-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_16661301-16824247 -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 15551, 15688 Sorry, prediction pasa_asmbl_41998.p1 fails validation. (CCA) CC 15551-15688 GT AGG (ATC) AG 15858-16038 GT AGG (ACT) AG 16163-16285 GT AGG (TGA) AG 16688-16881 GT TGG (ATT) AG 17612-17759 GT AGG (CTA) AG 17979-18100 GT CAG (CGC) AG 18338-18419 GT ACG (CTG) AG 18632-18763 GT CGG (ATA) AG 19140-19214 GT AGG (TGT) AG 19290-20089 AC GAA -recovered pasa_asmbl_41998.p1, terminal, 19290, 20089 -recovered pasa_asmbl_41998.p1, internal, 15858, 16038 -recovered pasa_asmbl_41998.p1, internal, 16163, 16285 -recovered pasa_asmbl_41998.p1, internal, 16688, 16881 -recovered pasa_asmbl_41998.p1, internal, 17612, 17759 -recovered pasa_asmbl_41998.p1, internal, 17979, 18100 -recovered pasa_asmbl_41998.p1, internal, 18338, 18419 -recovered pasa_asmbl_41998.p1, internal, 18632, 18763 -recovered pasa_asmbl_41998.p1, internal, 19140, 19214 Valid prediction for snap_scaffold_4-snap.3415-T1 Valid prediction for GlimmerHMM_glimmerT_10904-T1 Valid prediction for snap_scaffold_4-snap.3416-T1 Valid prediction for HiQ_model.g7139.t1 Valid prediction for snap_scaffold_4-snap.3389-T1 Valid prediction for CodingQuarry_transcript_49285-T1 Valid prediction for Augustus_model.g7145.t1 Couldn't classify 34336, 34441 Couldn't classify 35514, 35558 Sorry, prediction pasa_asmbl_42244.p1 fails validation. (CTG) GT 34336-34441 GT AAG (CAC) AG 34838-34974 GT GGG (GAG) AG 35125-35151 GT GGG (TGG) AG 35273-35398 GT GTG (GAG) AG 35514-35558 CA GCC -recovered pasa_asmbl_42244.p1, internal, 34838, 34974 -recovered pasa_asmbl_42244.p1, internal, 35125, 35151 -recovered pasa_asmbl_42244.p1, internal, 35273, 35398 Valid prediction for snap_scaffold_4-snap.3384-T1 Valid prediction for snap_scaffold_4-snap.3391-T1 Valid prediction for snap_scaffold_4-snap.3392-T1 Couldn't classify 149051, 149203 Sorry, prediction pasa_asmbl_42003.p1 fails validation. (AGC) CA 149051-149203 GT AGG (GTT) AG 149368-149469 GT AGG (TGT) AG 149554-149695 GT GGG (TCC) AG 149859-150067 GT CCG (GTG) AG 150271-150384 GG GAG -recovered pasa_asmbl_42003.p1, terminal, 150271, 150384 -recovered pasa_asmbl_42003.p1, internal, 149368, 149469 -recovered pasa_asmbl_42003.p1, internal, 149554, 149695 -recovered pasa_asmbl_42003.p1, internal, 149859, 150067 Valid prediction for Augustus_model.g7141.t1 Valid prediction for Augustus_model.g7144.t1 Valid prediction for snap_scaffold_4-snap.3396-T1 Valid prediction for snap_scaffold_4-snap.3388-T1 Valid prediction for snap_scaffold_4-snap.3408-T1 Valid prediction for snap_scaffold_4-snap.3402-T1 Valid prediction for HiQ_model.g7137.t1 Valid prediction for snap_scaffold_4-snap.3394-T1 Valid prediction for GlimmerHMM_glimmerT_10901-T1 Valid prediction for CodingQuarry_transcript_49295-T1 Valid prediction for snap_scaffold_4-snap.3407-T1 Valid prediction for snap_scaffold_4-snap.3417-T1 Valid prediction for snap_scaffold_4-snap.3424-T1 Valid prediction for GlimmerHMM_glimmerT_10910-T1 Valid prediction for snap_scaffold_4-snap.3413-T1 