-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_3116129-3285059 -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_4-snap.715-T1 Valid prediction for Augustus_model.g5789.t1 Valid prediction for snap_scaffold_4-snap.737-T1 Sorry, intron length (8) is less than minimum required (10) Couldn't classify 158236, 158387 Sorry, prediction pasa_asmbl_41162.p1 fails validation. (ATG) CT 153948-154013 GT GGG (GAC) AG 154149-154232 GT AGG (GGT) AG 154414-154460 GT GAG (TTT) AG 154690-154801 GT AGG (TTC) AG 154903-155090 GT AGG (GCA) AG 155602-155784 GT AGG (GAA) AG 155972-156066 GT AGG (GGC) AG 156200-156315 GT AGG (GTG) AG 156468-156543 GC AGG (ATA) AG 156639-156732 GT GGG (CTC) AG 156849-157019 GT TGG (GGA) AG 157197-157432 GT TGG (AGG) AG 158236-158387 AA CCA -recovered pasa_asmbl_41162.p1, initial, 153948, 154013 -recovered pasa_asmbl_41162.p1, internal, 154149, 154232 -recovered pasa_asmbl_41162.p1, internal, 154414, 154460 -recovered pasa_asmbl_41162.p1, internal, 154690, 154801 -recovered pasa_asmbl_41162.p1, internal, 154903, 155090 -recovered pasa_asmbl_41162.p1, internal, 155602, 155784 -recovered pasa_asmbl_41162.p1, internal, 155972, 156066 -recovered pasa_asmbl_41162.p1, internal, 156200, 156315 -recovered pasa_asmbl_41162.p1, internal, 156468, 156543 -recovered pasa_asmbl_41162.p1, internal, 156639, 156732 -recovered pasa_asmbl_41162.p1, internal, 156849, 157019 -recovered pasa_asmbl_41162.p1, internal, 157197, 157432 Valid prediction for snap_scaffold_4-snap.731-T1 Couldn't classify 31028, 31276 Couldn't classify 32138, 32327 Sorry, prediction pasa_asmbl_41161.p1 fails validation. (AGG) AG 31028-31276 GT AGG (GAC) AG 31365-31501 GT CGG (GCT) AG 32138-32327 CC CGC -recovered pasa_asmbl_41161.p1, internal, 31028, 31276 -recovered pasa_asmbl_41161.p1, internal, 31365, 31501 Valid prediction for snap_scaffold_4-snap.732-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_9027-T1 Valid prediction for GlimmerHMM_glimmerT_9050-T1 Valid prediction for GlimmerHMM_glimmerT_9031-T1 Couldn't classify 26841, 27148 Couldn't classify 27450, 27483 Sorry, prediction pasa_asmbl_41160.p1 fails validation. (ACC) GC 26841-27148 GT AGG (GTA) AG 27450-27483 GA GAG Valid prediction for GlimmerHMM_glimmerT_9039-T1 Valid prediction for HiQ_model.g5802.t1 Valid prediction for snap_scaffold_4-snap.705-T1 Valid prediction for CodingQuarry_transcript_48903-T1 Valid prediction for snap_scaffold_4-snap.709-T1 Valid prediction for GlimmerHMM_glimmerT_9025-T1 Valid prediction for GlimmerHMM_glimmerT_9042-T1 Valid prediction for snap_scaffold_4-snap.702-T1 Valid prediction for snap_scaffold_4-snap.707-T1 Valid prediction for snap_scaffold_4-snap.743-T1 Valid prediction for snap_scaffold_4-snap.711-T1 Valid prediction for snap_scaffold_4-snap.721-T1 Valid prediction for snap_scaffold_4-snap.722-T1 Valid prediction for GlimmerHMM_glimmerT_9020-T1 Valid prediction for GlimmerHMM_glimmerT_9028-T1 Valid prediction for GlimmerHMM_glimmerT_9045-T1 Valid prediction for Augustus_model.g5787.t1 Valid prediction for snap_scaffold_4-snap.713-T1 Valid prediction for snap_scaffold_4-snap.704-T1 Valid prediction for snap_scaffold_4-snap.736-T1 Valid prediction for CodingQuarry_transcript_48906-T1 Valid prediction for snap_scaffold_4-snap.724-T1 Valid prediction for Augustus_model.g5798.t1 Valid prediction for snap_scaffold_4-snap.720-T1 Valid prediction for snap_scaffold_4-snap.738-T1 Valid prediction for Augustus_model.g5803.t1 Valid prediction for GlimmerHMM_glimmerT_9044-T1 Valid prediction for pasa_asmbl_41168.p1 Valid prediction for pasa_asmbl_42409.p1 Valid prediction for GlimmerHMM_glimmerT_9022-T1 Valid prediction for Augustus_model.g5801.t1 Valid prediction for GlimmerHMM_glimmerT_9034-T1 Valid prediction for snap_scaffold_4-snap.735-T1 Valid prediction for snap_scaffold_4-snap.719-T1 