-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_3316257-3527059 -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_12-snap.675-T1 Valid prediction for Augustus_model.g19189.t1 Valid prediction for snap_scaffold_12-snap.687-T1 Valid prediction for GlimmerHMM_glimmerT_29094-T1 Valid prediction for snap_scaffold_12-snap.706-T1 Valid prediction for snap_scaffold_12-snap.696-T1 Valid prediction for GlimmerHMM_glimmerT_29081-T1 Valid prediction for GlimmerHMM_glimmerT_29080-T1 Valid prediction for GlimmerHMM_glimmerT_29097-T1 Valid prediction for snap_scaffold_12-snap.699-T1 Valid prediction for CodingQuarry_transcript_10152-T1 Valid prediction for CodingQuarry_transcript_10154-T1 Valid prediction for snap_scaffold_12-snap.697-T1 Valid prediction for Augustus_model.g19190.t1 Valid prediction for snap_scaffold_12-snap.685-T1 Valid prediction for snap_scaffold_12-snap.682-T1 Valid prediction for snap_scaffold_12-snap.688-T1 Valid prediction for Augustus_model.g19182.t1 Valid prediction for snap_scaffold_12-snap.702-T1 Valid prediction for snap_scaffold_12-snap.674-T1 Valid prediction for GlimmerHMM_glimmerT_29074-T1 Couldn't classify 84033, 84033 Sorry, prediction CodingQuarry_transcript_10157-T1 fails validation. (ATG) AA 82031-82046 GT AGG (CTC) AG 83027-83102 GT GAG (TAA) AG 83325-83511 GT TTG (ATT) AG 83741-83853 GT TGG (AAT) AG 84033-84033 AT GAA -recovered CodingQuarry_transcript_10157-T1, initial, 82031, 82046 -recovered CodingQuarry_transcript_10157-T1, internal, 83027, 83102 -recovered CodingQuarry_transcript_10157-T1, internal, 83325, 83511 -recovered CodingQuarry_transcript_10157-T1, internal, 83741, 83853 Couldn't classify 35563, 35679 Sorry, prediction pasa_asmbl_7552.p1 fails validation. (ATG) TC 34625-34747 GT AGG (ACA) AG 34885-35177 GT AAG (TGG) AG 35278-35386 GT AGG (GTG) AG 35563-35679 TT ACT -recovered pasa_asmbl_7552.p1, initial, 34625, 34747 -recovered pasa_asmbl_7552.p1, internal, 34885, 35177 -recovered pasa_asmbl_7552.p1, internal, 35278, 35386 Valid prediction for HiQ_model.g19188.t1 Couldn't classify 36844, 36916 Sorry, prediction pasa_asmbl_8256.p2 fails validation. (GGC) AT 36844-36916 GT AGG (AGT) AG 37163-37389 CG GAC -recovered pasa_asmbl_8256.p2, terminal, 37163, 37389 Valid prediction for CodingQuarry_transcript_10150-T1 Valid prediction for Augustus_model.g19194.t1 Valid prediction for GlimmerHMM_glimmerT_29087-T1 Valid prediction for snap_scaffold_12-snap.689-T1 Valid prediction for GlimmerHMM_glimmerT_29088-T1 Valid prediction for CodingQuarry_transcript_10151-T1 Couldn't classify 84033, 84033 Sorry, prediction pasa_asmbl_7560.p1 fails validation. (ATG) AA 82031-82046 GT AGG (CTC) AG 83027-83102 GT GAG (TAA) AG 83325-83511 GT TTG (ATT) AG 83741-83853 GT TGG (AAT) AG 84033-84033 AT GAA -recovered pasa_asmbl_7560.p1, initial, 82031, 82046 -recovered pasa_asmbl_7560.p1, internal, 83027, 83102 -recovered pasa_asmbl_7560.p1, internal, 83325, 83511 -recovered pasa_asmbl_7560.p1, internal, 