-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_8088375-8263777 -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 GlimmerHMM_glimmerT_48156-T1 Valid prediction for snap_scaffold_21-snap.1733-T1 Valid prediction for HiQ_model.g32173.t1 Valid prediction for snap_scaffold_21-snap.1713-T1 Valid prediction for snap_scaffold_21-snap.1724-T1 Valid prediction for GlimmerHMM_glimmerT_48174-T1 Valid prediction for snap_scaffold_21-snap.1723-T1 Valid prediction for Augustus_model.g32179.t1 Valid prediction for GlimmerHMM_glimmerT_48167-T1 Valid prediction for snap_scaffold_21-snap.1740-T1 Valid prediction for GlimmerHMM_glimmerT_48182-T1 Valid prediction for snap_scaffold_21-snap.1741-T1 Valid prediction for pasa_asmbl_28788.p1 Valid prediction for HiQ_model.g32172.t1 Valid prediction for GlimmerHMM_glimmerT_48154-T1 Couldn't classify 81641, 81759 Couldn't classify 82094, 82261 Sorry, prediction CodingQuarry_transcript_32655-T1 fails validation. (ATG) AT 78630-78906 GT AGG (CAG) AG 79108-79165 GT AAG (CAA) AG 79324-79379 GT AGG (AGC) AG 79497-79623 GT GGG (GAA) AG 79740-79842 GT GAG (GCC) AG 79966-80043 GT AGG (GTA) AG 80202-80301 GT AGG (GTG) AG 80397-80539 GT TGG (CTG) AG 80661-80867 GT TGG (GTG) AG 81054-81166 GT AGG (GTC) AG 81303-81436 GT AGG (AGG) AG 81641-81759 GG GAG (GAA) CT 82094-82261 GT TGG (GAT) AG 82565-82675 GT ATG (TTC) AG 82938-83025 GT GGG (GCC) AG 83273-83363 GT ATG (GAC) AG 83490-83625 GT AGG (GCT) AG 83903-83992 GT CCG (CTG) AG 84102-84223 GT GCG (AAA) AG 84490-84508 GC GAG -recovered CodingQuarry_transcript_32655-T1, initial, 78630, 78906 -recovered CodingQuarry_transcript_32655-T1, terminal, 84490, 84508 -recovered CodingQuarry_transcript_32655-T1, internal, 79108, 79165 -recovered CodingQuarry_transcript_32655-T1, internal, 79324, 79379 -recovered CodingQuarry_transcript_32655-T1, internal, 79497, 79623 -recovered CodingQuarry_transcript_32655-T1, internal, 79740, 79842 -recovered CodingQuarry_transcript_32655-T1, internal, 79966, 80043 -recovered CodingQuarry_transcript_32655-T1, internal, 80202, 80301 -recovered CodingQuarry_transcript_32655-T1, internal, 80397, 80539 -recovered CodingQuarry_transcript_32655-T1, internal, 80661, 80867 -recovered CodingQuarry_transcript_32655-T1, internal, 81054, 81166 -recovered CodingQuarry_transcript_32655-T1, internal, 81303, 81436 -recovered CodingQuarry_transcript_32655-T1, internal, 82565, 82675 -recovered CodingQuarry_transcript_32655-T1, internal, 82938, 83025 -recovered CodingQuarry_transcript_32655-T1, internal, 83273, 83363 -recovered CodingQuarry_transcript_32655-T1, internal, 83490, 83625 -recovered CodingQuarry_transcript_32655-T1, internal, 83903, 83992 -recovered CodingQuarry_transcript_32655-T1, internal, 84102, 84223 -recovered CodingQuarry_transcript_32655-T1, internal, 84490, 84508 Valid prediction for Augustus_model.g32170.t1 Valid prediction for snap_scaffold_21-snap.1729-T1 Couldn't classify 81641, 81759 Couldn't classify 82094, 82261 Sorry, prediction CodingQuarry_transcript_32654-T1 fails validation. (ATG) AT 78630-78906 GT AGG (ACG) AG 79111-79165 GT AAG (CAA) AG 79324-79379 GT AGG (AGC) AG 79497-79623 GT GGG (GAA) AG 79740-79842 GT GAG (GCC) AG 79966-80043 GT AGG (GTA) AG 80202-80301 GT AGG (GTG) AG 80397-80539 GT TGG (CTG) AG 