-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_2436065-2667206 -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: +)Couldn't classify 115663, 115738 Sorry, prediction pasa_asmbl_45177.p1 fails validation. (ATG) TA 108961-108984 GT AGG (ATC) AG 109959-110178 GT CGG (GCG) AG 112263-112398 GT AGG (CAT) AG 112629-112716 GT AGG (GAG) AG 113386-113530 GT TGG (TCT) AG 114489-114714 GC AGG (CCT) AG 115663-115738 AC CCA -recovered pasa_asmbl_45177.p1, initial, 108961, 108984 -recovered pasa_asmbl_45177.p1, internal, 109959, 110178 -recovered pasa_asmbl_45177.p1, internal, 112263, 112398 -recovered pasa_asmbl_45177.p1, internal, 112629, 112716 -recovered pasa_asmbl_45177.p1, internal, 113386, 113530 -recovered pasa_asmbl_45177.p1, internal, 114489, 114714 Valid prediction for CodingQuarry_transcript_51995-T1 Couldn't classify 202523, 202545 Couldn't classify 206295, 206375 Sorry, prediction pasa_asmbl_45195.p2 fails validation. (CTG) AC 202523-202545 GT AGG (TCC) AG 202802-202857 GT AGG (TCC) AG 205167-205275 GT GAG (GTA) AG 205501-205567 GT AGG (GGT) AG 206295-206375 GT TAG -recovered pasa_asmbl_45195.p2, internal, 202802, 202857 -recovered pasa_asmbl_45195.p2, internal, 205167, 205275 -recovered pasa_asmbl_45195.p2, internal, 205501, 205567 -recovered pasa_asmbl_45195.p2, internal, 206295, 206375 Valid prediction for snap_scaffold_5-snap.515-T1 Valid prediction for snap_scaffold_5-snap.510-T1 Valid prediction for snap_scaffold_5-snap.491-T1 Valid prediction for GlimmerHMM_glimmerT_11575-T1 Valid prediction for GlimmerHMM_glimmerT_11589-T1 Valid prediction for GlimmerHMM_glimmerT_11596-T1 Valid prediction for snap_scaffold_5-snap.512-T1 Valid prediction for Augustus_model.g7572.t1 Valid prediction for GlimmerHMM_glimmerT_11582-T1 Couldn't classify 98452, 98535 Sorry, prediction pasa_asmbl_45171.p1 fails validation. (TTT) AT 98452-98535 GT AGG (GTG) AG 98628-98754 GT AGG (GAA) AG 100090-100206 GT TGG (GCC) AG 100489-100672 GT CGG (ACA) AG 101903-102030 GT AGG (ATG) AG 103378-103787 GG GAG -recovered pasa_asmbl_45171.p1, terminal, 103378, 103787 -recovered pasa_asmbl_45171.p1, internal, 98628, 98754 -recovered pasa_asmbl_45171.p1, internal, 100090, 100206 -recovered pasa_asmbl_45171.p1, internal, 100489, 100672 -recovered pasa_asmbl_45171.p1, internal, 101903, 102030 Valid prediction for snap_scaffold_5-snap.509-T1 Valid prediction for snap_scaffold_5-snap.504-T1 Valid prediction for snap_scaffold_5-snap.481-T1 Valid prediction for snap_scaffold_5-snap.511-T1 Valid prediction for snap_scaffold_5-snap.513-T1 Valid prediction for snap_scaffold_5-snap.505-T1 Valid prediction for GlimmerHMM_glimmerT_11588-T1 Valid prediction for snap_scaffold_5-snap.486-T1 Valid prediction for snap_scaffold_5-snap.475-T1 Valid prediction for snap_scaffold_5-snap.479-T1 Valid prediction for GlimmerHMM_glimmerT_11598-T1 Valid prediction for Augustus_model.g7571.t1 Valid prediction for snap_scaffold_5-snap.516-T1 Valid prediction for snap_scaffold_5-snap.494-T1 Valid prediction for GlimmerHMM_glimmerT_11591-T1 