-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_18297934-18468829 -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_2-snap.3575-T1 Valid prediction for GlimmerHMM_glimmerT_5531-T1 Valid prediction for snap_scaffold_2-snap.3584-T1 Valid prediction for snap_scaffold_2-snap.3563-T1 Valid prediction for snap_scaffold_2-snap.3577-T1 Valid prediction for GlimmerHMM_glimmerT_5515-T1 Valid prediction for snap_scaffold_2-snap.3557-T1 Valid prediction for GlimmerHMM_glimmerT_5528-T1 Valid prediction for snap_scaffold_2-snap.3581-T1 Valid prediction for snap_scaffold_2-snap.3572-T1 Valid prediction for Augustus_model.g3711.t1 Valid prediction for Augustus_model.g3714.t1 Valid prediction for snap_scaffold_2-snap.3586-T1 Valid prediction for snap_scaffold_2-snap.3561-T1 Valid prediction for snap_scaffold_2-snap.3574-T1 Valid prediction for GlimmerHMM_glimmerT_5520-T1 Valid prediction for snap_scaffold_2-snap.3567-T1 Valid prediction for Augustus_model.g3712.t1 Valid prediction for snap_scaffold_2-snap.3570-T1 Valid prediction for snap_scaffold_2-snap.3569-T1 Valid prediction for GlimmerHMM_glimmerT_5519-T1 Valid prediction for snap_scaffold_2-snap.3550-T1 Valid prediction for snap_scaffold_2-snap.3552-T1 Valid prediction for snap_scaffold_2-snap.3560-T1 Valid prediction for GlimmerHMM_glimmerT_5533-T1 Valid prediction for snap_scaffold_2-snap.3587-T1 Valid prediction for snap_scaffold_2-snap.3582-T1 Valid prediction for snap_scaffold_2-snap.3583-T1 Valid prediction for snap_scaffold_2-snap.3565-T1 Valid prediction for GlimmerHMM_glimmerT_5523-T1 Valid prediction for snap_scaffold_2-snap.3554-T1 Valid prediction for GlimmerHMM_glimmerT_5524-T1 Valid prediction for snap_scaffold_2-snap.3558-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 GlimmerHMM_glimmerT_5530-T1 Valid prediction for GlimmerHMM_glimmerT_5514-T1 Valid prediction for snap_scaffold_2-snap.3562-T1 Valid prediction for GlimmerHMM_glimmerT_5534-T1 Valid prediction for snap_scaffold_2-snap.3573-T1 Valid prediction for snap_scaffold_2-snap.3555-T1 Valid prediction for GlimmerHMM_glimmerT_5518-T1 Couldn't classify 57240, 57283 Sorry, prediction pasa_asmbl_23779.p1 fails validation. (GGA) TA 57240-57283 GT AGG (CAT) AG 59202-59313 GT AGG (GAG) AG 61928-62081 GT CAG (ACT) AG 62913-62980 GT AGG (CAA) AG 63393-63450 GT AAG (CAT) AG 63657-63810 GT GGG (ACC) AG 64186-64298 GT AGG (GGA) AG 65759-65905 GT CGG (AGC) AG 66243-66511 GT AGG (TTC) AG 66713-66838 GT AGG (AAA) AG 66997-67114 GT AGG (AGA) AG 67270-67521 GT AGG (AGG) AG 67964-68040 GT TGG (GAC) AG 68369-68550 GT ATG (AGA) AG 69012-69094 GT AGG (AAA) AG 69458-69646 GT AGG (TGG) AG 70037-70183 GT GAG (ACG) AG 70538-70608 GT AGG (GGG) AG 70948-70989 GT AGG (GTT) AG 71555-71602 GT AGG (GCT) AG 71843-72313 GT AGG (GCA) AG 72571-72898 GT TGG (ACG) AG 73252-73307 CC GAC -recovered pasa_asmbl_23779.p1, terminal, 73252, 73307 -recovered pasa_asmbl_23779.p1, internal, 59202, 59313 -recovered pasa_asmbl_23779.p1, internal, 61928, 62081 -recovered pasa_asmbl_23779.p1, internal, 62913, 62980 -recovered pasa_asmbl_23779.p1, internal, 63393, 63450 -recovered pasa_asmbl_23779.p1, internal, 63657, 63810 -recovered pasa_asmbl_23779.p1, internal, 64186, 64298 -recovered pasa_asmbl_23779.p1, internal, 65759, 65905 -recovered pasa_asmbl_23779.p1, internal, 66243, 66511 -recovered pasa_asmbl_23779.p1, internal, 66713, 66838 -recovered pasa_asmbl_23779.p1, internal, 66997, 67114 -recovered pasa_asmbl_23779.p1, internal, 67270, 67521 -recovered pasa_asmbl_23779.p1, internal, 67964, 68040 -recovered pasa_asmbl_23779.p1, internal, 68369, 68550 -recovered pasa_asmbl_23779.p1, internal, 69012, 69094 -recovered pasa_asmbl_23779.p1, internal, 69458, 69646 -recovered pasa_asmbl_23779.p1, internal, 70037, 70183 -recovered pasa_asmbl_23779.p1, internal, 70538, 70608 -recovered pasa_asmbl_23779.p1, internal, 70948, 70989 -recovered pasa_asmbl_23779.p1, internal, 71555, 71602 -recovered pasa_asmbl_23779.p1, internal, 71843, 72313 -recovered pasa_asmbl_23779.p1, internal, 72571, 72898 Valid prediction for snap_scaffold_2-snap.3579-T1 Valid prediction for snap_scaffold_2-snap.3559-T1 Valid prediction for snap_scaffold_2-snap.3556-T1 Valid prediction for GlimmerHMM_glimmerT_5522-T1 