83741, 83853 Valid prediction for pasa_asmbl_7546.p1 Valid prediction for GlimmerHMM_glimmerT_29079-T1 Valid prediction for Augustus_model.g19193.t1 Valid prediction for snap_scaffold_12-snap.695-T1 Valid prediction for snap_scaffold_12-snap.667-T1 Valid prediction for Augustus_model.g19183.t1 Valid prediction for snap_scaffold_12-snap.670-T1 Valid prediction for GlimmerHMM_glimmerT_29082-T1 Valid prediction for HiQ_model.g19180.t1 Couldn't classify 49018, 49177 Couldn't classify 49543, 49715 Sorry, prediction pasa_asmbl_7555.p1 fails validation. (GCC) CA 49018-49177 GT AGG (GGC) AG 49543-49715 GG AAG Valid prediction for snap_scaffold_12-snap.681-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for Augustus_model.g19191.t1 Couldn't classify 50800, 50862 Couldn't classify 52647, 52751 Sorry, prediction pasa_asmbl_7556.p1 fails validation. (GGC) CT 50800-50862 GT AGG (AAA) AG 51091-51228 GT AGG (GGG) AG 51778-51882 GT ACG (GTG) AG 52032-52124 GT TGG (ACG) AG 52647-52751 TA AGT -recovered pasa_asmbl_7556.p1, internal, 51091, 51228 -recovered pasa_asmbl_7556.p1, internal, 51778, 51882 -recovered pasa_asmbl_7556.p1, internal, 52032, 52124 Valid prediction for snap_scaffold_12-snap.672-T1 Valid prediction for snap_scaffold_12-snap.671-T1 Valid prediction for HiQ_model.g19184.t1 Valid prediction for GlimmerHMM_glimmerT_29090-T1 Valid prediction for GlimmerHMM_glimmerT_29077-T1 Valid prediction for snap_scaffold_12-snap.679-T1 Valid prediction for snap_scaffold_12-snap.707-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_12-snap.705-T1 Valid prediction for Augustus_model.g19185.t1 Valid prediction for snap_scaffold_12-snap.700-T1 Valid prediction for snap_scaffold_12-snap.686-T1 Valid prediction for GlimmerHMM_glimmerT_29084-T1 Valid prediction for GlimmerHMM_glimmerT_29089-T1 Valid prediction for snap_scaffold_12-snap.708-T1 Valid prediction for snap_scaffold_12-snap.683-T1 Valid prediction for GlimmerHMM_glimmerT_29076-T1 Valid prediction for snap_scaffold_12-snap.680-T1 Valid prediction for GlimmerHMM_glimmerT_29078-T1 Valid prediction for GlimmerHMM_glimmerT_29098-T1 Valid prediction for snap_scaffold_12-snap.693-T1 Valid prediction for GlimmerHMM_glimmerT_29083-T1 Valid prediction for snap_scaffold_12-snap.709-T1 Couldn't classify 187432, 187499 Sorry, prediction pasa_asmbl_8357.p1 fails validation. (ATG) GC 183919-184049 GT AGG (TTT) AG 184315-184478 GT AGG (AGC) AG 185142-185300 GT CAG (AGG) AG 186062-186166 GT AGG (ATG) AG 186617-186708 GT AGG (TTT) AG 186953-187091 GT AGG (ACA) AG 187432-187499 GG GGG -recovered pasa_asmbl_8357.p1, initial, 183919, 184049 add_exon() Sorry, pasa_asmbl_8357.p1 186617-186708-initial-1 is invalid. -recovered pasa_asmbl_8357.p1, initial, 186617, 186708 add_exon() Sorry, pasa_asmbl_8357.p1 186953-187091-terminal-3 is invalid. -recovered pasa_asmbl_8357.p1, terminal, 186953, 187091 -recovered pasa_asmbl_8357.p1, internal, 184315, 184478 -recovered pasa_asmbl_8357.p1, internal, 185142, 