80661-80867 GT TGG (GTG) AG 81054-81166 GT AGG (GTC) AG 81303-81436 GT AGG (AGG) AG 81641-81759 GG GAG (GAA) CT 82094-82261 GT TGG (GAT) AG 82565-82675 GT ATG (TTC) AG 82938-83025 GT GGG (GCC) AG 83273-83363 GT ATG (GAC) AG 83490-83625 GT AGG (GCT) AG 83903-83992 GT CCG (CTG) AG 84102-84223 GT GCG (AAA) AG 84490-84508 GC GAG -recovered CodingQuarry_transcript_32654-T1, initial, 78630, 78906 -recovered CodingQuarry_transcript_32654-T1, terminal, 84490, 84508 -recovered CodingQuarry_transcript_32654-T1, internal, 79111, 79165 -recovered CodingQuarry_transcript_32654-T1, internal, 79324, 79379 -recovered CodingQuarry_transcript_32654-T1, internal, 79497, 79623 -recovered CodingQuarry_transcript_32654-T1, internal, 79740, 79842 -recovered CodingQuarry_transcript_32654-T1, internal, 79966, 80043 -recovered CodingQuarry_transcript_32654-T1, internal, 80202, 80301 -recovered CodingQuarry_transcript_32654-T1, internal, 80397, 80539 -recovered CodingQuarry_transcript_32654-T1, internal, 80661, 80867 -recovered CodingQuarry_transcript_32654-T1, internal, 81054, 81166 -recovered CodingQuarry_transcript_32654-T1, internal, 81303, 81436 -recovered CodingQuarry_transcript_32654-T1, internal, 82565, 82675 -recovered CodingQuarry_transcript_32654-T1, internal, 82938, 83025 -recovered CodingQuarry_transcript_32654-T1, internal, 83273, 83363 -recovered CodingQuarry_transcript_32654-T1, internal, 83490, 83625 -recovered CodingQuarry_transcript_32654-T1, internal, 83903, 83992 -recovered CodingQuarry_transcript_32654-T1, internal, 84102, 84223 -recovered CodingQuarry_transcript_32654-T1, internal, 84490, 84508 Valid prediction for CodingQuarry_transcript_32653-T1 Couldn't classify 91793, 91803 Sorry, prediction pasa_asmbl_28794.p1 fails validation. (TAC) AC 91793-91803 GT AGG (GAC) AG 92023-92101 GT AGG (GTC) AG 92334-92477 GT CGG (GCA) AG 92906-93040 GT CTG (TAT) AG 93318-93415 GT AGG (GTA) AG 93653-93794 GT GGG (GTC) AG 93917-93995 GT GGG (CAA) AG 94087-94152 GT TGG (GGG) AG 94390-94458 GT AGG (GCT) AG 94651-94859 TT GAT -recovered pasa_asmbl_28794.p1, terminal, 94651, 94859 -recovered pasa_asmbl_28794.p1, internal, 92023, 92101 -recovered pasa_asmbl_28794.p1, internal, 92334, 92477 -recovered pasa_asmbl_28794.p1, internal, 92906, 93040 -recovered pasa_asmbl_28794.p1, internal, 93318, 93415 -recovered pasa_asmbl_28794.p1, internal, 93653, 93794 -recovered pasa_asmbl_28794.p1, internal, 93917, 93995 -recovered pasa_asmbl_28794.p1, internal, 94087, 94152 -recovered pasa_asmbl_28794.p1, internal, 94390, 94458 Valid prediction for snap_scaffold_21-snap.1727-T1 Valid prediction for snap_scaffold_21-snap.1719-T1 Valid prediction for GlimmerHMM_glimmerT_48164-T1 Valid prediction for GlimmerHMM_glimmerT_48155-T1 Valid prediction for GlimmerHMM_glimmerT_48168-T1 Valid prediction for Augustus_model.g32171.t1 Valid prediction for snap_scaffold_21-snap.1722-T1 Valid prediction for HiQ_model.g32167.t1 Valid prediction for GlimmerHMM_glimmerT_48178-T1 Valid prediction for snap_scaffold_21-snap.1734-T1 Valid prediction for GlimmerHMM_glimmerT_48180-T1 Valid prediction for CodingQuarry_transcript_32658-T1 Valid prediction for pasa_asmbl_28797.p1 Valid prediction for GlimmerHMM_glimmerT_48162-T1 Valid prediction for Augustus_model.g32185.t1 