Valid prediction for GlimmerHMM_glimmerT_9048-T1 Valid prediction for snap_scaffold_4-snap.741-T1 Valid prediction for Augustus_model.g5792.t1 Valid prediction for GlimmerHMM_glimmerT_9024-T1 Valid prediction for snap_scaffold_4-snap.717-T1 Valid prediction for GlimmerHMM_glimmerT_9049-T1 Valid prediction for GlimmerHMM_glimmerT_9023-T1 Couldn't classify 159203, 159343 Sorry, prediction pasa_asmbl_41167.p1 fails validation. (GAC) TG 159203-159343 GT AGG (ACG) AG 159856-160053 AG AGA -recovered pasa_asmbl_41167.p1, terminal, 159856, 160053 Valid prediction for GlimmerHMM_glimmerT_9033-T1 Valid prediction for snap_scaffold_4-snap.742-T1 Valid prediction for GlimmerHMM_glimmerT_9021-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_4-snap.723-T1 Valid prediction for snap_scaffold_4-snap.712-T1 Valid prediction for GlimmerHMM_glimmerT_9035-T1 Valid prediction for GlimmerHMM_glimmerT_9040-T1 Valid prediction for snap_scaffold_4-snap.727-T1 Valid prediction for Augustus_model.g5791.t1 Valid prediction for snap_scaffold_4-snap.706-T1 Valid prediction for GlimmerHMM_glimmerT_9030-T1 Valid prediction for CodingQuarry_transcript_48896-T1 Valid prediction for GlimmerHMM_glimmerT_9043-T1 Valid prediction for snap_scaffold_4-snap.740-T1 Valid prediction for CodingQuarry_transcript_48900-T1 Valid prediction for CodingQuarry_transcript_48898-T1 Valid prediction for GlimmerHMM_glimmerT_9041-T1 Valid prediction for Augustus_model.g5796.t1 Valid prediction for GlimmerHMM_glimmerT_9019-T1 Valid prediction for CodingQuarry_transcript_48897-T1 Valid prediction for GlimmerHMM_glimmerT_9047-T1 Valid prediction for snap_scaffold_4-snap.728-T1 Valid prediction for GlimmerHMM_glimmerT_9032-T1 Valid prediction for CodingQuarry_transcript_48899-T1 Valid prediction for snap_scaffold_4-snap.726-T1 Valid prediction for snap_scaffold_4-snap.708-T1 Couldn't classify 63400, 63506 Couldn't classify 65394, 65450 Sorry, prediction pasa_asmbl_42414.p1 fails validation. (CTC) AG 63400-63506 GT AGG (TCT) AG 64172-64322 GT AGG (TTT) AG 65394-65450 CG TCC -recovered pasa_asmbl_42414.p1, internal, 63400, 63506 -recovered pasa_asmbl_42414.p1, internal, 64172, 64322 Couldn't classify 50528, 50629 Sorry, prediction pasa_asmbl_42416.p1 fails validation. (GCA) GG 50528-50629 GT CAG (ATC) AG 52560-52747 GT AAG (AAT) AG 52943-53051 GT AAG (GTG) AG 53277-53444 GT AGG (GCG) AG 54029-54170 GT CCG (AGA) AG 55412-55542 CA AGC -recovered pasa_asmbl_42416.p1, terminal, 55412, 55542 -recovered pasa_asmbl_42416.p1, internal, 52560, 52747 -recovered pasa_asmbl_42416.p1, internal, 52943, 53051 -recovered pasa_asmbl_42416.p1, internal, 53277, 53444 -recovered pasa_asmbl_42416.p1, internal, 54029, 54170 Valid prediction for Augustus_model.g5793.t1 Couldn't classify 69959, 69968 Couldn't classify 71797, 71838 Sorry, prediction pasa_asmbl_42411.p1 fails validation. (CAT) AG 69959-69968 GT GGG (GCA) AG 70113-70309 GT AGG (GCA) AG 70608-70739 GT TGG (GAG) AG 71429-71527 GT AGG (TGG) AG 71797-71838 GT GGG -recovered pasa_asmbl_42411.p1, internal, 69959, 69968 -recovered pasa_asmbl_42411.p1, internal, 70113, 70309 -recovered pasa_asmbl_42411.p1, internal, 70608, 70739 -recovered pasa_asmbl_42411.p1, internal, 71429, 71527 -recovered pasa_asmbl_42411.p1, internal, 71797, 71838 Valid prediction for snap_scaffold_4-snap.730-T1 Valid prediction for GlimmerHMM_glimmerT_9029-T1 Valid prediction for snap_scaffold_4-snap.718-T1 Valid prediction for snap_scaffold_4-snap.733-T1 Valid prediction for pasa_asmbl_42429.p1 Valid prediction for Augustus_model.g5788.t1 Valid prediction for pasa_asmbl_42423.p1 Valid prediction for GlimmerHMM_glimmerT_9046-T1 Couldn't classify 24869, 25020 Sorry, prediction pasa_asmbl_42434.p1 fails validation. (ATG) AA 17227-17269 GT AGG (TTG) AG 17347-17478 GT AGG (ATT) AG 20060-20883 GT AGG (TTA) AG 20976-21106 