185300 -recovered pasa_asmbl_8357.p1, internal, 186062, 186166 -recovered pasa_asmbl_8357.p1, internal, 186617, 186708 -recovered pasa_asmbl_8357.p1, internal, 186953, 187091 Valid prediction for snap_scaffold_12-snap.704-T1 Valid prediction for Augustus_model.g19198.t1 Couldn't classify 142133, 142245 Sorry, prediction pasa_asmbl_8359.p1 fails validation. (GAG) AG 142133-142245 GT AGG (GCC) AG 142805-142946 GT AGG (AAA) AG 143480-143614 GT TGG (GTT) AG 143849-143971 CT AGC -recovered pasa_asmbl_8359.p1, terminal, 143849, 143971 -recovered pasa_asmbl_8359.p1, internal, 142133, 142245 -recovered pasa_asmbl_8359.p1, internal, 142805, 142946 -recovered pasa_asmbl_8359.p1, internal, 143480, 143614 Valid prediction for snap_scaffold_12-snap.701-T1 Valid prediction for HiQ_model.g19179.t1 Valid prediction for GlimmerHMM_glimmerT_29092-T1 Valid prediction for CodingQuarry_transcript_10155-T1 Valid prediction for snap_scaffold_12-snap.703-T1 Valid prediction for GlimmerHMM_glimmerT_29091-T1 Valid prediction for snap_scaffold_12-snap.694-T1 Valid prediction for snap_scaffold_12-snap.684-T1 Valid prediction for snap_scaffold_12-snap.668-T1 Valid prediction for Augustus_model.g19197.t1 Valid prediction for GlimmerHMM_glimmerT_29099-T1 Couldn't classify 187888, 187984 Sorry, prediction pasa_asmbl_8356.p1 fails validation. (TAC) GT 187888-187984 GT TGG (CCC) AG 188270-188440 GT AGG (TGT) AG 188720-188876 GT ACG (GGG) AG 189021-189135 GT AGG (ACT) AG 189591-189792 GT AGG (GTG) AG 190033-190202 GT AGG (GGT) AG 190411-190513 GT TGG (GTG) AG 190827-190960 GT AAG (GTG) AG 191223-191292 GT AGG (GGG) AG 191635-191810 GT AGG (GTG) AG 192697-192832 GT GGG (ATG) AG 192953-193047 GC GAG add_exon() Sorry, pasa_asmbl_8356.p1 192953-193047-initial-1 is invalid. -recovered pasa_asmbl_8356.p1, initial, 192953, 193047 -recovered pasa_asmbl_8356.p1, terminal, 192953, 193047 -recovered pasa_asmbl_8356.p1, internal, 188270, 188440 -recovered pasa_asmbl_8356.p1, internal, 188720, 188876 -recovered pasa_asmbl_8356.p1, internal, 189021, 189135 -recovered pasa_asmbl_8356.p1, internal, 189591, 189792 -recovered pasa_asmbl_8356.p1, internal, 190033, 190202 -recovered pasa_asmbl_8356.p1, internal, 190411, 190513 -recovered pasa_asmbl_8356.p1, internal, 190827, 190960 -recovered pasa_asmbl_8356.p1, internal, 191223, 191292 -recovered pasa_asmbl_8356.p1, internal, 191635, 191810 -recovered pasa_asmbl_8356.p1, internal, 192697, 192832 -recovered pasa_asmbl_8356.p1, internal, 192953, 193047 Valid prediction for CodingQuarry_transcript_10156-T1 Couldn't classify 129317, 129419 Sorry, prediction pasa_asmbl_9147.p1 fails validation. (AAG) TA 129317-129419 GT AAG (TTC) AG 130079-130199 GT AGG (TGA) AG 130384-130507 GT TGG (CTG) AG 130917-131060 GT CGG (GAT) AG 131243-131354 GT GGG (ATC) AG 131460-131491 GT CTG (GAC) AG 131728-131852 GT AAG (GCC) AG 132161-132218 GT AGG (GAC) AG 132352-132483 GT AGG (GCT) AG 132758-132886 GT AGG (CAC) AG 133378-133450 GT AGG (GTC) AG 133758-133822 