Valid prediction for GlimmerHMM_glimmerT_10913-T1 Valid prediction for snap_scaffold_4-snap.3423-T1 Valid prediction for snap_scaffold_4-snap.3385-T1 Valid prediction for snap_scaffold_4-snap.3403-T1 Couldn't classify 24037, 24054 Sorry, prediction pasa_asmbl_41999.p1 fails validation. (GGA) AG 24037-24054 GT TGG (GAT) AG 24222-24300 GT CAG (TAC) AG 24381-24515 GT AGG (CGA) AG 24872-24946 GT AGG (TGT) AG 25451-25659 GT AGG (GTT) AG 25830-26047 GT GGG (ATT) AG 26156-26498 AA GAA -recovered pasa_asmbl_41999.p1, terminal, 26156, 26498 -recovered pasa_asmbl_41999.p1, internal, 24037, 24054 -recovered pasa_asmbl_41999.p1, internal, 24222, 24300 -recovered pasa_asmbl_41999.p1, internal, 24381, 24515 -recovered pasa_asmbl_41999.p1, internal, 24872, 24946 -recovered pasa_asmbl_41999.p1, internal, 25451, 25659 -recovered pasa_asmbl_41999.p1, internal, 25830, 26047 Valid prediction for GlimmerHMM_glimmerT_10895-T1 Valid prediction for HiQ_model.g7156.t1 Valid prediction for GlimmerHMM_glimmerT_10893-T1 Valid prediction for snap_scaffold_4-snap.3411-T1 Couldn't classify 27764, 27962 Couldn't classify 28653, 28801 Sorry, prediction pasa_asmbl_42000.p1 fails validation. (CGC) GC 27764-27962 GT GGG (TGG) AG 28189-28389 GT CGG (TAC) AG 28653-28801 AT TCA -recovered pasa_asmbl_42000.p1, internal, 28189, 28389 Valid prediction for Augustus_model.g7140.t1 Valid prediction for GlimmerHMM_glimmerT_10898-T1 Valid prediction for pasa_asmbl_41996.p1 Valid prediction for GlimmerHMM_glimmerT_10906-T1 Valid prediction for snap_scaffold_4-snap.3398-T1 Valid prediction for snap_scaffold_4-snap.3420-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 Augustus_model.g7157.t1 Valid prediction for Augustus_model.g7142.t1 Valid prediction for GlimmerHMM_glimmerT_10897-T1 Valid prediction for GlimmerHMM_glimmerT_10903-T1 Valid prediction for snap_scaffold_4-snap.3409-T1 Valid prediction for Augustus_model.g7153.t1 Couldn't classify 15994, 16089 Couldn't classify 16158, 16193 Sorry, prediction CodingQuarry_transcript_49294-T1 fails validation. (ATG) TC 14526-14631 GT GGG (AGG) AG 14776-14818 GT CGG (TGC) AG 14950-15017 GT AGG (GAT) AG 15150-15424 GT AAG (CTC) AG 15533-15734 GT AGG (CCG) AG 15994-16089 AT GGA (ATC) TC 16158-16193 GT AGG (CTG) AG 16339-16346 TT GAT -recovered CodingQuarry_transcript_49294-T1, initial, 14526, 14631 -recovered CodingQuarry_transcript_49294-T1, terminal, 16339, 16346 -recovered CodingQuarry_transcript_49294-T1, internal, 14776, 14818 -recovered CodingQuarry_transcript_49294-T1, internal, 14950, 15017 -recovered CodingQuarry_transcript_49294-T1, internal, 15150, 15424 -recovered CodingQuarry_transcript_49294-T1, internal, 15533, 15734 Valid prediction for HiQ_model.g7151.t1 Valid prediction for pasa_asmbl_43542.p1 Valid prediction for Augustus_model.g7158.t1 Valid prediction for HiQ_model.g7147.t1 Valid prediction for Augustus_model.g7152.t1 Valid prediction for CodingQuarry_transcript_49291-T1 Valid prediction for GlimmerHMM_glimmerT_10914-T1 Valid prediction for GlimmerHMM_glimmerT_10902-T1 Couldn't classify 102583, 