Couldn't classify 185289, 185678 Sorry, prediction pasa_asmbl_45191.p1 fails validation. (GAC) TG 185289-185678 CC GCC Valid prediction for GlimmerHMM_glimmerT_11595-T1 Valid prediction for HiQ_model.g7579.t1 Valid prediction for GlimmerHMM_glimmerT_11581-T1 Valid prediction for CodingQuarry_transcript_51996-T1 Valid prediction for HiQ_model.g7576.t1 Couldn't classify 185682, 186428 Sorry, prediction pasa_asmbl_45192.p1 fails validation. (CAT) CC 185682-186428 AA AGA Valid prediction for snap_scaffold_5-snap.503-T1 Valid prediction for snap_scaffold_5-snap.487-T1 Couldn't classify 116376, 116677 Couldn't classify 126733, 126831 Sorry, prediction pasa_asmbl_45178.p1 fails validation. (CCC) CC 116376-116677 GT AGG (CCC) AG 117676-117786 GT AGG (CTT) AG 119947-120088 GT AGG (ATG) AG 121546-121646 GT AGG (GAA) AG 122417-122531 GT AGG (ATC) AG 124499-124582 GT TGG (GCA) AG 125076-125132 GT TGG (ATG) AG 125669-125785 GT ATG (GCC) AG 126733-126831 GT GAG -recovered pasa_asmbl_45178.p1, initial, 121546, 121646 -recovered pasa_asmbl_45178.p1, initial, 125669, 125785 -recovered pasa_asmbl_45178.p1, internal, 117676, 117786 -recovered pasa_asmbl_45178.p1, internal, 119947, 120088 -recovered pasa_asmbl_45178.p1, internal, 121546, 121646 -recovered pasa_asmbl_45178.p1, internal, 122417, 122531 -recovered pasa_asmbl_45178.p1, internal, 124499, 124582 -recovered pasa_asmbl_45178.p1, internal, 125076, 125132 -recovered pasa_asmbl_45178.p1, internal, 125669, 125785 -recovered pasa_asmbl_45178.p1, internal, 126733, 126831 Valid prediction for Augustus_model.g7569.t1 Couldn't classify 212569, 212630 Sorry, prediction pasa_asmbl_45197.p1 fails validation. (CTC) CC 212569-212630 GT AAG (GAC) AG 213237-213389 GT GGG (GTC) AG 213943-214135 GT AGG (ACC) AG 214601-214719 GT CGG (GTC) AG 215156-215198 TG GAT -recovered pasa_asmbl_45197.p1, terminal, 215156, 215198 -recovered pasa_asmbl_45197.p1, internal, 213237, 213389 -recovered pasa_asmbl_45197.p1, internal, 213943, 214135 -recovered pasa_asmbl_45197.p1, internal, 214601, 214719 Valid prediction for Augustus_model.g7580.t1 Valid prediction for GlimmerHMM_glimmerT_11592-T1 Valid prediction for snap_scaffold_5-snap.522-T1 Valid prediction for GlimmerHMM_glimmerT_11579-T1 Valid prediction for Augustus_model.g7577.t1 Valid prediction for Augustus_model.g7575.t1 Valid prediction for HiQ_model.g7574.t1 Valid prediction for HiQ_model.g7581.t1 Couldn't classify 206772, 206854 Couldn't classify 210576, 210682 Sorry, prediction pasa_asmbl_45196.p1 fails validation. (GTG) AG 206772-206854 GT AGG (GAC) AG 209736-209850 GT AGG (CTT) AG 209964-210097 GT TGG (TAA) AG 210223-210284 GT AGG (GAA) AG 210576-210682 CA AGC -recovered pasa_asmbl_45196.p1, internal, 206772, 206854 -recovered pasa_asmbl_45196.p1, internal, 209736, 209850 -recovered pasa_asmbl_45196.p1, internal, 209964, 210097 -recovered pasa_asmbl_45196.p1, internal, 210223, 210284 Couldn't classify 89778, 89963 Sorry, prediction pasa_asmbl_46421.p1 fails validation. (GTG) CA 89778-89963 GT AGG (ACA) AG 90451-90645 AC AGA -recovered pasa_asmbl_46421.p1, terminal, 90451, 90645 Valid prediction for snap_scaffold_5-snap.484-T1 Valid prediction for GlimmerHMM_glimmerT_11594-T1 Valid prediction for GlimmerHMM_glimmerT_11585-T1 Valid prediction for snap_scaffold_5-snap.501-T1 Valid prediction for GlimmerHMM_glimmerT_11586-T1 Valid prediction for Augustus_model.g7568.t1 Valid prediction for Augustus_model.g7567.t1 Valid prediction for GlimmerHMM_glimmerT_11590-T1 Valid prediction for snap_scaffold_5-snap.490-T1 Valid prediction for snap_scaffold_5-snap.508-T1 Couldn't classify 128352, 128553 Sorry, prediction pasa_asmbl_45183.p1 fails validation. (CAG) TC 128352-128553 GT GCG (ATG) AG 128852-128990 GT AGG (GAC) AG 129829-129928 GT AGG (AAA) AG 130341-130468 GT CAG (CAT) AG 130809-130907 GT CAG (GTA) AG 131469-131704 GT CGG (ACG) AG 131868-131994 GT AAG (TTC) AG 132557-132701 GT GGG (GAG) AG 132931-133065 GT CTG (GAG) AG 133367-133558 GT AGG (CGG) AG 133934-134108 GC AGG (ATC) AG 135098-135244 GT AGG (TCC) AG 136493-136560 CC GAC add_exon() Sorry, pasa_asmbl_45183.p1 128852-128990-initial-1 is invalid. -recovered pasa_asmbl_45183.p1, initial, 128852, 128990 -recovered pasa_asmbl_45183.p1, terminal, 136493, 136560 -recovered pasa_asmbl_45183.p1, internal, 128852, 128990 -recovered pasa_asmbl_45183.p1, internal, 129829, 129928 -recovered pasa_asmbl_45183.p1, internal, 130341, 130468 -recovered pasa_asmbl_45183.p1, internal, 130809, 130907 -recovered pasa_asmbl_45183.p1, internal, 131469, 131704 -recovered pasa_asmbl_45183.p1, internal, 131868, 131994 -recovered pasa_asmbl_45183.p1, internal, 132557, 132701 -recovered pasa_asmbl_45183.p1, internal, 132931, 133065 -recovered pasa_asmbl_45183.p1, internal, 133367, 133558 -recovered pasa_asmbl_45183.p1, internal, 133934, 134108 -recovered pasa_asmbl_45183.p1, internal, 135098, 135244 Couldn't classify 184749, 185159 Sorry, prediction pasa_asmbl_45187.p1 fails validation. (ATG) TC 175376-175417 GT AGG (GAA) AG 177795-177874 GT AGG (AGA) AG 178345-178420 GT AGG (ACT) AG 180030-180109 GT AGG (GGT) AG 180767-180873 GT CGG (TCG) AG 181214-181297 GT AGG (GAA) AG 181460-181640 GT AGG (ACT) AG 182034-182106 GT TGG (GAT) AG 184749-185159 GG TCG -recovered pasa_asmbl_45187.p1, initial, 175376, 175417 -recovered pasa_asmbl_45187.p1, internal, 177795, 177874 -recovered pasa_asmbl_45187.p1, internal, 178345, 178420 -recovered pasa_asmbl_45187.p1, internal, 180030, 180109 -recovered pasa_asmbl_45187.p1, internal, 180767, 180873 -recovered pasa_asmbl_45187.p1, internal, 181214, 181297 -recovered pasa_asmbl_45187.p1, internal, 181460, 181640 -recovered pasa_asmbl_45187.p1, internal, 182034, 182106 Valid prediction for snap_scaffold_5-snap.495-T1 Valid prediction for GlimmerHMM_glimmerT_11584-T1 Valid prediction for pasa_asmbl_45199.p1 Valid prediction for snap_scaffold_5-snap.496-T1 Sorry, intron length (7) is less than minimum required (10) -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_5-snap.506-T1 Valid prediction for snap_scaffold_5-snap.507-T1 Valid prediction for