-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_2341024-2552284 -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_6-snap.582-T1 Valid prediction for snap_scaffold_6-snap.589-T1 Valid prediction for GlimmerHMM_glimmerT_14171-T1 Valid prediction for GlimmerHMM_glimmerT_14169-T1 Valid prediction for CodingQuarry_transcript_54942-T1 Valid prediction for HiQ_model.g9397.t1 Valid prediction for snap_scaffold_6-snap.563-T1 Valid prediction for GlimmerHMM_glimmerT_14172-T1 Valid prediction for snap_scaffold_6-snap.554-T1 Couldn't classify 161544, 161906 Sorry, prediction pasa_asmbl_46761.p1 fails validation. (CCT) CT 161544-161906 AG AAA Valid prediction for Augustus_model.g9396.t1 Valid prediction for snap_scaffold_6-snap.573-T1 Valid prediction for GlimmerHMM_glimmerT_14168-T1 Valid prediction for snap_scaffold_6-snap.581-T1 Valid prediction for snap_scaffold_6-snap.550-T1 Valid prediction for GlimmerHMM_glimmerT_14185-T1 Valid prediction for pasa_asmbl_46762.p1 Valid prediction for GlimmerHMM_glimmerT_14178-T1 Valid prediction for Augustus_model.g9390.t1 Valid prediction for snap_scaffold_6-snap.559-T1 Valid prediction for snap_scaffold_6-snap.578-T1 Valid prediction for GlimmerHMM_glimmerT_14175-T1 Valid prediction for GlimmerHMM_glimmerT_14162-T1 Valid prediction for snap_scaffold_6-snap.544-T1 Valid prediction for snap_scaffold_6-snap.543-T1 Valid prediction for CodingQuarry_transcript_54941-T1 Valid prediction for GlimmerHMM_glimmerT_14182-T1 Valid prediction for GlimmerHMM_glimmerT_14179-T1 Valid prediction for snap_scaffold_6-snap.579-T1 Valid prediction for snap_scaffold_6-snap.565-T1 Valid prediction for snap_scaffold_6-snap.557-T1 Valid prediction for snap_scaffold_6-snap.561-T1 Valid prediction for GlimmerHMM_glimmerT_14181-T1 Valid prediction for GlimmerHMM_glimmerT_14160-T1 Valid prediction for snap_scaffold_6-snap.576-T1 Valid prediction for snap_scaffold_6-snap.548-T1 Valid prediction for snap_scaffold_6-snap.542-T1 Valid prediction for snap_scaffold_6-snap.566-T1 Valid prediction for GlimmerHMM_glimmerT_14164-T1 Valid prediction for Augustus_model.g9387.t1 Valid prediction for snap_scaffold_6-snap.545-T1 Valid prediction for GlimmerHMM_glimmerT_14170-T1 Valid prediction for Augustus_model.g9394.t1 Valid prediction for snap_scaffold_6-snap.562-T1 Valid prediction for snap_scaffold_6-snap.551-T1 Valid prediction for snap_scaffold_6-snap.593-T1 Valid prediction for snap_scaffold_6-snap.571-T1 Valid prediction for GlimmerHMM_glimmerT_14167-T1 Valid prediction for snap_scaffold_6-snap.585-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for Augustus_model.g9389.t1 Valid prediction for snap_scaffold_6-snap.587-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_6-snap.555-T1 Valid prediction for snap_scaffold_6-snap.541-T1 Valid prediction for Augustus_model.g9401.t1 Valid prediction for snap_scaffold_6-snap.569-T1 Valid prediction for snap_scaffold_6-snap.547-T1 Valid prediction for Augustus_model.g9400.t1 Valid prediction for snap_scaffold_6-snap.577-T1 Valid prediction for CodingQuarry_transcript_54939-T1 Valid prediction for snap_scaffold_6-snap.553-T1 Valid prediction for snap_scaffold_6-snap.549-T1 Valid prediction for snap_scaffold_6-snap.540-T1 Couldn't classify 4832, 5025 Couldn't classify 8018, 8158 Sorry, prediction pasa_asmbl_49435.p1 fails validation. (TGC) GG 4832-5025 GT AGG (TGC) AG 5233-5386 GT AGG (GAT) AG 6287-6433 GT AGG (AAC) AG 8018-8158 AG GCA -recovered pasa_asmbl_49435.p1, internal, 5233, 5386 -recovered pasa_asmbl_49435.p1, internal, 6287, 6433 Valid prediction for Augustus_model.g9398.t1 Valid prediction for snap_scaffold_6-snap.570-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_14163-T1 Valid prediction for snap_scaffold_6-snap.588-T1 Valid prediction for snap_scaffold_6-snap.572-T1 Valid prediction for GlimmerHMM_glimmerT_14177-T1 Valid prediction for GlimmerHMM_glimmerT_14166-T1 Valid prediction for snap_scaffold_6-snap.567-T1 Valid prediction for GlimmerHMM_glimmerT_14183-T1 Valid prediction for snap_scaffold_6-snap.575-T1 Valid prediction for Augustus_model.g9388.t1 Valid prediction for GlimmerHMM_glimmerT_14161-T1 Valid prediction for snap_scaffold_6-snap.592-T1 Valid prediction for Augustus_model.g9399.t1 Valid prediction for snap_scaffold_6-snap.558-T1 Valid prediction for snap_scaffold_6-snap.552-T1 Valid prediction for snap_scaffold_6-snap.584-T1 Valid prediction for GlimmerHMM_glimmerT_14184-T1 Valid prediction for GlimmerHMM_glimmerT_14165-T1 Couldn't classify 69649, 69882 Sorry, prediction pasa_asmbl_48127.p1 fails validation. (AAA) AG 69649-69882 GT AGG (AAT) AG 