl_54803.p1 Couldn't classify 6983, 7072 Couldn't classify 7875, 8025 Sorry, prediction pasa_asmbl_54806.p1 fails validation. (GAG) TG 6983-7072 GT AGG (CTG) AG 7372-7499 GT GTG (CCA) AG 7631-7771 GT AAG (GAA) AG 7875-8025 GT CGG -recovered pasa_asmbl_54806.p1, internal, 7372, 7499 -recovered pasa_asmbl_54806.p1, internal, 7631, 7771 -recovered pasa_asmbl_54806.p1, internal, 7875, 8025 Couldn't classify 13888, 13941 Sorry, prediction pasa_asmbl_55776.p1 fails validation. (AAG) TG 13888-13941 GT AGG (GGG) AG 14212-14385 GT AGG (GGT) AG 15077-15259 GT AGG (GAG) AG 15655-15887 GT AGG (TGT) AG 16130-16313 GT ACG (GAG) AG 16791-16955 GG GAG -recovered pasa_asmbl_55776.p1, terminal, 16791, 16955 -recovered pasa_asmbl_55776.p1, internal, 14212, 14385 -recovered pasa_asmbl_55776.p1, internal, 15077, 15259 -recovered pasa_asmbl_55776.p1, internal, 15655, 15887 -recovered pasa_asmbl_55776.p1, internal, 16130, 16313 Valid prediction for Augustus_model.g14310.t1 Valid prediction for snap_scaffold_9-snap.132-T1 Valid prediction for GlimmerHMM_glimmerT_21498-T1 Valid prediction for GlimmerHMM_glimmerT_21505-T1 Valid prediction for Augustus_model.g14303.t1 Valid prediction for snap_scaffold_9-snap.138-T1 Couldn't classify 9027, 9161 Couldn't classify 11980, 11993 Sorry, prediction pasa_asmbl_54805.p1 fails validation. (GAG) AG 9027-9161 GT TGG (GGT) AG 10643-10804 GT AGG (ATG) AG 11491-11716 GT TGG (GCA) AG 11980-11993 GG GAG -recovered pasa_asmbl_54805.p1, initial, 11491, 11716 -recovered pasa_asmbl_54805.p1, internal, 9027, 9161 -recovered pasa_asmbl_54805.p1, internal, 10643, 10804 -recovered pasa_asmbl_54805.p1, internal, 11491, 11716 Valid prediction for snap_scaffold_9-snap.155-T1 Valid prediction for GlimmerHMM_glimmerT_21506-T1 Valid prediction for snap_scaffold_9-snap.157-T1 Valid prediction for snap_scaffold_9-snap.123-T1 Valid prediction for snap_scaffold_9-snap.140-T1 Valid prediction for snap_scaffold_9-snap.130-T1 Valid prediction for snap_scaffold_9-snap.136-T1 Valid prediction for Augustus_model.g14307.t1 Valid prediction for snap_scaffold_9-snap.146-T1 Valid prediction for Augustus_model.g14316.t1 Valid prediction for GlimmerHMM_glimmerT_21520-T1 Valid prediction for Augustus_model.g14300.t1 Valid prediction for snap_scaffold_9-snap.152-T1 Valid prediction for GlimmerHMM_glimmerT_21501-T1 Valid prediction for GlimmerHMM_glimmerT_21508-T1 Valid prediction for snap_scaffold_9-snap.126-T1 Valid prediction for snap_scaffold_9-snap.150-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_9-snap.133-T1 Valid prediction for snap_scaffold_9-snap.134-T1 Valid prediction for snap_scaffold_9-snap.148-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9279, rend_intergenic: 5657 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 15523, rend_intergenic: 10740 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24135, rend_intergenic: 17809 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51294, rend_intergenic: 30915 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59575, rend_intergenic: 57778 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59756, rend_intergenic: 59660 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 62036, rend_intergenic: 60443 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76167, rend_intergenic: 67012 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 80455, rend_intergenic: 79486 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 92876, rend_intergenic: 80695 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 93030, rend_intergenic: 92878 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105231, rend_intergenic: 93086 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 108865, rend_intergenic: 106604 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119441, rend_intergenic: 113022 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120312, rend_intergenic: 119773 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 124200, rend_intergenic: 120415 