102588 Sorry, prediction pasa_asmbl_43208.p1 fails validation. (GCC) GA 102583-102588 GT TGG (TTG) AG 103079-103216 GT AGG (CAT) AG 103314-103433 GT AAG (GTG) AG 103560-103692 GT CTG (GTT) AG 104180-104295 GT AGG (GAG) AG 104397-104465 GT AGG (TCC) AG 106830-106889 AG GAA -recovered pasa_asmbl_43208.p1, terminal, 106830, 106889 -recovered pasa_asmbl_43208.p1, internal, 103079, 103216 -recovered pasa_asmbl_43208.p1, internal, 103314, 103433 -recovered pasa_asmbl_43208.p1, internal, 103560, 103692 -recovered pasa_asmbl_43208.p1, internal, 104180, 104295 -recovered pasa_asmbl_43208.p1, internal, 104397, 104465 Valid prediction for snap_scaffold_4-snap.3397-T1 Valid prediction for snap_scaffold_4-snap.3404-T1 Valid prediction for GlimmerHMM_glimmerT_10917-T1 Valid prediction for snap_scaffold_4-snap.3390-T1 Valid prediction for snap_scaffold_4-snap.3387-T1 Valid prediction for GlimmerHMM_glimmerT_10899-T1 Valid prediction for HiQ_model.g7155.t1 Valid prediction for pasa_asmbl_43214.p1 Valid prediction for snap_scaffold_4-snap.3418-T1 Valid prediction for HiQ_model.g7154.t1 Valid prediction for pasa_asmbl_43203.p1 Valid prediction for GlimmerHMM_glimmerT_10909-T1 Valid prediction for Augustus_model.g7148.t1 Valid prediction for CodingQuarry_transcript_49292-T1 Valid prediction for snap_scaffold_4-snap.3401-T1 Valid prediction for pasa_asmbl_43204.p1 Valid prediction for Augustus_model.g7149.t1 Valid prediction for CodingQuarry_transcript_49289-T1 Valid prediction for GlimmerHMM_glimmerT_10907-T1 Valid prediction for snap_scaffold_4-snap.3405-T1 Valid prediction for CodingQuarry_transcript_49293-T1 Valid prediction for GlimmerHMM_glimmerT_10912-T1 Valid prediction for snap_scaffold_4-snap.3400-T1 Valid prediction for snap_scaffold_4-snap.3412-T1 Valid prediction for GlimmerHMM_glimmerT_10896-T1 Valid prediction for GlimmerHMM_glimmerT_10911-T1 Valid prediction for HiQ_model.g7138.t1 Valid prediction for snap_scaffold_4-snap.3399-T1 Valid prediction for GlimmerHMM_glimmerT_10900-T1 Couldn't classify 21552, 21573 Sorry, prediction CodingQuarry_transcript_49290-T1 fails validation. (ATG) CC 20150-20167 GT TGG (GTG) AG 20604-20718 GT AAG (GCG) AG 20809-20923 GT CCG (AGG) AG 21050-21194 GT ACG (TGT) AG 21310-21371 GT TGG (TTT) TG 21552-21573 GT AGG -recovered CodingQuarry_transcript_49290-T1, initial, 20150, 20167 -recovered CodingQuarry_transcript_49290-T1, internal, 20604, 20718 -recovered CodingQuarry_transcript_49290-T1, internal, 20809, 20923 -recovered CodingQuarry_transcript_49290-T1, internal, 21050, 21194 -recovered CodingQuarry_transcript_49290-T1, internal, 21310, 21371 Couldn't classify 43279, 43416 Sorry, prediction pasa_asmbl_43213.p1 fails validation. (ATG) TG 35279-35480 GT AGG (TGA) AG 35851-36005 GT AGG (CAA) AG 36750-36861 GT CGG (AGG) AG 37518-37641 GT AGG (CCC) AG 37814-37969 GT AGG (GCT) AG 40007-40184 GT AGG (GAC) AG 41305-41399 GT AAG (GCA) AG 41993-42073 GT AAG (GAC) AG 42804-42987 GT GGG (GCC) AG 43279-43416 GG GGG -recovered pasa_asmbl_43213.p1, initial, 35279, 35480 -recovered pasa_asmbl_43213.p1, internal, 