70432-70549 GT AGG (AGC) AG 72186-72265 GT ATG (TAC) AG 73388-73559 GT AAG (TGT) AG 73832-73899 GT AGG (AGC) AG 74929-75009 CT AAC -recovered pasa_asmbl_48127.p1, terminal, 74929, 75009 -recovered pasa_asmbl_48127.p1, internal, 69649, 69882 -recovered pasa_asmbl_48127.p1, internal, 70432, 70549 -recovered pasa_asmbl_48127.p1, internal, 72186, 72265 -recovered pasa_asmbl_48127.p1, internal, 73388, 73559 -recovered pasa_asmbl_48127.p1, internal, 73832, 73899 Valid prediction for Augustus_model.g9391.t1 Valid prediction for CodingQuarry_transcript_54938-T1 Valid prediction for HiQ_model.g9393.t1 Valid prediction for snap_scaffold_6-snap.580-T1 Valid prediction for GlimmerHMM_glimmerT_14186-T1 Valid prediction for snap_scaffold_6-snap.538-T1 Valid prediction for snap_scaffold_6-snap.564-T1 Valid prediction for snap_scaffold_6-snap.586-T1 Valid prediction for GlimmerHMM_glimmerT_14176-T1 Valid prediction for snap_scaffold_6-snap.568-T1 Valid prediction for snap_scaffold_6-snap.560-T1 Valid prediction for snap_scaffold_6-snap.556-T1 Valid prediction for GlimmerHMM_glimmerT_14174-T1 Valid prediction for snap_scaffold_6-snap.583-T1 Valid prediction for GlimmerHMM_glimmerT_14180-T1 Valid prediction for snap_scaffold_6-snap.590-T1 Valid prediction for snap_scaffold_6-snap.546-T1 Couldn't classify 25047, 25279 Sorry, prediction pasa_asmbl_48139.p1 fails validation. (ATG) CC 23596-23710 GT AGG (CGT) AG 25047-25279 CT CCC -recovered pasa_asmbl_48139.p1, initial, 23596, 23710 Valid prediction for GlimmerHMM_glimmerT_14173-T1 Valid prediction for snap_scaffold_6-snap.591-T1 Valid prediction for Augustus_model.g9392.t1 Valid prediction for snap_scaffold_6-snap.574-T1 Couldn't classify 30995, 31213 Sorry, prediction pasa_asmbl_48136.p1 fails validation. (GCC) CA 30995-31213 GT AGG (GAC) AG 32507-32722 AC GAA -recovered pasa_asmbl_48136.p1, terminal, 32507, 32722 Valid prediction for snap_scaffold_6-snap.539-T1 Valid prediction for Augustus_model.g9395.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29939, rend_intergenic: 24204 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 39274, rend_intergenic: 35547 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47358, rend_intergenic: 40347 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50116, rend_intergenic: 48319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 56376, rend_intergenic: 50216 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59176, rend_intergenic: 56781 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59776, rend_intergenic: 59310 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 64639, rend_intergenic: 59830 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 69024, rend_intergenic: 65132 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 72140, rend_intergenic: 70996 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76826, rend_intergenic: 72251 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81998, rend_intergenic: 78058 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91975, rend_intergenic: 90792 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105559, rend_intergenic: 99937 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118836, rend_intergenic: 118132 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123829, rend_intergenic: 119183 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127864, rend_intergenic: 123834 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 141508, rend_intergenic: 138150 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 152743, rend_intergenic: 146190 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 161906, rend_intergenic: 159046 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 173287, rend_intergenic: 171107 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179526, rend_intergenic: 177428 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 180451, rend_intergenic: 179587 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 187657, rend_intergenic: 180508 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 193375, rend_intergenic: 189394 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 195850, rend_intergenic: 193707 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 208475, rend_intergenic: 203237 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 211261 -exon list size: 335 building trellis 0.3 0.6 0.9 1.2 1.5 1.8 2.1 2.4 2.7 3.0 3.3 3.6 3.9 4.2 4.5 4.7 5.0 5.3 5.6 5.9 6.2 6.5 6.8 7.1 7.4 7.7 8.0 8.3 8.6 8.9 9.2 9.5 9.8 10.1 10.4 10.7 11.0 11.3 11.6 11.9 12.2 12.5 12.8 13.1 13.4 13.6 13.9 14.2 14.5 14.8 15.1 15.4 15.7 16.0 16.3 16.6 16.9 17.2 17.5 17.8 18.1 18.4 