GT TGG (ATC) AG 133959-134054 GT AGG (CCT) AG 134172-134275 GT AAG (GCA) AG 134480-134557 GT TCG (CCT) AG 134759-134896 GT GGG (CCA) AG 135133-135170 GT AGG (GCA) AG 135291-135450 GT CTG (GGA) AG 135743-135917 TC AGT -recovered pasa_asmbl_9147.p1, terminal, 135743, 135917 -recovered pasa_asmbl_9147.p1, internal, 130079, 130199 -recovered pasa_asmbl_9147.p1, internal, 130384, 130507 -recovered pasa_asmbl_9147.p1, internal, 130917, 131060 -recovered pasa_asmbl_9147.p1, internal, 131243, 131354 -recovered pasa_asmbl_9147.p1, internal, 131460, 131491 -recovered pasa_asmbl_9147.p1, internal, 131728, 131852 -recovered pasa_asmbl_9147.p1, internal, 132161, 132218 -recovered pasa_asmbl_9147.p1, internal, 132352, 132483 -recovered pasa_asmbl_9147.p1, internal, 132758, 132886 -recovered pasa_asmbl_9147.p1, internal, 133378, 133450 -recovered pasa_asmbl_9147.p1, internal, 133758, 133822 -recovered pasa_asmbl_9147.p1, internal, 133959, 134054 -recovered pasa_asmbl_9147.p1, internal, 134172, 134275 -recovered pasa_asmbl_9147.p1, internal, 134480, 134557 -recovered pasa_asmbl_9147.p1, internal, 134759, 134896 -recovered pasa_asmbl_9147.p1, internal, 135133, 135170 -recovered pasa_asmbl_9147.p1, internal, 135291, 135450 Valid prediction for snap_scaffold_12-snap.698-T1 Valid prediction for GlimmerHMM_glimmerT_29095-T1 Valid prediction for pasa_asmbl_8354.p1 Valid prediction for Augustus_model.g19196.t1 Valid prediction for snap_scaffold_12-snap.677-T1 Sorry, intron length (8) is less than minimum required (10) Valid prediction for HiQ_model.g19187.t1 Valid prediction for snap_scaffold_12-snap.678-T1 Valid prediction for GlimmerHMM_glimmerT_29100-T1 Valid prediction for snap_scaffold_12-snap.676-T1 Valid prediction for GlimmerHMM_glimmerT_29093-T1 Valid prediction for pasa_asmbl_8360.p1 Valid prediction for HiQ_model.g19186.t1 Valid prediction for snap_scaffold_12-snap.673-T1 Valid prediction for GlimmerHMM_glimmerT_29075-T1 Valid prediction for snap_scaffold_12-snap.692-T1 Valid prediction for GlimmerHMM_glimmerT_29085-T1 Valid prediction for Augustus_model.g19195.t1 Valid prediction for snap_scaffold_12-snap.691-T1 Valid prediction for Augustus_model.g19192.t1 Valid prediction for GlimmerHMM_glimmerT_29086-T1 Valid prediction for GlimmerHMM_glimmerT_29096-T1 Valid prediction for GlimmerHMM_glimmerT_29073-T1 Valid prediction for snap_scaffold_12-snap.669-T1 Valid prediction for Augustus_model.g19181.t1 Valid prediction for snap_scaffold_12-snap.690-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26885, rend_intergenic: 18955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 32641, rend_intergenic: 27633 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46775, rend_intergenic: 41552 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48426, rend_intergenic: 46972 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55296, rend_intergenic: 52519 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75964, rend_intergenic: 