35851, 36005 -recovered pasa_asmbl_43213.p1, internal, 36750, 36861 -recovered pasa_asmbl_43213.p1, internal, 37518, 37641 -recovered pasa_asmbl_43213.p1, internal, 37814, 37969 -recovered pasa_asmbl_43213.p1, internal, 40007, 40184 -recovered pasa_asmbl_43213.p1, internal, 41305, 41399 -recovered pasa_asmbl_43213.p1, internal, 41993, 42073 -recovered pasa_asmbl_43213.p1, internal, 42804, 42987 Valid prediction for Augustus_model.g7150.t1 Valid prediction for snap_scaffold_4-snap.3414-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_10915-T1 Valid prediction for snap_scaffold_4-snap.3386-T1 Valid prediction for GlimmerHMM_glimmerT_10916-T1 Valid prediction for snap_scaffold_4-snap.3410-T1 Valid prediction for Augustus_model.g7146.t1 Valid prediction for snap_scaffold_4-snap.3395-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_4-snap.3393-T1 Valid prediction for CodingQuarry_transcript_49287-T1 Valid prediction for GlimmerHMM_glimmerT_10905-T1 Valid prediction for pasa_asmbl_43211.p1 Valid prediction for GlimmerHMM_glimmerT_10894-T1 Valid prediction for snap_scaffold_4-snap.3421-T1 Valid prediction for GlimmerHMM_glimmerT_10908-T1 Valid prediction for snap_scaffold_4-snap.3406-T1 Valid prediction for HiQ_model.g7143.t1 Valid prediction for CodingQuarry_transcript_49288-T1 Valid prediction for CodingQuarry_transcript_49286-T1 Valid prediction for snap_scaffold_4-snap.3419-T1 Valid prediction for pasa_asmbl_43218.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13726, rend_intergenic: 12630 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 26498, rend_intergenic: 19934 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35822, rend_intergenic: 32079 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48835, rend_intergenic: 47019 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50072, rend_intergenic: 48955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55320, rend_intergenic: 53171 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70339, rend_intergenic: 58420 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95222, rend_intergenic: 86529 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99899, rend_intergenic: 96546 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105274, rend_intergenic: 100934 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 126232, rend_intergenic: 114856 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 139894, rend_intergenic: 126728 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 162947 -exon list size: 485 building trellis 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.1 2.3 2.5 2.7 2.9 3.1 3.3 3.5 3.7 3.9 4.1 4.3 4.5 4.7 4.9 5.1 5.3 5.5 5.7 6.0 6.2 6.4 6.6 6.8 7.0 7.2 7.4 7.6 7.8 8.0 8.2 8.4 8.6 8.8 9.0 9.2 9.4 9.7 9.9 10.1 10.3 10.5 10.7 10.9 11.1 11.3 11.5 11.7 11.9 12.1 12.3 12.5 12.7 12.9 13.1 13.3 13.6 13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.6 15.8 16.0 16.2 16.4 16.6 16.8 17.0 17.2 17.5 17.7 17.9 18.1 18.3 18.5 18.7 18.9 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.5 20.7 20.9 21.1 21.4 21.6 21.8 