-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_782775-1097384 -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 Augustus_model.g31339.t1 Valid prediction for Augustus_model.g31348.t1 Valid prediction for snap_scaffold_21-snap.143-T1 Valid prediction for GlimmerHMM_glimmerT_47055-T1 Valid prediction for snap_scaffold_21-snap.172-T1 Valid prediction for HiQ_model.g31346.t1 Valid prediction for snap_scaffold_21-snap.133-T1 Valid prediction for GlimmerHMM_glimmerT_47038-T1 Valid prediction for snap_scaffold_21-snap.137-T1 Valid prediction for Augustus_model.g31328.t1 Valid prediction for CodingQuarry_transcript_32432-T1 Valid prediction for GlimmerHMM_glimmerT_47046-T1 Valid prediction for snap_scaffold_21-snap.160-T1 Valid prediction for Augustus_model.g31331.t1 Couldn't classify 150824, 151270 Sorry, prediction pasa_asmbl_28225.p1 fails validation. (GGG) TG 150824-151270 CC TTC Valid prediction for Augustus_model.g31336.t1 Valid prediction for snap_scaffold_21-snap.176-T1 Couldn't classify 292459, 292576 Sorry, prediction pasa_asmbl_28325.p1 fails validation. (CAG) CT 292459-292576 GT AGG (ACT) AG 292917-292996 GT AGG (GGT) AG 293939-294054 GT CTG (GTG) AG 294282-294312 AG AAA -recovered pasa_asmbl_28325.p1, terminal, 294282, 294312 -recovered pasa_asmbl_28325.p1, internal, 292917, 292996 -recovered pasa_asmbl_28325.p1, internal, 293939, 294054 Valid prediction for snap_scaffold_21-snap.134-T1 Valid prediction for GlimmerHMM_glimmerT_47036-T1 Valid prediction for GlimmerHMM_glimmerT_47058-T1 Valid prediction for snap_scaffold_21-snap.168-T1 Valid prediction for snap_scaffold_21-snap.146-T1 Valid prediction for Augustus_model.g31343.t1 Valid prediction for GlimmerHMM_glimmerT_47040-T1 Valid prediction for snap_scaffold_21-snap.170-T1 Valid prediction for pasa_asmbl_28320.p1 Couldn't classify 200961, 201116 Sorry, prediction pasa_asmbl_28317.p1 fails validation. (TCT) TC 200961-201116 GT AGG (GGC) AG 202165-202297 GT CTG (ACC) AG 203212-203324 GT AGG (GAC) AG 203597-203723 GT AGG (GAA) AG 203968-204089 GT ACG (GAG) AG 204881-205010 GT CTG (TAT) AG 205665-205691 GT AGG (GGA) AG 206223-206337 GT AGG (ACA) AG 206421-206511 AG AGA -recovered pasa_asmbl_28317.p1, terminal, 206421, 206511 -recovered pasa_asmbl_28317.p1, internal, 202165, 202297 -recovered pasa_asmbl_28317.p1, internal, 203212, 203324 -recovered pasa_asmbl_28317.p1, internal, 203597, 203723 -recovered pasa_asmbl_28317.p1, internal, 203968, 204089 -recovered pasa_asmbl_28317.p1, internal, 204881, 205010 -recovered pasa_asmbl_28317.p1, internal, 205665, 205691 -recovered pasa_asmbl_28317.p1, internal, 206223, 206337 Valid prediction for GlimmerHMM_glimmerT_47051-T1 Valid prediction for snap_scaffold_21-snap.157-T1 Valid prediction for GlimmerHMM_glimmerT_47054-T1 Valid prediction for CodingQuarry_transcript_32426-T1 Valid prediction for snap_scaffold_21-snap.151-T1 