-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_4970499-5195176 -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_40260-T1 Valid prediction for snap_scaffold_17-snap.1060-T1 Valid prediction for CodingQuarry_transcript_21976-T1 Valid prediction for GlimmerHMM_glimmerT_40254-T1 Valid prediction for snap_scaffold_17-snap.1065-T1 Valid prediction for pasa_asmbl_19454.p1 Valid prediction for Augustus_model.g26818.t1 Valid prediction for GlimmerHMM_glimmerT_40266-T1 Valid prediction for GlimmerHMM_glimmerT_40263-T1 Valid prediction for snap_scaffold_17-snap.1051-T1 Valid prediction for GlimmerHMM_glimmerT_40272-T1 Couldn't classify 103275, 103334 Sorry, prediction pasa_asmbl_18805.p1 fails validation. (ATG) CG 102079-102175 GT CGG (GTC) AG 102450-102544 GT AGG (ATT) AG 102654-102761 GT CGG (GTG) AG 102949-103101 GT AGG (ATC) AG 103275-103334 TA ATT -recovered pasa_asmbl_18805.p1, initial, 102079, 102175 -recovered pasa_asmbl_18805.p1, internal, 102450, 102544 -recovered pasa_asmbl_18805.p1, internal, 102654, 102761 -recovered pasa_asmbl_18805.p1, internal, 102949, 103101 Valid prediction for snap_scaffold_17-snap.1042-T1 Valid prediction for snap_scaffold_17-snap.1054-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_17-snap.1040-T1 Valid prediction for GlimmerHMM_glimmerT_40267-T1 Couldn't classify 104043, 104261 Sorry, prediction pasa_asmbl_18810.p1 fails validation. (CAG) AT 104043-104261 GT AGG (GCC) AG 104473-104643 AG AGA -recovered pasa_asmbl_18810.p1, terminal, 104473, 104643 Valid prediction for snap_scaffold_17-snap.1036-T1 Valid prediction for Augustus_model.g26815.t1 Valid prediction for GlimmerHMM_glimmerT_40264-T1 Valid prediction for Augustus_model.g26820.t1 Valid prediction for snap_scaffold_17-snap.1033-T1 Valid prediction for GlimmerHMM_glimmerT_40269-T1 Valid prediction for GlimmerHMM_glimmerT_40248-T1 Valid prediction for Augustus_model.g26805.t1 Valid prediction for HiQ_model.g26823.t1 Valid prediction for snap_scaffold_17-snap.1049-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for CodingQuarry_transcript_21973-T1 Valid prediction for Augustus_model.g26821.t1 Valid prediction for CodingQuarry_transcript_21974-T1 Couldn't classify 137442, 137510 Couldn't classify 138011, 138149 Sorry, prediction pasa_asmbl_19514.p1 fails validation. (GAG) CA 137442-137510 GT AGG (GAG) AG 137731-137885 GT ACG (GCT) AG 138011-138149 AT GCA -recovered pasa_asmbl_19514.p1, internal, 137731, 137885 Valid prediction for snap_scaffold_17-snap.1064-T1 Valid prediction for snap_scaffold_17-snap.1062-T1 Valid prediction for snap_scaffold_17-snap.1055-T1 Valid prediction for pasa_asmbl_18811.p1 Valid prediction for GlimmerHMM_glimmerT_40250-T1 Valid prediction for snap_scaffold_17-snap.1037-T1 Valid prediction for snap_scaffold_17-snap.1058-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_40265-T1 Couldn't classify 140116, 140336 Couldn't classify 140468, 141197 Sorry, prediction pasa_asmbl_18467.p1 fails validation. (GGT) CA 140116-140336 GT AGG (GAG) AG 140468-141197 TC CCT Valid prediction for snap_scaffold_17-snap.1048-T1 Valid prediction for Augustus_model.g26824.t1 Valid prediction for snap_scaffold_17-snap.1052-T1 Valid prediction for GlimmerHMM_glimmerT_40251-T1 Valid prediction for GlimmerHMM_glimmerT_40256-T1 Valid prediction for GlimmerHMM_glimmerT_40249-T1 Couldn't classify 182470, 182495 Couldn't classify 186041, 186098 Sorry, prediction pasa_asmbl_17896.p1 fails validation. (CAC) GC 182470-182495 GT GAG (GTG) AG 184286-184455 GT AGG (CCT) AG 185234-185423 