Couldn't classify 34705, 35278 Couldn't classify 36676, 36713 Sorry, prediction pasa_asmbl_23782.p1 fails validation. (TCG) GC 34705-35278 GT AGG (ACT) AG 36676-36713 GC AGG -recovered pasa_asmbl_23782.p1, internal, 36676, 36713 Valid prediction for Augustus_model.g3710.t1 Valid prediction for snap_scaffold_2-snap.3564-T1 Valid prediction for snap_scaffold_2-snap.3580-T1 Valid prediction for GlimmerHMM_glimmerT_5527-T1 Valid prediction for GlimmerHMM_glimmerT_5517-T1 Valid prediction for GlimmerHMM_glimmerT_5529-T1 Valid prediction for GlimmerHMM_glimmerT_5526-T1 Valid prediction for snap_scaffold_2-snap.3566-T1 Valid prediction for snap_scaffold_2-snap.3553-T1 Valid prediction for GlimmerHMM_glimmerT_5521-T1 Valid prediction for Augustus_model.g3713.t1 Valid prediction for Augustus_model.g3716.t1 Couldn't classify 33241, 33654 Sorry, prediction pasa_asmbl_23784.p1 fails validation. (AAA) CC 33241-33654 CA GAC Valid prediction for snap_scaffold_2-snap.3578-T1 Valid prediction for snap_scaffold_2-snap.3571-T1 Valid prediction for snap_scaffold_2-snap.3551-T1 Couldn't classify 34087, 34548 Sorry, prediction pasa_asmbl_23783.p1 fails validation. (CCA) AG 34087-34548 CT GCC Valid prediction for GlimmerHMM_glimmerT_5532-T1 Valid prediction for GlimmerHMM_glimmerT_5516-T1 Valid prediction for snap_scaffold_2-snap.3585-T1 Valid prediction for snap_scaffold_2-snap.3568-T1 Couldn't classify 45039, 45093 Couldn't classify 54557, 54579 Sorry, prediction pasa_asmbl_23781.p1 fails validation. (TTC) CG 45039-45093 GT AGG (AGC) AG 47251-47375 GT AGG (GTA) AG 49701-50092 GT AGG (TTG) AG 50891-50947 GT AGG (TAT) AG 52028-52087 GT AGG (TTG) AG 52533-52716 GT AGG (AGG) AG 53196-53298 GT CGG (TAA) AG 54557-54579 AG GGA -recovered pasa_asmbl_23781.p1, internal, 47251, 47375 -recovered pasa_asmbl_23781.p1, internal, 49701, 50092 -recovered pasa_asmbl_23781.p1, internal, 50891, 50947 -recovered pasa_asmbl_23781.p1, internal, 52028, 52087 -recovered pasa_asmbl_23781.p1, internal, 52533, 52716 -recovered pasa_asmbl_23781.p1, internal, 53196, 53298 Valid prediction for snap_scaffold_2-snap.3576-T1 Valid prediction for Augustus_model.g3715.t1 Valid prediction for GlimmerHMM_glimmerT_5525-T1 Couldn't classify 169637, 169673 Sorry, prediction pasa_asmbl_23775.p1 fails validation. (ATG) TG 161759-161809 GT AGG (GAT) AG 164742-164805 GT AGG (GCA) AG 165189-165335 GT AGG (ACC) AG 166455-166586 GT TGG (TTT) AG 167516-167609 GT AAG (GGC) AG 169637-169673 AG CAA -recovered pasa_asmbl_23775.p1, initial, 161759, 161809 -recovered pasa_asmbl_23775.p1, internal, 164742, 164805 -recovered pasa_asmbl_23775.p1, internal, 165189, 165335 -recovered pasa_asmbl_23775.p1, internal, 166455, 166586 -recovered pasa_asmbl_23775.p1, internal, 167516, 167609 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4992, rend_intergenic: 3284 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 14652, rend_intergenic: 5530 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24284, rend_intergenic: 15802 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31196, rend_intergenic: 27783 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 32684, rend_intergenic: 32061 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40610, rend_intergenic: 32740 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48273, rend_intergenic: 46235 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50627, rend_intergenic: 48278 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51439, rend_intergenic: 50649 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91327, rend_intergenic: 64869 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 93550, rend_intergenic: 91708 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95249, rend_intergenic: 94062 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100891, rend_intergenic: 95420 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103614, rend_intergenic: 100891 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 109421, rend_intergenic: 106916 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110426, rend_intergenic: 109691 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 121133, rend_intergenic: 111213 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125407, rend_intergenic: 