Valid prediction for snap_scaffold_21-snap.1731-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_21-snap.1721-T1 Valid prediction for CodingQuarry_transcript_32656-T1 Valid prediction for GlimmerHMM_glimmerT_48165-T1 Valid prediction for Augustus_model.g32181.t1 Valid prediction for snap_scaffold_21-snap.1728-T1 Valid prediction for snap_scaffold_21-snap.1720-T1 Valid prediction for pasa_asmbl_28799.p1 Valid prediction for Augustus_model.g32175.t1 Valid prediction for GlimmerHMM_glimmerT_48163-T1 Valid prediction for GlimmerHMM_glimmerT_48171-T1 Valid prediction for snap_scaffold_21-snap.1725-T1 Valid prediction for snap_scaffold_21-snap.1736-T1 Valid prediction for GlimmerHMM_glimmerT_48161-T1 Valid prediction for HiQ_model.g32176.t1 Valid prediction for snap_scaffold_21-snap.1710-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 snap_scaffold_21-snap.1742-T1 Couldn't classify 166010, 166122 Sorry, prediction GlimmerHMM_glimmerT_48153-T1 fails validation. (ATG) CC 153143-153451 GT AGG (GTG) AG 153822-154847 GT AGG (GTG) AG 155042-155559 GT ATG (GAA) AG 164937-165043 GT CGG (GAG) AG 166010-166122 NT CNN (AAC) AG 166570-166669 GT CGG (GTG) AG 167105-167377 GT AGG (ACA) AG 167748-168127 AC GAA -recovered GlimmerHMM_glimmerT_48153-T1, initial, 153143, 153451 -recovered GlimmerHMM_glimmerT_48153-T1, terminal, 167748, 168127 -recovered GlimmerHMM_glimmerT_48153-T1, internal, 153822, 154847 -recovered GlimmerHMM_glimmerT_48153-T1, internal, 155042, 155559 -recovered GlimmerHMM_glimmerT_48153-T1, internal, 164937, 165043 -recovered GlimmerHMM_glimmerT_48153-T1, internal, 166570, 166669 -recovered GlimmerHMM_glimmerT_48153-T1, internal, 167105, 167377 Valid prediction for HiQ_model.g32177.t1 Valid prediction for pasa_asmbl_27898.p1 Valid prediction for Augustus_model.g32169.t1 Valid prediction for HiQ_model.g32178.t1 Valid prediction for GlimmerHMM_glimmerT_48177-T1 Valid prediction for GlimmerHMM_glimmerT_48172-T1 Valid prediction for GlimmerHMM_glimmerT_48157-T1 Valid prediction for GlimmerHMM_glimmerT_48169-T1 Valid prediction for snap_scaffold_21-snap.1709-T1 Valid prediction for GlimmerHMM_glimmerT_48166-T1 Valid prediction for GlimmerHMM_glimmerT_48173-T1 Valid prediction for snap_scaffold_21-snap.1739-T1 Valid prediction for GlimmerHMM_glimmerT_48160-T1 Valid prediction for snap_scaffold_21-snap.1711-T1 Valid prediction for GlimmerHMM_glimmerT_48170-T1 Valid prediction for snap_scaffold_21-snap.1718-T1 Valid prediction for HiQ_model.g32187.t1 Valid prediction for snap_scaffold_21-snap.1726-T1 Valid prediction for Augustus_model.g32186.t1 Valid prediction for HiQ_model.g32183.t1 Valid prediction for Augustus_model.g32184.t1 Valid prediction for GlimmerHMM_glimmerT_48181-T1 Valid prediction for snap_scaffold_21-snap.1717-T1 Valid prediction for Augustus_model.g32165.t1 Valid prediction for GlimmerHMM_glimmerT_48159-T1 Valid prediction for Augustus_model.g32174.t1 Valid prediction for Augustus_model.g32168.t1 Valid prediction for CodingQuarry_transcript_32659-T1 Valid prediction for snap_scaffold_21-snap.1737-T1 Valid prediction for pasa_asmbl_27911.p1 Valid prediction for GlimmerHMM_glimmerT_48176-T1 Valid prediction for CodingQuarry_transcript_32657-T1 Valid prediction for GlimmerHMM_glimmerT_48158-T1 Valid