18.7 19.0 19.3 19.6 19.9 20.2 20.5 20.8 21.1 21.4 21.7 22.0 22.3 22.6 22.8 23.1 23.4 23.7 24.0 24.3 24.6 24.9 25.2 25.5 25.8 26.1 26.4 26.7 27.0 27.3 27.6 27.9 28.2 28.5 28.8 29.1 29.4 29.7 30.0 30.3 30.6 30.9 31.2 31.5 31.8 32.0 32.3 32.6 32.9 33.2 33.5 33.8 34.1 34.4 34.7 35.0 35.3 35.6 35.9 36.2 36.5 36.8 37.1 37.4 37.7 38.0 38.3 38.6 38.9 39.2 39.5 39.8 40.1 40.4 40.7 40.9 41.2 41.5 41.8 42.1 42.4 42.7 43.0 43.3 43.6 43.9 44.2 44.5 44.8 45.1 45.4 45.7 46.0 46.3 46.6 46.9 47.2 47.5 47.8 48.1 48.4 48.7 49.0 49.3 49.6 49.9 50.1 50.4 50.7 51.0 51.3 51.6 51.9 52.2 52.5 52.8 53.1 53.4 53.7 54.0 54.3 54.6 54.9 55.2 55.5 55.8 56.1 56.4 56.7 57.0 57.3 57.6 57.9 58.2 58.5 58.8 59.1 59.3 59.6 59.9 60.2 60.5 60.8 61.1 61.4 61.7 62.0 62.3 62.6 62.9 63.2 63.5 63.8 64.1 64.4 64.7 65.0 65.3 65.6 65.9 66.2 66.5 66.8 67.1 67.4 67.7 68.0 68.2 68.5 68.8 69.1 69.4 69.7 70.0 70.3 70.6 70.9 71.2 71.5 71.8 72.1 72.4 72.7 73.0 73.3 73.6 73.9 74.2 74.5 74.8 75.1 75.4 75.7 76.0 76.3 76.6 76.9 77.2 77.4 77.7 78.0 78.3 78.6 78.9 79.2 79.5 79.8 80.1 80.4 80.7 81.0 81.3 81.6 81.9 82.2 82.5 82.8 83.1 83.4 83.7 84.0 84.3 84.6 84.9 85.2 85.5 85.8 86.1 86.4 86.6 86.9 87.2 87.5 87.8 88.1 88.4 88.7 89.0 89.3 89.6 89.9 90.2 90.5 90.8 91.1 91.4 91.7 92.0 92.3 92.6 92.9 93.2 93.5 93.8 94.1 94.4 94.7 95.0 95.3 95.5 95.8 96.1 96.4 96.7 97.0 97.3 97.6 97.9 98.2 98.5 98.8 99.1 99.4 99.7 -found 30 predictions from path traversal Error with prediction: snap lend_intergenic: 29939, rend_intergenic: 24204 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 39274, rend_intergenic: 35547 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 47358, rend_intergenic: 40347 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 50116, rend_intergenic: 48319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 56376, rend_intergenic: 50216 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59176, rend_intergenic: 56781 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 59776, rend_intergenic: 59310 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 64639, rend_intergenic: 59830 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 69024, rend_intergenic: 65132 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 72140, rend_intergenic: 70996 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 76826, rend_intergenic: 72251 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81998, rend_intergenic: 78058 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91975, rend_intergenic: 90792 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105559, rend_intergenic: 99937 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118836, rend_intergenic: 118132 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123829, rend_intergenic: 119183 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127864, rend_intergenic: 123834 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 141508, rend_intergenic: 138150 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 152743, rend_intergenic: 146190 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 161906, rend_intergenic: 159046 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 173287, rend_intergenic: 171107 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179526, rend_intergenic: 177428 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 180451, rend_intergenic: 179587 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 187657, rend_intergenic: 180508 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 193375, rend_intergenic: 189394 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 195850, rend_intergenic: 193707 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 208475, rend_intergenic: 203237 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 16 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 22634 -exon list size: 11 building trellis 7.7 15.4 23.1 30.8 38.5 46.2 53.8 61.5 69.2 76.9 84.6 92.3 -found 2 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 - 21795 -exon list size: 8 building trellis 10.0 20.0 30.0 40.0 50.0 60.0 70.0 80.0 90.0 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 21720 -exon list size: 7 building trellis 11.1 22.2 33.3 44.4 55.6 66.7 77.8 88.9 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 3733 - 21720 -exon list size: 5 building trellis 14.3 28.6 42.9 57.1 71.4 85.7 -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 3733 - 15691 -exon list size: 3 building trellis 20.0 40.0 60.0 80.0 -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 4114 - 15691 -exon list size: 2 building trellis 25.0 50.0 75.0 -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