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129361, rend_intergenic: 126164 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133136, rend_intergenic: 131254 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143727, rend_intergenic: 133194 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 148208 -exon list size: 398 building trellis 0.2 0.5 0.8 1.0 1.2 1.5 1.8 2.0 2.2 2.5 2.8 3.0 3.2 3.5 3.8 4.0 4.2 4.5 4.8 5.0 5.2 5.5 5.8 6.0 6.2 6.5 6.8 7.0 7.2 7.5 7.8 8.0 8.2 8.5 8.8 9.0 9.2 9.5 9.8 10.0 10.2 10.5 10.8 11.0 11.2 11.5 11.8 12.0 12.2 12.5 12.8 13.0 13.2 13.5 13.8 14.0 14.2 14.5 14.8 15.0 15.2 15.5 15.8 16.0 16.2 16.5 16.8 17.0 17.2 17.5 17.8 18.0 18.2 18.5 18.8 19.0 19.2 19.5 19.8 20.0 20.2 20.5 20.8 21.0 21.2 21.5 21.8 22.0 22.2 22.5 22.8 23.0 23.2 23.5 23.8 24.0 24.2 24.5 24.8 25.0 25.2 25.5 25.8 26.0 26.2 26.5 26.8 27.0 27.3 27.5 27.8 28.0 28.2 28.5 28.7 29.0 29.2 29.5 29.8 30.0 30.2 30.5 30.8 31.0 31.2 31.5 31.8 32.0 32.2 32.5 32.8 33.0 33.2 33.5 33.8 34.0 34.2 34.5 34.8 35.0 35.2 35.5 35.8 36.0 36.2 36.5 36.8 37.0 37.2 37.5 37.8 38.0 38.2 38.5 38.8 39.0 39.2 39.5 39.8 40.0 40.2 40.5 40.8 41.0 41.2 41.5 41.8 42.0 42.2 42.5 42.8 43.0 43.2 43.5 43.8 44.0 44.2 44.5 44.8 45.0 45.2 45.5 45.8 46.0 46.2 46.5 46.8 47.0 47.2 47.5 47.8 48.0 48.2 48.5 48.8 49.0 49.2 49.5 49.8 50.0 50.2 50.5 50.7 51.0 51.2 51.5 51.7 52.0 52.2 52.5 52.8 53.0 53.2 53.5 53.8 54.0 54.2 54.5 54.8 55.0 55.2 55.5 55.8 56.0 56.2 56.5 56.8 57.0 57.2 57.5 57.8 58.0 58.2 58.5 58.8 59.0 59.2 59.5 59.8 60.0 60.2 60.5 60.8 61.0 61.3 61.5 61.8 62.0 62.3 62.5 62.7 63.0 63.2 63.5 63.7 64.0 64.2 64.5 64.8 65.0 65.2 65.5 65.8 66.0 66.2 66.5 66.8 67.0 67.2 67.5 67.8 68.0 68.2 68.5 68.8 69.0 69.2 69.5 69.8 70.0 70.2 70.5 70.8 71.0 71.2 71.5 71.8 72.0 72.2 72.5 72.8 73.0 73.2 73.5 73.8 74.0 74.2 74.5 74.8 75.0 75.2 75.5 75.8 76.0 76.2 76.5 76.8 77.0 77.2 77.5 77.8 78.0 78.2 78.5 78.8 79.0 79.2 79.5 79.8 80.0 80.2 80.5 80.8 81.0 81.2 81.5 81.8 82.0 82.2 82.5 82.8 83.0 83.2 83.5 83.8 84.0 84.2 84.5 84.8 85.0 85.2 85.5 85.8 86.0 86.2 86.5 86.8 87.0 87.2 87.5 87.8 88.0 88.2 88.5 88.8 89.0 89.2 89.5 89.8 90.0 90.2 90.5 90.8 91.0 91.2 91.5 91.8 92.0 92.2 92.5 92.8 93.0 93.2 93.5 93.8 94.0 94.2 94.5 94.8 95.0 95.2 95.5 95.8 96.0 96.2 96.5 96.8 97.0 97.2 97.5 97.8 98.0 98.2 98.5 98.8 99.0 99.2 99.5 99.8 -found 19 predictions from path traversal Error with prediction: snap lend_intergenic: 9279, rend_intergenic: 5657 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 15523, rend_intergenic: 10740 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24135, rend_intergenic: 17809 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51294, rend_intergenic: 30915 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59575, rend_intergenic: 57778 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59756, rend_intergenic: 59660 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 62036, rend_intergenic: 60443 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76167, rend_intergenic: 67012 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 80455, rend_intergenic: 79486 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 92876, rend_intergenic: 80695 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 93030, rend_intergenic: 92878 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105231, rend_intergenic: 93086 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 108865, rend_intergenic: 106604 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119441, rend_intergenic: 113022 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120312, rend_intergenic: 119773 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 124200, rend_intergenic: 120415 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129361, rend_intergenic: 126164 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 133136, rend_intergenic: 131254 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 143727, rend_intergenic: 133194 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 16 predictions persist after filtering for low support