prediction for GlimmerHMM_glimmerT_48179-T1 Valid prediction for snap_scaffold_21-snap.1730-T1 Couldn't classify 129844, 129872 Sorry, prediction pasa_asmbl_27891.p1 fails validation. (CCC) GC 129844-129872 GC AGG (CAC) AG 131389-131652 GT AGG (AAA) AG 132324-132350 GT AGG (ACC) AG 134618-135044 GA GAG -recovered pasa_asmbl_27891.p1, terminal, 134618, 135044 -recovered pasa_asmbl_27891.p1, internal, 131389, 131652 -recovered pasa_asmbl_27891.p1, internal, 132324, 132350 Valid prediction for snap_scaffold_21-snap.1715-T1 Valid prediction for snap_scaffold_21-snap.1716-T1 Couldn't classify 6485, 6722 Couldn't classify 6750, 6823 Sorry, prediction CodingQuarry_transcript_32664-T1 fails validation. (ATG) AG 3477-3542 GT AGG (GTG) AG 3733-3857 GT AGG (TTC) AG 4407-4467 GT CAG (GTA) AG 4553-4696 GT ATG (GTG) AG 5113-5214 GT AGG (GTA) AG 5387-5543 GT AGG (GGC) AG 5862-6004 GT AGG (GTG) AG 6175-6228 GT AGG (CTG) AG 6485-6722 AT GAA (GCG) GA 6750-6823 CA GAC -recovered CodingQuarry_transcript_32664-T1, initial, 3477, 3542 -recovered CodingQuarry_transcript_32664-T1, internal, 3477, 3542 -recovered CodingQuarry_transcript_32664-T1, internal, 3733, 3857 -recovered CodingQuarry_transcript_32664-T1, internal, 4407, 4467 -recovered CodingQuarry_transcript_32664-T1, internal, 4553, 4696 -recovered CodingQuarry_transcript_32664-T1, internal, 5113, 5214 -recovered CodingQuarry_transcript_32664-T1, internal, 5387, 5543 -recovered CodingQuarry_transcript_32664-T1, internal, 5862, 6004 -recovered CodingQuarry_transcript_32664-T1, internal, 6175, 6228 Couldn't classify 34901, 35013 Sorry, prediction CodingQuarry_transcript_32663-T1 fails validation. (ATG) TC 33432-33641 GT AGG (AAT) AG 33795-33865 GT AAG (GAG) AG 33956-34011 GT ACG (TTG) AG 34101-34171 GT AGG (GAC) AG 34453-34569 GT AGG (TCA) AG 34674-34730 GT AGG (AAC) AG 34901-35013 CT ACC (GTA) AG 35231-35234 TT AAT -recovered CodingQuarry_transcript_32663-T1, initial, 33432, 33641 add_exon() Sorry, CodingQuarry_transcript_32663-T1 33795-33865-terminal-2 is invalid. -recovered CodingQuarry_transcript_32663-T1, terminal, 33795, 33865 -recovered CodingQuarry_transcript_32663-T1, terminal, 35231, 35234 -recovered CodingQuarry_transcript_32663-T1, internal, 33795, 33865 -recovered CodingQuarry_transcript_32663-T1, internal, 33956, 34011 -recovered CodingQuarry_transcript_32663-T1, internal, 34101, 34171 -recovered CodingQuarry_transcript_32663-T1, internal, 34453, 34569 -recovered CodingQuarry_transcript_32663-T1, internal, 34674, 34730 Valid prediction for CodingQuarry_transcript_32661-T1 Valid prediction for GlimmerHMM_glimmerT_48175-T1 Valid prediction for CodingQuarry_transcript_32660-T1 Valid prediction for GlimmerHMM_glimmerT_48183-T1 Valid prediction for CodingQuarry_transcript_32662-T1 Valid prediction for Augustus_model.g32166.t1 Valid prediction for snap_scaffold_21-snap.1712-T1 Couldn't classify 23667, 24080 Sorry, prediction pasa_asmbl_27909.p1 fails validation. (GGT) CA 23667-24080 GT AGG (GTC) AG 24280-24444 GT AGG (GAG) AG 24640-25161 AC AGA -recovered pasa_asmbl_27909.p1, terminal, 24640, 25161 -recovered pasa_asmbl_27909.p1, internal, 24280, 24444 Valid prediction for pasa_asmbl_27904.p1 Valid prediction for snap_scaffold_21-snap.1732-T1 Valid prediction for snap_scaffold_21-snap.1738-T1 Valid prediction for snap_scaffold_21-snap.1714-T1 Valid prediction for HiQ_model.g32182.t1 Valid prediction for snap_scaffold_21-snap.1735-T1 Valid prediction for Augustus_model.g32180.t1 Valid prediction for pasa_asmbl_27906.