123003 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 130010, rend_intergenic: 126300 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 144302, rend_intergenic: 130111 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 145717, rend_intergenic: 144383 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 162530, rend_intergenic: 145867 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 170896 -exon list size: 304 building trellis 0.3 0.7 1.0 1.3 1.6 2.0 2.3 2.6 2.9 3.3 3.6 3.9 4.2 4.6 4.9 5.2 5.6 5.9 6.2 6.5 6.9 7.2 7.5 7.8 8.2 8.5 8.8 9.2 9.5 9.8 10.1 10.5 10.8 11.1 11.4 11.8 12.1 12.4 12.7 13.1 13.4 13.7 14.1 14.4 14.7 15.0 15.4 15.7 16.0 16.3 16.7 17.0 17.3 17.6 18.0 18.3 18.6 19.0 19.3 19.6 19.9 20.3 20.6 20.9 21.2 21.6 21.9 22.2 22.5 22.9 23.2 23.5 23.9 24.2 24.5 24.8 25.2 25.5 25.8 26.1 26.5 26.8 27.1 27.5 27.8 28.1 28.4 28.8 29.1 29.4 29.7 30.1 30.4 30.7 31.0 31.4 31.7 32.0 32.4 32.7 33.0 33.3 33.7 34.0 34.3 34.6 35.0 35.3 35.6 35.9 36.3 36.6 36.9 37.3 37.6 37.9 38.2 38.6 38.9 39.2 39.5 39.9 40.2 40.5 40.8 41.2 41.5 41.8 42.2 42.5 42.8 43.1 43.5 43.8 44.1 44.4 44.8 45.1 45.4 45.8 46.1 46.4 46.7 47.1 47.4 47.7 48.0 48.4 48.7 49.0 49.3 49.7 50.0 50.3 50.7 51.0 51.3 51.6 52.0 52.3 52.6 52.9 53.3 53.6 53.9 54.2 54.6 54.9 55.2 55.6 55.9 56.2 56.5 56.9 57.2 57.5 57.8 58.2 58.5 58.8 59.2 59.5 59.8 60.1 60.5 60.8 61.1 61.4 61.8 62.1 62.4 62.7 63.1 63.4 63.7 64.1 64.4 64.7 65.0 65.4 65.7 66.0 66.3 66.7 67.0 67.3 67.6 68.0 68.3 68.6 69.0 69.3 69.6 69.9 70.3 70.6 70.9 71.2 71.6 71.9 72.2 72.5 72.9 73.2 73.5 73.9 74.2 74.5 74.8 75.2 75.5 75.8 76.1 76.5 76.8 77.1 77.5 77.8 78.1 78.4 78.8 79.1 79.4 79.7 80.1 80.4 80.7 81.0 81.4 81.7 82.0 82.4 82.7 83.0 83.3 83.7 84.0 84.3 84.6 85.0 85.3 85.6 85.9 86.3 86.6 86.9 87.3 87.6 87.9 88.2 88.6 88.9 89.2 89.5 89.9 90.2 90.5 90.8 91.2 91.5 91.8 92.2 92.5 92.8 93.1 93.5 93.8 94.1 94.4 94.8 95.1 95.4 95.8 96.1 96.4 96.7 97.1 97.4 97.7 98.0 98.4 98.7 99.0 99.3 99.7 -found 19 predictions from path traversal Error with prediction: snap lend_intergenic: 4992, rend_intergenic: 3284 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 14652, rend_intergenic: 5530 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24284, rend_intergenic: 15802 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31196, rend_intergenic: 27783 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 32684, rend_intergenic: 32061 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40610, rend_intergenic: 32740 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48273, rend_intergenic: 46235 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50627, rend_intergenic: 48278 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51439, rend_intergenic: 50649 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91327, rend_intergenic: 64869 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 93550, rend_intergenic: 91708 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 95249, rend_intergenic: 94062 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100891, rend_intergenic: 95420 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 103614, rend_intergenic: 100891 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 109421, rend_intergenic: 106916 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110426, rend_intergenic: 109691 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 121133, rend_intergenic: 111213 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125407, rend_intergenic: 123003 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 130010, rend_intergenic: 126300 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 144302, rend_intergenic: 130111 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 145717, rend_intergenic: 144383 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 162530, rend_intergenic: 145867 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 8 predictions persist after filtering for low support -building DP trellis -building trellis in range 158230 - 170896 -exon list size: 17 building trellis 5.3 10.5 15.8 21.1 26.3 31.6 36.8 42.1 47.4 52.6 57.9 63.2 68.4 73.7 78.9 84.2 89.5 94.7 -found 3 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support