Valid prediction for GlimmerHMM_glimmerT_47039-T1 Valid prediction for GlimmerHMM_glimmerT_47063-T1 Valid prediction for GlimmerHMM_glimmerT_47052-T1 Valid prediction for snap_scaffold_21-snap.148-T1 Valid prediction for CodingQuarry_transcript_32429-T1 Valid prediction for GlimmerHMM_glimmerT_47047-T1 Valid prediction for snap_scaffold_21-snap.144-T1 Valid prediction for GlimmerHMM_glimmerT_47053-T1 Valid prediction for GlimmerHMM_glimmerT_47061-T1 Valid prediction for snap_scaffold_21-snap.174-T1 Valid prediction for snap_scaffold_21-snap.145-T1 Valid prediction for snap_scaffold_21-snap.154-T1 Valid prediction for HiQ_model.g31344.t1 Couldn't classify 52598, 52901 Sorry, prediction pasa_asmbl_28315.p1 fails validation. (TTG) GT 52598-52901 GT AGG (GCG) AG 53084-53172 GG AGG -recovered pasa_asmbl_28315.p1, terminal, 53084, 53172 Valid prediction for snap_scaffold_21-snap.149-T1 Valid prediction for CodingQuarry_transcript_32424-T1 Valid prediction for snap_scaffold_21-snap.175-T1 Valid prediction for GlimmerHMM_glimmerT_47045-T1 Valid prediction for CodingQuarry_transcript_32425-T1 Valid prediction for CodingQuarry_transcript_32422-T1 Valid prediction for HiQ_model.g31335.t1 Valid prediction for snap_scaffold_21-snap.136-T1 Valid prediction for Augustus_model.g31329.t1 Valid prediction for Augustus_model.g31340.t1 Valid prediction for Augustus_model.g31347.t1 Valid prediction for GlimmerHMM_glimmerT_47062-T1 Valid prediction for snap_scaffold_21-snap.139-T1 Valid prediction for snap_scaffold_21-snap.169-T1 Valid prediction for pasa_asmbl_28308.p1 Valid prediction for snap_scaffold_21-snap.158-T1 Couldn't classify 265962, 266108 Couldn't classify 266260, 266279 Sorry, prediction CodingQuarry_transcript_32430-T1 fails validation. (ATG) CC 263697-263766 GT CGG (AGG) AG 264021-264202 GT AGG (AGT) AG 265143-265292 GT AGG (GTG) AG 265545-265812 GT AGG (GGA) AG 265962-266108 TA GGT (TTA) GT 266260-266279 AG GAA -recovered CodingQuarry_transcript_32430-T1, initial, 263697, 263766 -recovered CodingQuarry_transcript_32430-T1, internal, 264021, 264202 -recovered CodingQuarry_transcript_32430-T1, internal, 265143, 265292 -recovered CodingQuarry_transcript_32430-T1, internal, 265545, 265812 Valid prediction for snap_scaffold_21-snap.138-T1 Valid prediction for snap_scaffold_21-snap.142-T1 Valid prediction for pasa_asmbl_28307.p1 Valid prediction for Augustus_model.g31338.t1 Valid prediction for HiQ_model.g31332.t1 Couldn't classify 285627, 285781 Couldn't classify 288382, 288471 Sorry, prediction pasa_asmbl_28324.p1 fails validation. (ATG) TC 276428-276473 GT AGG (CTA) AG 279184-279304 GT AGG (GTT) AG 282040-282127 GT ATG (CTT) AG 283544-283608 GT AGG (GCT) AG 283879-284054 GT CAG (ACC) AG 285627-285781 AT AGA (ATC) AC 288382-288471 GT AGG -recovered pasa_asmbl_28324.p1, initial, 276428, 276473 -recovered pasa_asmbl_28324.p1, internal, 