snap_scaffold_5-snap.523-T1 Valid prediction for GlimmerHMM_glimmerT_11576-T1 Valid prediction for HiQ_model.g7573.t1 Valid prediction for snap_scaffold_5-snap.499-T1 Valid prediction for pasa_asmbl_43889.p1 Valid prediction for snap_scaffold_5-snap.498-T1 Valid prediction for snap_scaffold_5-snap.497-T1 Valid prediction for snap_scaffold_5-snap.493-T1 Valid prediction for CodingQuarry_transcript_51994-T1 Valid prediction for GlimmerHMM_glimmerT_11577-T1 Valid prediction for Augustus_model.g7570.t1 Valid prediction for GlimmerHMM_glimmerT_11574-T1 Valid prediction for GlimmerHMM_glimmerT_11583-T1 Valid prediction for snap_scaffold_5-snap.520-T1 Valid prediction for GlimmerHMM_glimmerT_11593-T1 Valid prediction for snap_scaffold_5-snap.482-T1 Valid prediction for snap_scaffold_5-snap.477-T1 Valid prediction for snap_scaffold_5-snap.485-T1 Valid prediction for snap_scaffold_5-snap.480-T1 Valid prediction for snap_scaffold_5-snap.519-T1 Valid prediction for snap_scaffold_5-snap.489-T1 Valid prediction for snap_scaffold_5-snap.514-T1 Valid prediction for snap_scaffold_5-snap.492-T1 Valid prediction for snap_scaffold_5-snap.517-T1 Valid prediction for snap_scaffold_5-snap.502-T1 Valid prediction for snap_scaffold_5-snap.478-T1 Valid prediction for GlimmerHMM_glimmerT_11587-T1 Valid prediction for snap_scaffold_5-snap.488-T1 Valid prediction for Augustus_model.g7578.t1 Valid prediction for snap_scaffold_5-snap.500-T1 Valid prediction for snap_scaffold_5-snap.521-T1 Valid prediction for GlimmerHMM_glimmerT_11578-T1 Valid prediction for snap_scaffold_5-snap.483-T1 Valid prediction for snap_scaffold_5-snap.476-T1 Valid prediction for snap_scaffold_5-snap.518-T1 Valid prediction for CodingQuarry_transcript_51993-T1 Valid prediction for GlimmerHMM_glimmerT_11597-T1 Valid prediction for snap_scaffold_5-snap.524-T1 Valid prediction for GlimmerHMM_glimmerT_11580-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22559, rend_intergenic: 6009 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28482, rend_intergenic: 22921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51936, rend_intergenic: 41535 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81199, rend_intergenic: 72530 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 85777, rend_intergenic: 82743 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91601, rend_intergenic: 86506 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131998, rend_intergenic: 110527 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149431, rend_intergenic: 142508 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192918, rend_intergenic: 190153 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 215905, rend_intergenic: 196666 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 228826, rend_intergenic: 221071 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 231142 -exon list size: 435 building trellis 0.2 0.5 0.7 0.9 1.1 1.4 1.6 1.8 2.1 2.3 2.5 2.7 3.0 3.2 3.4 3.7 3.9 4.1 4.3 4.6 4.8 5.0 5.3 5.5 5.7 5.9 6.2 6.4 6.6 6.9 7.1 7.3 7.6 7.8 8.0 8.2 8.5 8.7 8.9 