GT AGG (GAT) AG 185673-185858 GT AGG (GTC) AG 186041-186098 GG TGG add_exon() Sorry, pasa_asmbl_17896.p1 185673-185858-terminal-1 is invalid. -recovered pasa_asmbl_17896.p1, terminal, 185673, 185858 -recovered pasa_asmbl_17896.p1, internal, 184286, 184455 -recovered pasa_asmbl_17896.p1, internal, 185234, 185423 -recovered pasa_asmbl_17896.p1, internal, 185673, 185858 Valid prediction for snap_scaffold_17-snap.1035-T1 Valid prediction for snap_scaffold_17-snap.1053-T1 Valid prediction for Augustus_model.g26808.t1 Valid prediction for snap_scaffold_17-snap.1032-T1 Valid prediction for HiQ_model.g26819.t1 Valid prediction for pasa_asmbl_17898.p1 Valid prediction for Augustus_model.g26802.t1 Valid prediction for snap_scaffold_17-snap.1057-T1 Valid prediction for snap_scaffold_17-snap.1038-T1 Valid prediction for HiQ_model.g26812.t1 Valid prediction for CodingQuarry_transcript_21977-T1 Valid prediction for Augustus_model.g26807.t1 Couldn't classify 103896, 103955 Sorry, prediction pasa_asmbl_17911.p1 fails validation. (GTC) CA 103896-103955 GT AGG (TGG) AG 104242-104387 GT AGG (GAC) AG 104512-104658 GT AGG (GTC) AG 104768-104852 GT AGG (AGG) AG 104970-105076 GT GGG (GCG) AG 105269-105415 GT GGG (ACA) AG 105538-105634 GT AAG (GAC) AG 105815-106027 GT AGG (ATC) AG 106224-106334 GT AGG (GTT) AG 106444-106555 GT TGG (GAG) AG 106671-106789 GT TGG (GGC) AG 106947-107078 GT AGG (GCC) AG 107526-107663 GT AGG (AAA) AG 107754-107858 GT AGG (GTG) AG 107982-108117 GT CGG (GCC) AG 108221-108347 GT CGG (GCT) AG 108538-108748 GT ATG (TTT) AG 109326-109436 GT AGG (GTG) AG 109760-109978 GT AGG (GGC) AG 110625-110765 GT TGG (CCT) AG 111484-111684 GG GAG -recovered pasa_asmbl_17911.p1, terminal, 111484, 111684 -recovered pasa_asmbl_17911.p1, internal, 104242, 104387 -recovered pasa_asmbl_17911.p1, internal, 104512, 104658 -recovered pasa_asmbl_17911.p1, internal, 104768, 104852 -recovered pasa_asmbl_17911.p1, internal, 104970, 105076 -recovered pasa_asmbl_17911.p1, internal, 105269, 105415 -recovered pasa_asmbl_17911.p1, internal, 105538, 105634 -recovered pasa_asmbl_17911.p1, internal, 105815, 106027 -recovered pasa_asmbl_17911.p1, internal, 106224, 106334 -recovered pasa_asmbl_17911.p1, internal, 106444, 106555 -recovered pasa_asmbl_17911.p1, internal, 106671, 106789 -recovered pasa_asmbl_17911.p1, internal, 106947, 107078 -recovered pasa_asmbl_17911.p1, internal, 107526, 107663 -recovered pasa_asmbl_17911.p1, internal, 107754, 107858 -recovered pasa_asmbl_17911.p1, internal, 107982, 108117 -recovered pasa_asmbl_17911.p1, internal, 108221, 108347 -recovered pasa_asmbl_17911.p1, internal, 108538, 108748 -recovered pasa_asmbl_17911.p1, internal, 109326, 109436 -recovered pasa_asmbl_17911.p1, internal, 109760, 109978 -recovered pasa_asmbl_17911.p1, internal, 110625, 110765 Valid prediction for HiQ_model.g26811.t1 Valid prediction for Augustus_model.g26806.t1 Valid prediction for CodingQuarry_transcript_21971-T1 Valid prediction for snap_scaffold_17-snap.1047-T1 Valid prediction for CodingQuarry_transcript_21968-T1 Valid prediction for snap_scaffold_17-snap.1043-T1 Valid prediction for CodingQuarry_transcript_21980-T1 Couldn't classify 141276, 142265 Sorry, prediction pasa_asmbl_17903.p1 fails validation. (CCC) AC 141276-142265 AG CCA Couldn't classify 137927, 138221 Couldn't classify 139685, 139933 Sorry, prediction pasa_asmbl_17904.p1 fails validation. (GAG) AT 137927-138221 GT TGG (ACG) AG 138838-139091 GT AGG (GAG) AG 139685-139933 GG AGG -recovered pasa_asmbl_17904.p1, internal, 138838, 139091 