22.0 22.2 22.4 22.6 22.8 23.0 23.2 23.4 23.6 23.8 24.0 24.2 24.4 24.6 24.8 25.1 25.3 25.5 25.7 25.9 26.1 26.3 26.5 26.7 26.9 27.1 27.3 27.5 27.7 27.9 28.1 28.3 28.5 28.7 29.0 29.2 29.4 29.6 29.8 30.0 30.2 30.4 30.6 30.8 31.0 31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6 32.9 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.5 34.7 34.9 35.1 35.3 35.5 35.7 35.9 36.1 36.3 36.6 36.8 37.0 37.2 37.4 37.6 37.8 38.0 38.2 38.4 38.6 38.8 39.0 39.2 39.4 39.6 39.8 40.0 40.2 40.5 40.7 40.9 41.1 41.3 41.5 41.7 41.9 42.1 42.3 42.5 42.7 42.9 43.1 43.3 43.5 43.7 43.9 44.1 44.4 44.6 44.8 45.0 45.2 45.4 45.6 45.8 46.0 46.2 46.4 46.6 46.8 47.0 47.2 47.4 47.6 47.8 48.0 48.3 48.5 48.7 48.9 49.1 49.3 49.5 49.7 49.9 50.1 50.3 50.5 50.7 50.9 51.1 51.3 51.5 51.7 52.0 52.2 52.4 52.6 52.8 53.0 53.2 53.4 53.6 53.8 54.0 54.2 54.4 54.6 54.8 55.0 55.2 55.4 55.6 55.9 56.1 56.3 56.5 56.7 56.9 57.1 57.3 57.5 57.7 57.9 58.1 58.3 58.5 58.7 58.9 59.1 59.3 59.5 59.8 60.0 60.2 60.4 60.6 60.8 61.0 61.2 61.4 61.6 61.8 62.0 62.2 62.4 62.6 62.8 63.0 63.2 63.4 63.7 63.9 64.1 64.3 64.5 64.7 64.9 65.1 65.3 65.5 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.1 67.4 67.6 67.8 68.0 68.2 68.4 68.6 68.8 69.0 69.2 69.4 69.6 69.8 70.0 70.2 70.4 70.6 70.8 71.0 71.3 71.5 71.7 71.9 72.1 72.3 72.5 72.7 72.9 73.1 73.3 73.5 73.7 73.9 74.1 74.3 74.5 74.7 74.9 75.2 75.4 75.6 75.8 76.0 76.2 76.4 76.6 76.8 77.0 77.2 77.4 77.6 77.8 78.0 78.2 78.4 78.6 78.9 79.1 79.3 79.5 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.1 81.3 81.5 81.7 81.9 82.1 82.3 82.5 82.8 83.0 83.2 83.4 83.6 83.8 84.0 84.2 84.4 84.6 84.8 85.0 85.2 85.4 85.6 85.8 86.0 86.2 86.4 86.7 86.9 87.1 87.3 87.5 87.7 87.9 88.1 88.3 88.5 88.7 88.9 89.1 89.3 89.5 89.7 89.9 90.1 90.3 90.6 90.8 91.0 91.2 91.4 91.6 91.8 92.0 92.2 92.4 92.6 92.8 93.0 93.2 93.4 93.6 93.8 94.0 94.3 94.5 94.7 94.9 95.1 95.3 95.5 95.7 95.9 96.1 96.3 96.5 96.7 96.9 97.1 97.3 97.5 97.7 97.9 98.2 98.4 98.6 98.8 99.0 99.2 99.4 99.6 99.8 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 13726, rend_intergenic: 12630 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 26498, rend_intergenic: 19934 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35822, rend_intergenic: 32079 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48835, rend_intergenic: 47019 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50072, rend_intergenic: 48955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55320, rend_intergenic: 53171 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70339, rend_intergenic: 58420 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95222, rend_intergenic: 86529 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99899, rend_intergenic: 96546 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105274, rend_intergenic: 100934 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 126232, rend_intergenic: 114856 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 139894, rend_intergenic: 126728 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 26 predictions persist after filtering for low support