74887 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 98502, rend_intergenic: 96622 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 198273, rend_intergenic: 193825 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 210803 -exon list size: 385 building trellis 0.3 0.5 0.8 1.0 1.3 1.6 1.8 2.1 2.3 2.6 2.8 3.1 3.4 3.6 3.9 4.1 4.4 4.7 4.9 5.2 5.4 5.7 5.9 6.2 6.5 6.7 7.0 7.2 7.5 7.8 8.0 8.3 8.5 8.8 9.0 9.3 9.6 9.8 10.1 10.3 10.6 10.9 11.1 11.4 11.6 11.9 12.1 12.4 12.7 12.9 13.2 13.4 13.7 14.0 14.2 14.5 14.7 15.0 15.2 15.5 15.8 16.0 16.3 16.5 16.8 17.1 17.3 17.6 17.8 18.1 18.3 18.6 18.9 19.1 19.4 19.6 19.9 20.2 20.4 20.7 20.9 21.2 21.4 21.7 22.0 22.2 22.5 22.7 23.0 23.3 23.5 23.8 24.0 24.3 24.5 24.8 25.1 25.3 25.6 25.8 26.1 26.4 26.6 26.9 27.1 27.4 27.6 27.9 28.2 28.4 28.7 28.9 29.2 29.5 29.7 30.0 30.2 30.5 30.7 31.0 31.3 31.5 31.8 32.0 32.3 32.6 32.8 33.1 33.3 33.6 33.9 34.1 34.4 34.6 34.9 35.1 35.4 35.7 35.9 36.2 36.4 36.7 37.0 37.2 37.5 37.7 38.0 38.2 38.5 38.8 39.0 39.3 39.5 39.8 40.1 40.3 40.6 40.8 41.1 41.3 41.6 41.9 42.1 42.4 42.6 42.9 43.2 43.4 43.7 43.9 44.2 44.4 44.7 45.0 45.2 45.5 45.7 46.0 46.3 46.5 46.8 47.0 47.3 47.5 47.8 48.1 48.3 48.6 48.8 49.1 49.4 49.6 49.9 50.1 50.4 50.6 50.9 51.2 51.4 51.7 51.9 52.2 52.5 52.7 53.0 53.2 53.5 53.7 54.0 54.3 54.5 54.8 55.0 55.3 55.6 55.8 56.1 56.3 56.6 56.8 57.1 57.4 57.6 57.9 58.1 58.4 58.7 58.9 59.2 59.4 59.7 59.9 60.2 60.5 60.7 61.0 61.2 61.5 61.8 62.0 62.3 62.5 62.8 63.0 63.3 63.6 63.8 64.1 64.3 64.6 64.9 65.1 65.4 65.6 65.9 66.1 66.4 66.7 66.9 67.2 67.4 67.7 68.0 68.2 68.5 68.7 69.0 69.3 69.5 69.8 70.0 70.3 70.5 70.8 71.1 71.3 71.6 71.8 72.1 72.4 72.6 72.9 73.1 73.4 73.6 73.9 74.2 74.4 74.7 74.9 75.2 75.5 75.7 76.0 76.2 76.5 76.7 77.0 77.3 77.5 77.8 78.0 78.3 78.6 78.8 79.1 79.3 79.6 79.8 80.1 80.4 80.6 80.9 81.1 81.4 81.7 81.9 82.2 82.4 82.7 82.9 83.2 83.5 83.7 84.0 84.2 84.5 84.8 85.0 85.3 85.5 85.8 86.0 86.3 86.6 86.8 87.1 87.3 87.6 87.9 88.1 88.4 88.6 88.9 89.1 89.4 89.7 89.9 90.2 90.4 90.7 91.0 91.2 91.5 91.7 92.0 92.2 92.5 92.8 93.0 93.3 93.5 93.8 94.1 94.3 94.6 94.8 95.1 95.3 95.6 95.9 96.1 96.4 96.6 96.9 97.2 97.4 97.7 97.9 98.2 98.4 98.7 99.0 99.2 99.5 99.7 -found 29 predictions from path traversal Error with prediction: snap lend_intergenic: 26885, rend_intergenic: 18955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 32641, rend_intergenic: 27633 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 46775, rend_intergenic: 41552 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48426, rend_intergenic: 46972 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55296, rend_intergenic: 52519 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 75964, rend_intergenic: 74887 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 98502, rend_intergenic: 96622 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 198273, rend_intergenic: 193825 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 23 predictions persist after filtering for low support