Valid prediction for GlimmerHMM_glimmerT_40261-T1 Valid prediction for CodingQuarry_transcript_21978-T1 Valid prediction for HiQ_model.g26814.t1 Valid prediction for snap_scaffold_17-snap.1063-T1 Couldn't classify 135736, 135800 Couldn't classify 136913, 137012 Sorry, prediction pasa_asmbl_17905.p1 fails validation. (TTC) CC 135736-135800 GT AGG (GTT) AG 135914-136086 GT AGG (GCC) AG 136666-136780 GT CGG (GGA) AG 136913-137012 CC GTC -recovered pasa_asmbl_17905.p1, internal, 135914, 136086 -recovered pasa_asmbl_17905.p1, internal, 136666, 136780 Valid prediction for Augustus_model.g26810.t1 Valid prediction for snap_scaffold_17-snap.1056-T1 Valid prediction for pasa_asmbl_17909.p1 Valid prediction for GlimmerHMM_glimmerT_40262-T1 Valid prediction for snap_scaffold_17-snap.1034-T1 Valid prediction for Augustus_model.g26813.t1 Valid prediction for CodingQuarry_transcript_21975-T1 Valid prediction for GlimmerHMM_glimmerT_40255-T1 Valid prediction for CodingQuarry_transcript_21979-T1 Couldn't classify 160432, 160549 Sorry, prediction pasa_asmbl_17897.p1 fails validation. (TCG) CA 160432-160549 GT GGG (CTG) AG 161182-161292 GT AAG (CCT) AG 161577-161797 TC AAT -recovered pasa_asmbl_17897.p1, terminal, 161577, 161797 -recovered pasa_asmbl_17897.p1, internal, 161182, 161292 Couldn't classify 95644, 95928 Sorry, prediction pasa_asmbl_17915.p1 fails validation. (ATG) AG 94221-94424 GT AGG (GTA) AG 94835-95029 GT AGG (AGC) AG 95366-95512 GT AGG (GTG) AG 95644-95928 GG GGG -recovered pasa_asmbl_17915.p1, initial, 94221, 94424 -recovered pasa_asmbl_17915.p1, internal, 94221, 94424 -recovered pasa_asmbl_17915.p1, internal, 94835, 95029 -recovered pasa_asmbl_17915.p1, internal, 95366, 95512 Valid prediction for HiQ_model.g26809.t1 Valid prediction for GlimmerHMM_glimmerT_40270-T1 Valid prediction for GlimmerHMM_glimmerT_40257-T1 Couldn't classify 95935, 96705 Sorry, prediction pasa_asmbl_17914.p1 fails validation. (GGG) GG 95935-96705 TG GAT Valid prediction for GlimmerHMM_glimmerT_40259-T1 Valid prediction for snap_scaffold_17-snap.1046-T1 Valid prediction for snap_scaffold_17-snap.1041-T1 Valid prediction for GlimmerHMM_glimmerT_40253-T1 Valid prediction for GlimmerHMM_glimmerT_40271-T1 Valid prediction for pasa_asmbl_17921.p1 Valid prediction for Augustus_model.g26817.t1 Valid prediction for Augustus_model.g26803.t1 Valid prediction for snap_scaffold_17-snap.1061-T1 Valid prediction for snap_scaffold_17-snap.1039-T1 Valid prediction for snap_scaffold_17-snap.1059-T1 Valid prediction for CodingQuarry_transcript_21969-T1 Valid prediction for Augustus_model.g26816.t1 Valid prediction for HiQ_model.g26822.t1 Valid prediction for GlimmerHMM_glimmerT_40247-T1 Valid prediction for Augustus_model.g26804.t1 Valid prediction for GlimmerHMM_glimmerT_40252-T1 Couldn't classify 134227, 134299 Sorry, prediction pasa_asmbl_17908.p1 fails validation. (ATG) CA 132524-132638 GT TGG (TTC) AG 133727-133904 GT AGG (TAC) AG 134227-134299 CG CCC -recovered pasa_asmbl_17908.p1, initial, 132524, 132638 -recovered pasa_asmbl_17908.p1, internal, 133727, 133904 Valid prediction for pasa_asmbl_17917.p1 Valid prediction for GlimmerHMM_glimmerT_40273-T1 Valid prediction for snap_scaffold_17-snap.1050-T1 Valid prediction for snap_scaffold_17-snap.1044-T1 Valid prediction for snap_scaffold_17-snap.1045-T1 Valid prediction for CodingQuarry_transcript_21972-T1 Valid prediction for pasa_asmbl_17899.p1 Valid prediction for GlimmerHMM_glimmerT_40268-T1 Couldn't classify 142269, 143420 Sorry, prediction pasa_asmbl_17902.p1 fails