GT AGG (ACA) AG 21316-21433 GT AGG (GAG) AG 21839-22024 GT GGG (ATC) AG 22452-22604 GT AGG (CTG) AG 22856-23010 GT AGG (CCT) AG 23201-23318 GT AGG (GTG) AG 23410-23460 GT GGG (ACG) AG 23912-24019 GT AGG (ATG) AG 24328-24565 GT CTG (CGC) AG 24869-25020 AC TTA -recovered pasa_asmbl_42434.p1, initial, 17227, 17269 -recovered pasa_asmbl_42434.p1, initial, 24328, 24565 -recovered pasa_asmbl_42434.p1, terminal, 22856, 23010 -recovered pasa_asmbl_42434.p1, internal, 17347, 17478 -recovered pasa_asmbl_42434.p1, internal, 20060, 20883 -recovered pasa_asmbl_42434.p1, internal, 20976, 21106 -recovered pasa_asmbl_42434.p1, internal, 21316, 21433 -recovered pasa_asmbl_42434.p1, internal, 21839, 22024 -recovered pasa_asmbl_42434.p1, internal, 22452, 22604 -recovered pasa_asmbl_42434.p1, internal, 22856, 23010 -recovered pasa_asmbl_42434.p1, internal, 23201, 23318 -recovered pasa_asmbl_42434.p1, internal, 23410, 23460 -recovered pasa_asmbl_42434.p1, internal, 23912, 24019 -recovered pasa_asmbl_42434.p1, internal, 24328, 24565 Valid prediction for Augustus_model.g5790.t1 Valid prediction for snap_scaffold_4-snap.725-T1 Valid prediction for snap_scaffold_4-snap.710-T1 Valid prediction for snap_scaffold_4-snap.734-T1 Valid prediction for Augustus_model.g5794.t1 Valid prediction for HiQ_model.g5799.t1 Valid prediction for GlimmerHMM_glimmerT_9038-T1 Valid prediction for snap_scaffold_4-snap.739-T1 Valid prediction for snap_scaffold_4-snap.729-T1 Valid prediction for GlimmerHMM_glimmerT_9026-T1 Valid prediction for GlimmerHMM_glimmerT_9037-T1 Valid prediction for snap_scaffold_4-snap.714-T1 Valid prediction for snap_scaffold_4-snap.703-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for CodingQuarry_transcript_48902-T1 Couldn't classify 26098, 26268 Couldn't classify 26349, 26507 Sorry, prediction CodingQuarry_transcript_48901-T1 fails validation. (ATG) GT 26098-26268 AT CCA (ATG) TC 26349-26507 CG GAC Valid prediction for HiQ_model.g5797.t1 Valid prediction for pasa_asmbl_42427.p1 Valid prediction for HiQ_model.g5795.t1 Valid prediction for snap_scaffold_4-snap.716-T1 Valid prediction for GlimmerHMM_glimmerT_9036-T1 Valid prediction for HiQ_model.g5800.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7757, rend_intergenic: 7634 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 32648, rend_intergenic: 8249 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36095, rend_intergenic: 32745 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51385, rend_intergenic: 50007 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53805, rend_intergenic: 52118 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55045, rend_intergenic: 53956 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58270, rend_intergenic: 55644 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 64777, rend_intergenic: 58661 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 85644, rend_intergenic: 69027 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103743, rend_intergenic: 89056 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107511, rend_intergenic: 104049 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 109704, rend_intergenic: 107818 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125236, rend_intergenic: 122463 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131036, rend_intergenic: 127806 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 136711, rend_intergenic: 135187 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149128, rend_intergenic: 143903 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 168931 -exon list size: 431 building trellis 0.2 0.5 0.7 0.9 1.2 1.4 1.6 1.8 2.1 2.3 2.5 2.8 3.0 3.2 3.5 3.7 3.9 4.2 4.4 4.6 4.8 5.1 5.3 5.5 5.8 6.0 6.2 6.5 6.7 6.9 7.2 7.4 7.6 7.9 8.1 8.3 8.5 8.8 9.0 9.2 9.5 9.7 9.9 10.2 10.4 10.6 10.9 11.1 11.3 11.5 11.8 