279184, 279304 -recovered pasa_asmbl_28324.p1, internal, 282040, 282127 -recovered pasa_asmbl_28324.p1, internal, 283544, 283608 -recovered pasa_asmbl_28324.p1, internal, 283879, 284054 Valid prediction for Augustus_model.g31330.t1 Couldn't classify 40885, 41034 Sorry, prediction pasa_asmbl_28309.p1 fails validation. (TGG) GC 40885-41034 GT AGG (GAT) AG 41333-41469 GT TGG (CTG) AG 42133-42259 GT GGG (GGG) AG 42567-42602 GT AGG (ATT) AG 42812-42933 GT GTG (ATG) AG 43860-43989 GT CTG (GAC) AG 46317-46465 GT GTG (ATG) AG 46933-47062 GT TGG (GAT) AG 47219-47251 GT TGG (CTA) AG 47605-47714 GT AGG (CTG) AG 48385-48511 GT ATG (AGT) AG 48757-48884 GT ATG (ATG) AG 50507-50630 GT AGG (CCC) AG 51921-52079 GT AGG (GCT) AG 52742-52901 GT AGG (GCG) AG 53084-53172 GG AGG add_exon() Sorry, pasa_asmbl_28309.p1 43860-43989-initial-1 is invalid. -recovered pasa_asmbl_28309.p1, initial, 43860, 43989 add_exon() Sorry, pasa_asmbl_28309.p1 46933-47062-initial-1 is invalid. -recovered pasa_asmbl_28309.p1, initial, 46933, 47062 add_exon() Sorry, pasa_asmbl_28309.p1 50507-50630-initial-1 is invalid. -recovered pasa_asmbl_28309.p1, initial, 50507, 50630 -recovered pasa_asmbl_28309.p1, terminal, 53084, 53172 -recovered pasa_asmbl_28309.p1, internal, 41333, 41469 -recovered pasa_asmbl_28309.p1, internal, 42133, 42259 -recovered pasa_asmbl_28309.p1, internal, 42567, 42602 -recovered pasa_asmbl_28309.p1, internal, 42812, 42933 -recovered pasa_asmbl_28309.p1, internal, 43860, 43989 -recovered pasa_asmbl_28309.p1, internal, 46317, 46465 -recovered pasa_asmbl_28309.p1, internal, 46933, 47062 -recovered pasa_asmbl_28309.p1, internal, 47219, 47251 -recovered pasa_asmbl_28309.p1, internal, 47605, 47714 -recovered pasa_asmbl_28309.p1, internal, 48385, 48511 -recovered pasa_asmbl_28309.p1, internal, 48757, 48884 -recovered pasa_asmbl_28309.p1, internal, 50507, 50630 -recovered pasa_asmbl_28309.p1, internal, 51921, 52079 -recovered pasa_asmbl_28309.p1, internal, 52742, 52901 Valid prediction for snap_scaffold_21-snap.164-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.150-T1 Valid prediction for snap_scaffold_21-snap.165-T1 Valid prediction for GlimmerHMM_glimmerT_47050-T1 Valid prediction for snap_scaffold_21-snap.167-T1 Couldn't classify 256350, 256478 Sorry, prediction pasa_asmbl_27363.p1 fails validation. (GTG) AG 256350-256478 GT AGG (GCT) AG 256818-256921 GT TCG (GTC) AG 257156-257258 GT TGG (GGA) AG 257779-257947 GT AGG (CTG) AG 258040-258128 GT CAG (GAC) AG 258225-258350 GT AGG (CCC) AG 258545-258703 CC GAC -recovered pasa_asmbl_27363.p1, terminal, 258545, 258703 -recovered pasa_asmbl_27363.p1, internal, 256350, 256478 -recovered pasa_asmbl_27363.p1, internal, 256818, 256921 -recovered pasa_asmbl_27363.p1, internal, 257156, 257258 -recovered pasa_asmbl_27363.p1, internal, 257779, 257947 -recovered pasa_asmbl_27363.p1, internal, 258040, 258128 -recovered pasa_asmbl_27363.p1, internal, 258225, 258350 Valid prediction for CodingQuarry_transcript_32428-T1 Valid prediction for snap_scaffold_21-snap.141-T1 Valid prediction for GlimmerHMM_glimmerT_47057-T1 Valid prediction for snap_scaffold_21-snap.147-T1 Valid prediction for Augustus_model.g31342.t1 Valid prediction for snap_scaffold_21-snap.173-T1 Valid prediction for snap_scaffold_21-snap.163-T1 Valid prediction for Augustus_model.g31345.t1 Valid prediction for Augustus_model.g31337.t1 Valid prediction for GlimmerHMM_glimmerT_47060-T1 Valid prediction for snap_scaffold_21-snap.140-T1 Valid prediction for snap_scaffold_21-snap.159-T1 Valid prediction for GlimmerHMM_glimmerT_47048-T1 Valid prediction for snap_scaffold_21-snap.161-T1 Valid prediction for GlimmerHMM_glimmerT_47041-T1 Valid prediction for snap_scaffold_21-snap.135-T1 Valid prediction for GlimmerHMM_glimmerT_47043-T1 Valid prediction for snap_scaffold_21-snap.171-T1 Valid prediction for snap_scaffold_21-snap.156-T1 Valid prediction for snap_scaffold_21-snap.153-T1 Valid prediction for CodingQuarry_transcript_32431-T1 Valid prediction for pasa_asmbl_27364.p1 Valid prediction for CodingQuarry_transcript_32427-T1 Valid prediction for Augustus_model.g31333.t1 Valid prediction for GlimmerHMM_glimmerT_47037-T1 Valid prediction for pasa_asmbl_27371.p1 Valid prediction for GlimmerHMM_glimmerT_47042-T1 Valid prediction for snap_scaffold_21-snap.155-T1 Valid prediction for snap_scaffold_21-snap.162-T1 Valid prediction for snap_scaffold_21-snap.131-T1 Couldn't classify 96217, 96363 Sorry, prediction pasa_asmbl_27368.p1 fails validation. (GAC) CA 96217-96363 GT GGG (CCC) AG 98649-98740 GT AAG (GCA) AG 100384-100488 GT AGG (GAA) AG 100845-100909 GT AGG (GTG) AG 101023-101133 GT AGG (TAG) AG 102355-102519 GT GGG (ACA) AG 102961-103074 GT AGG (ACT) AG 103303-103547 CT AGC add_exon() Sorry, pasa_asmbl_27368.p1 102961-103074-terminal-1 is invalid. -recovered pasa_asmbl_27368.p1, terminal, 102961, 103074 -recovered pasa_asmbl_27368.p1, terminal, 103303, 103547 -recovered pasa_asmbl_27368.p1, internal, 98649, 98740 -recovered pasa_asmbl_27368.p1, internal, 100384, 100488 -recovered pasa_asmbl_27368.p1, internal, 100845, 100909 -recovered pasa_asmbl_27368.p1, internal, 101023, 101133 -recovered pasa_asmbl_27368.p1, internal, 102355, 102519 -recovered pasa_asmbl_27368.p1, internal, 102961, 103074 Valid prediction for HiQ_model.g31334.t1 Valid prediction for snap_scaffold_21-snap.166-T1 Valid prediction for GlimmerHMM_glimmerT_47059-T1 Valid prediction for GlimmerHMM_glimmerT_47056-T1 Valid prediction for GlimmerHMM_glimmerT_47044-T1 Valid prediction for GlimmerHMM_glimmerT_47049-T1 Valid prediction for snap_scaffold_21-snap.132-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for snap_scaffold_21-snap.152-T1 Valid prediction for Augustus_model.g31341.