validation. (GGT) GT 142269-143420 GG GAG Couldn't classify 189084, 189140 Sorry, prediction pasa_asmbl_17895.p1 fails validation. (AGG) TG 189084-189140 GT CGG (GTT) AG 189284-189394 GT AGG (TAC) AG 190796-190948 GT ATG (GAT) AG 191255-191386 CA GAC -recovered pasa_asmbl_17895.p1, terminal, 191255, 191386 -recovered pasa_asmbl_17895.p1, internal, 189284, 189394 -recovered pasa_asmbl_17895.p1, internal, 190796, 190948 Valid prediction for GlimmerHMM_glimmerT_40258-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 24189, rend_intergenic: 24186 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27345, rend_intergenic: 24186 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 42545, rend_intergenic: 40774 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91698, rend_intergenic: 85570 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123420, rend_intergenic: 113915 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129026, rend_intergenic: 124918 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140192, rend_intergenic: 135936 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 224678 -exon list size: 361 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 4.1 4.4 4.7 5.0 5.2 5.5 5.8 6.1 6.3 6.6 6.9 7.2 7.4 7.7 8.0 8.3 8.5 8.8 9.1 9.4 9.6 9.9 10.2 10.5 10.7 11.0 11.3 11.6 11.8 12.1 12.4 12.7 12.9 13.2 13.5 13.8 14.0 14.3 14.6 14.9 15.2 15.4 15.7 16.0 16.3 16.5 16.8 17.1 17.4 17.6 17.9 18.2 18.5 18.7 19.0 19.3 19.6 19.8 20.1 20.4 20.7 20.9 21.2 21.5 21.8 22.0 22.3 22.6 22.9 23.1 23.4 23.7 24.0 24.2 24.5 24.8 25.1 25.3 25.6 25.9 26.2 26.4 26.7 27.0 27.3 27.5 27.8 28.1 28.4 28.7 28.9 29.2 29.5 29.8 30.0 30.3 30.6 30.9 31.1 31.4 31.7 32.0 32.2 32.5 32.8 33.1 33.3 33.6 33.9 34.2 34.4 34.7 35.0 35.3 35.5 35.8 36.1 36.4 36.6 36.9 37.2 37.5 37.7 38.0 38.3 38.6 38.8 39.1 39.4 39.7 39.9 40.2 40.5 40.8 41.0 41.3 41.6 41.9 42.1 42.4 42.7 43.0 43.3 43.5 43.8 44.1 44.4 44.6 44.9 45.2 45.5 45.7 46.0 46.3 46.6 46.8 47.1 47.4 47.7 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 52.3 52.6 52.9 53.2 53.4 53.7 54.0 54.3 54.5 54.8 55.1 55.4 55.6 55.9 56.2 56.5 56.7 57.0 57.3 57.6 57.9 58.1 58.4 58.7 59.0 59.2 59.5 59.8 60.1 60.3 60.6 60.9 61.2 61.4 61.7 62.0 62.3 62.5 62.8 63.1 63.4 63.6 63.9 64.2 64.5 64.7 65.0 65.3 65.6 65.8 66.1 66.4 66.7 66.9 67.2 67.5 67.8 68.0 68.3 68.6 68.9 69.1 69.4 69.7 70.0 70.2 70.5 70.8 71.1 71.3 71.6 71.9 72.2 72.5 72.7 73.0 73.3 73.6 73.8 74.1 74.4 74.7 74.9 75.2 75.5 75.8 76.0 76.3 76.6 76.9 77.1 77.4 77.7 78.0 78.2 78.5 78.8 79.1 79.3 79.6 79.9 80.2 80.4 80.7 81.0 81.3 81.5 81.8 82.1 82.4 82.6 82.9 83.2 83.5 83.7 84.0 84.3 84.6 84.8 85.1 85.4 85.7 86.0 86.2 86.5 86.8 87.1 87.3 87.6 87.9 88.2 88.4 88.7 89.0 89.3 89.5 89.8 90.1 90.4 90.6 90.9 91.2 91.5 91.7 92.0 92.3 92.6 92.8 93.1 93.4 93.7 93.9 94.2 94.5 94.8 95.0 95.3 95.6 95.9 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 27 predictions from path traversal Error with prediction: GlimmerHMM lend_intergenic: 24189, rend_intergenic: 24186 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27345, rend_intergenic: 24186 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 42545, rend_intergenic: 40774 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91698, rend_intergenic: 85570 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123420, rend_intergenic: 113915 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129026, rend_intergenic: 124918 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140192, rend_intergenic: 135936 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