12.0 12.2 12.5 12.7 12.9 13.2 13.4 13.6 13.9 14.1 14.3 14.5 14.8 15.0 15.2 15.5 15.7 15.9 16.2 16.4 16.6 16.9 17.1 17.3 17.6 17.8 18.0 18.2 18.5 18.7 18.9 19.2 19.4 19.6 19.9 20.1 20.3 20.6 20.8 21.0 21.2 21.5 21.7 21.9 22.2 22.4 22.6 22.9 23.1 23.3 23.6 23.8 24.0 24.2 24.5 24.7 24.9 25.2 25.4 25.6 25.9 26.1 26.3 26.6 26.8 27.0 27.3 27.5 27.7 27.9 28.2 28.4 28.6 28.9 29.1 29.3 29.6 29.8 30.0 30.3 30.5 30.7 30.9 31.2 31.4 31.6 31.9 32.1 32.3 32.6 32.8 33.0 33.3 33.5 33.7 33.9 34.2 34.4 34.6 34.9 35.1 35.3 35.6 35.8 36.0 36.3 36.5 36.7 37.0 37.2 37.4 37.6 37.9 38.1 38.3 38.6 38.8 39.0 39.3 39.5 39.7 40.0 40.2 40.4 40.6 40.9 41.1 41.3 41.6 41.8 42.0 42.3 42.5 42.7 43.0 43.2 43.4 43.6 43.9 44.1 44.3 44.6 44.8 45.0 45.3 45.5 45.7 46.0 46.2 46.4 46.7 46.9 47.1 47.3 47.6 47.8 48.0 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 52.0 52.2 52.4 52.7 52.9 53.1 53.3 53.6 53.8 54.0 54.3 54.5 54.7 55.0 55.2 55.4 55.7 55.9 56.1 56.4 56.6 56.8 57.0 57.3 57.5 57.7 58.0 58.2 58.4 58.7 58.9 59.1 59.4 59.6 59.8 60.0 60.3 60.5 60.7 61.0 61.2 61.4 61.7 61.9 62.1 62.4 62.6 62.8 63.0 63.3 63.5 63.7 64.0 64.2 64.4 64.7 64.9 65.1 65.4 65.6 65.8 66.1 66.3 66.5 66.7 67.0 67.2 67.4 67.7 67.9 68.1 68.4 68.6 68.8 69.1 69.3 69.5 69.7 70.0 70.2 70.4 70.7 70.9 71.1 71.4 71.6 71.8 72.1 72.3 72.5 72.7 73.0 73.2 73.4 73.7 73.9 74.1 74.4 74.6 74.8 75.1 75.3 75.5 75.8 76.0 76.2 76.4 76.7 76.9 77.1 77.4 77.6 77.8 78.1 78.3 78.5 78.8 79.0 79.2 79.4 79.7 79.9 80.1 80.4 80.6 80.8 81.1 81.3 81.5 81.8 82.0 82.2 82.4 82.7 82.9 83.1 83.4 83.6 83.8 84.1 84.3 84.5 84.8 85.0 85.2 85.5 85.7 85.9 86.1 86.4 86.6 86.8 87.1 87.3 87.5 87.8 88.0 88.2 88.5 88.7 88.9 89.1 89.4 89.6 89.8 90.1 90.3 90.5 90.8 91.0 91.2 91.5 91.7 91.9 92.1 92.4 92.6 92.8 93.1 93.3 93.5 93.8 94.0 94.2 94.5 94.7 94.9 95.2 95.4 95.6 95.8 96.1 96.3 96.5 96.8 97.0 97.2 97.5 97.7 97.9 98.2 98.4 98.6 98.8 99.1 99.3 99.5 99.8 -found 28 predictions from path traversal Error with prediction: snap lend_intergenic: 7757, rend_intergenic: 7634 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 32648, rend_intergenic: 8249 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36095, rend_intergenic: 32745 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51385, rend_intergenic: 50007 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53805, rend_intergenic: 52118 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55045, rend_intergenic: 53956 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 58270, rend_intergenic: 55644 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 64777, rend_intergenic: 58661 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 85644, rend_intergenic: 69027 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103743, rend_intergenic: 89056 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107511, rend_intergenic: 104049 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 109704, rend_intergenic: 107818 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125236, rend_intergenic: 122463 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131036, rend_intergenic: 127806 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 136711, rend_intergenic: 135187 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149128, rend_intergenic: 143903 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 16 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 13695 -exon list size: 12 building trellis 7.1 14.3 21.4 28.6 35.7 42.9 50.0 57.1 64.3 71.4 78.6 85.7 92.9 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 12815 -exon list size: 10 building trellis 8.3 16.7 25.0 33.3 41.7 50.0 58.3 66.7 75.0 83.3 91.7 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 12723 -exon list size: 9 building trellis 9.1 18.2 27.3 36.4 45.5 54.5 63.6 72.7 81.8 90.9 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support