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29829, rend_intergenic: 27267 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 152557, rend_intergenic: 150563 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 199930, rend_intergenic: 197196 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 230767, rend_intergenic: 220692 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 314610 -exon list size: 402 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 2.0 2.2 2.5 2.7 3.0 3.2 3.5 3.7 4.0 4.2 4.5 4.7 5.0 5.2 5.4 5.7 5.9 6.2 6.4 6.7 6.9 7.2 7.4 7.7 7.9 8.2 8.4 8.7 8.9 9.2 9.4 9.7 9.9 10.1 10.4 10.6 10.9 11.1 11.4 11.6 11.9 12.1 12.4 12.6 12.9 13.1 13.4 13.6 13.9 14.1 14.4 14.6 14.9 15.1 15.3 15.6 15.8 16.1 16.3 16.6 16.8 17.1 17.3 17.6 17.8 18.1 18.3 18.6 18.8 19.1 19.3 19.6 19.8 20.0 20.3 20.5 20.8 21.0 21.3 21.5 21.8 22.0 22.3 22.5 22.8 23.0 23.3 23.5 23.8 24.0 24.3 24.5 24.8 25.0 25.2 25.5 25.7 26.0 26.2 26.5 26.7 27.0 27.2 27.5 27.7 28.0 28.2 28.5 28.7 29.0 29.2 29.5 29.7 30.0 30.2 30.4 30.7 30.9 31.2 31.4 31.7 31.9 32.2 32.4 32.7 32.9 33.2 33.4 33.7 33.9 34.2 34.4 34.7 34.9 35.1 35.4 35.6 35.9 36.1 36.4 36.6 36.9 37.1 37.4 37.6 37.9 38.1 38.4 38.6 38.9 39.1 39.4 39.6 39.9 40.1 40.3 40.6 40.8 41.1 41.3 41.6 41.8 42.1 42.3 42.6 42.8 43.1 43.3 43.6 43.8 44.1 44.3 44.6 44.8 45.0 45.3 45.5 45.8 46.0 46.3 46.5 46.8 47.0 47.3 47.5 47.8 48.0 48.3 48.5 48.8 49.0 49.3 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 52.7 53.0 53.2 53.5 53.7 54.0 54.2 54.5 54.7 55.0 55.2 55.4 55.7 55.9 56.2 56.4 56.7 56.9 57.2 57.4 57.7 57.9 58.2 58.4 58.7 58.9 59.2 59.4 59.7 59.9 60.1 60.4 60.6 60.9 61.1 61.4 61.6 61.9 62.1 62.4 62.6 62.9 63.1 63.4 63.6 63.9 64.1 64.4 64.6 64.9 65.1 65.3 65.6 65.8 66.1 66.3 66.6 66.8 67.1 67.3 67.6 67.8 68.1 68.3 68.6 68.8 69.1 69.3 69.6 69.8 70.0 70.3 70.5 70.8 71.0 71.3 71.5 71.8 72.0 72.3 72.5 72.8 73.0 73.3 73.5 73.8 74.0 74.3 74.5 74.8 75.0 75.2 75.5 75.7 76.0 76.2 76.5 76.7 77.0 77.2 77.5 77.7 78.0 78.2 78.5 78.7 79.0 79.2 79.5 79.7 80.0 80.2 80.4 80.7 80.9 81.2 81.4 81.7 81.9 82.2 82.4 82.7 82.9 83.2 83.4 83.7 83.9 84.2 84.4 84.7 84.9 85.1 85.4 85.6 85.9 86.1 86.4 86.6 86.9 87.1 87.4 87.6 87.9 88.1 88.4 88.6 88.9 89.1 89.4 89.6 89.9 90.1 90.3 90.6 90.8 91.1 91.3 91.6 91.8 92.1 92.3 92.6 92.8 93.1 93.3 93.6 93.8 94.1 94.3 94.6 94.8 95.0 95.3 95.5 95.8 96.0 96.3 96.5 96.8 97.0 97.3 97.5 97.8 98.0 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 35 predictions from path traversal Error with prediction: snap lend_intergenic: 29829, rend_intergenic: 27267 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 152557, rend_intergenic: 150563 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 199930, rend_intergenic: 197196 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 230767, rend_intergenic: 220692 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 31 predictions persist after filtering for low support