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12789, rend_intergenic: 10050 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20318, rend_intergenic: 13703 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55414, rend_intergenic: 47212 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115621, rend_intergenic: 112994 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 158775, rend_intergenic: 155108 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 171941, rend_intergenic: 168581 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 175403 -exon list size: 359 building trellis 0.3 0.6 0.8 1.1 1.4 1.7 1.9 2.2 2.5 2.8 3.0 3.3 3.6 3.9 4.2 4.4 4.7 5.0 5.3 5.5 5.8 6.1 6.4 6.6 6.9 7.2 7.5 7.8 8.0 8.3 8.6 8.9 9.1 9.4 9.7 10.0 10.2 10.5 10.8 11.1 11.4 11.6 11.9 12.2 12.5 12.7 13.0 13.3 13.6 13.9 14.1 14.4 14.7 15.0 15.2 15.5 15.8 16.1 16.3 16.6 16.9 17.2 17.5 17.7 18.0 18.3 18.6 18.8 19.1 19.4 19.7 19.9 20.2 20.5 20.8 21.1 21.3 21.6 21.9 22.2 22.4 22.7 23.0 23.3 23.5 23.8 24.1 24.4 24.7 24.9 25.2 25.5 25.8 26.0 26.3 26.6 26.9 27.1 27.4 27.7 28.0 28.3 28.5 28.8 29.1 29.4 29.6 29.9 30.2 30.5 30.7 31.0 31.3 31.6 31.9 32.1 32.4 32.7 33.0 33.2 33.5 33.8 34.1 34.3 34.6 34.9 35.2 35.5 35.7 36.0 36.3 36.6 36.8 37.1 37.4 37.7 38.0 38.2 38.5 38.8 39.1 39.3 39.6 39.9 40.2 40.4 40.7 41.0 41.3 41.6 41.8 42.1 42.4 42.7 42.9 43.2 43.5 43.8 44.0 44.3 44.6 44.9 45.2 45.4 45.7 46.0 46.3 46.5 46.8 47.1 47.4 47.6 47.9 48.2 48.5 48.8 49.0 49.3 49.6 49.9 50.1 50.4 50.7 51.0 51.2 51.5 51.8 52.1 52.4 52.6 52.9 53.2 53.5 53.7 54.0 54.3 54.6 54.8 55.1 55.4 55.7 56.0 56.2 56.5 56.8 57.1 57.3 57.6 57.9 58.2 58.4 58.7 59.0 59.3 59.6 59.8 60.1 60.4 60.7 60.9 61.2 61.5 61.8 62.0 62.3 62.6 62.9 63.2 63.4 63.7 64.0 64.3 64.5 64.8 65.1 65.4 65.7 65.9 66.2 66.5 66.8 67.0 67.3 67.6 67.9 68.1 68.4 68.7 69.0 69.3 69.5 69.8 70.1 70.4 70.6 70.9 71.2 71.5 71.7 72.0 72.3 72.6 72.9 73.1 73.4 73.7 74.0 74.2 74.5 74.8 75.1 75.3 75.6 75.9 76.2 76.5 76.7 77.0 77.3 77.6 77.8 78.1 78.4 78.7 78.9 79.2 79.5 79.8 80.1 80.3 80.6 80.9 81.2 81.4 81.7 82.0 82.3 82.5 82.8 83.1 83.4 83.7 83.9 84.2 84.5 84.8 85.0 85.3 85.6 85.9 86.1 86.4 86.7 87.0 87.3 87.5 87.8 88.1 88.4 88.6 88.9 89.2 89.5 89.8 90.0 90.3 90.6 90.9 91.1 91.4 91.7 92.0 92.2 92.5 92.8 93.1 93.4 93.6 93.9 94.2 94.5 94.7 95.0 95.3 95.6 95.8 96.1 96.4 96.7 97.0 97.2 97.5 97.8 98.1 98.3 98.6 98.9 99.2 99.4 99.7 -found 35 predictions from path traversal Error with prediction: snap lend_intergenic: 12789, rend_intergenic: 10050 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20318, rend_intergenic: 13703 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55414, rend_intergenic: 47212 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115621, rend_intergenic: 112994 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 158775, rend_intergenic: 155108 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 171941, rend_intergenic: 168581 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 30 predictions persist after filtering for low support