9.2 9.4 9.6 9.8 10.1 10.3 10.5 10.8 11.0 11.2 11.4 11.7 11.9 12.1 12.4 12.6 12.8 13.0 13.3 13.5 13.7 14.0 14.2 14.4 14.6 14.9 15.1 15.3 15.6 15.8 16.0 16.2 16.5 16.7 16.9 17.2 17.4 17.6 17.8 18.1 18.3 18.5 18.8 19.0 19.2 19.5 19.7 19.9 20.1 20.4 20.6 20.8 21.1 21.3 21.5 21.7 22.0 22.2 22.4 22.7 22.9 23.1 23.3 23.6 23.8 24.0 24.3 24.5 24.7 24.9 25.2 25.4 25.6 25.9 26.1 26.3 26.5 26.8 27.0 27.2 27.5 27.7 27.9 28.1 28.4 28.6 28.8 29.1 29.3 29.5 29.7 30.0 30.2 30.4 30.7 30.9 31.1 31.4 31.6 31.8 32.0 32.3 32.5 32.7 33.0 33.2 33.4 33.6 33.9 34.1 34.3 34.6 34.8 35.0 35.2 35.5 35.7 35.9 36.2 36.4 36.6 36.8 37.1 37.3 37.5 37.8 38.0 38.2 38.4 38.7 38.9 39.1 39.4 39.6 39.8 40.0 40.3 40.5 40.7 41.0 41.2 41.4 41.6 41.9 42.1 42.3 42.6 42.8 43.0 43.2 43.5 43.7 43.9 44.2 44.4 44.6 44.9 45.1 45.3 45.5 45.8 46.0 46.2 46.5 46.7 46.9 47.1 47.4 47.6 47.8 48.1 48.3 48.5 48.7 49.0 49.2 49.4 49.7 49.9 50.1 50.3 50.6 50.8 51.0 51.3 51.5 51.7 51.9 52.2 52.4 52.6 52.9 53.1 53.3 53.5 53.8 54.0 54.2 54.5 54.7 54.9 55.1 55.4 55.6 55.8 56.1 56.3 56.5 56.8 57.0 57.2 57.4 57.7 57.9 58.1 58.4 58.6 58.8 59.0 59.3 59.5 59.7 60.0 60.2 60.4 60.6 60.9 61.1 61.3 61.6 61.8 62.0 62.2 62.5 62.7 62.9 63.2 63.4 63.6 63.8 64.1 64.3 64.5 64.8 65.0 65.2 65.4 65.7 65.9 66.1 66.4 66.6 66.8 67.0 67.3 67.5 67.7 68.0 68.2 68.4 68.6 68.9 69.1 69.3 69.6 69.8 70.0 70.3 70.5 70.7 70.9 71.2 71.4 71.6 71.9 72.1 72.3 72.5 72.8 73.0 73.2 73.5 73.7 73.9 74.1 74.4 74.6 74.8 75.1 75.3 75.5 75.7 76.0 76.2 76.4 76.7 76.9 77.1 77.3 77.6 77.8 78.0 78.3 78.5 78.7 78.9 79.2 79.4 79.6 79.9 80.1 80.3 80.5 80.8 81.0 81.2 81.5 81.7 81.9 82.2 82.4 82.6 82.8 83.1 83.3 83.5 83.8 84.0 84.2 84.4 84.7 84.9 85.1 85.4 85.6 85.8 86.0 86.3 86.5 86.7 87.0 87.2 87.4 87.6 87.9 88.1 88.3 88.6 88.8 89.0 89.2 89.5 89.7 89.9 90.2 90.4 90.6 90.8 91.1 91.3 91.5 91.8 92.0 92.2 92.4 92.7 92.9 93.1 93.4 93.6 93.8 94.1 94.3 94.5 94.7 95.0 95.2 95.4 95.7 95.9 96.1 96.3 96.6 96.8 97.0 97.3 97.5 97.7 97.9 98.2 98.4 98.6 98.9 99.1 99.3 99.5 99.8 -found 29 predictions from path traversal Error with prediction: snap lend_intergenic: 22559, rend_intergenic: 6009 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28482, rend_intergenic: 22921 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51936, rend_intergenic: 41535 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81199, rend_intergenic: 72530 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 85777, rend_intergenic: 82743 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91601, rend_intergenic: 86506 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131998, rend_intergenic: 110527 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149431, rend_intergenic: 142508 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 192918, rend_intergenic: 190153 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 215905, rend_intergenic: 196666 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 228826, rend_intergenic: 221071 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 20 predictions persist after filtering for low support