-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_6158340-6376697 -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 CodingQuarry_transcript_35688-T1 Valid prediction for snap_scaffold_23-snap.1136-T1 Valid prediction for snap_scaffold_23-snap.1106-T1 Valid prediction for GlimmerHMM_glimmerT_51133-T1 Valid prediction for snap_scaffold_23-snap.1119-T1 Couldn't classify 184980, 185188 Couldn't classify 185210, 185453 Sorry, prediction CodingQuarry_transcript_35687-T1 fails validation. (ATG) CC 184980-185188 GA GAG (CTC) AT 185210-185453 AC AGA Couldn't classify 174684, 175321 Couldn't classify 175487, 175672 Sorry, prediction CodingQuarry_transcript_35684-T1 fails validation. (ATG) CC 170430-170577 GT AGG (CAC) AG 170842-170981 GT AGG (GGC) AG 171203-171301 GT GAG (GTG) AG 171478-171609 GT AGG (GCC) AG 171709-171792 GT AGG (GGT) AG 172058-172084 GT AGG (AAT) AG 172167-172214 GT AAG (CCG) AG 172540-172602 GT CAG (TCT) AG 174461-174587 GC AGG (GCA) AG 174684-175321 AA ACA (GAC) AA 175487-175672 GT TGG (GCT) AG 175780-175851 AT AAA -recovered CodingQuarry_transcript_35684-T1, initial, 170430, 170577 add_exon() Sorry, CodingQuarry_transcript_35684-T1 174461-174587-terminal-3 is invalid. -recovered CodingQuarry_transcript_35684-T1, terminal, 174461, 174587 -recovered CodingQuarry_transcript_35684-T1, terminal, 175780, 175851 -recovered CodingQuarry_transcript_35684-T1, internal, 170842, 170981 -recovered CodingQuarry_transcript_35684-T1, internal, 171203, 171301 -recovered CodingQuarry_transcript_35684-T1, internal, 171478, 171609 -recovered CodingQuarry_transcript_35684-T1, internal, 171709, 171792 -recovered CodingQuarry_transcript_35684-T1, internal, 172058, 172084 -recovered CodingQuarry_transcript_35684-T1, internal, 172167, 172214 -recovered CodingQuarry_transcript_35684-T1, internal, 172540, 172602 -recovered CodingQuarry_transcript_35684-T1, internal, 174461, 174587 Valid prediction for snap_scaffold_23-snap.1146-T1 Valid prediction for GlimmerHMM_glimmerT_51145-T1 Valid prediction for Augustus_model.g34206.t1 Valid prediction for snap_scaffold_23-snap.1141-T1 Valid prediction for snap_scaffold_23-snap.1131-T1 Couldn't classify 183174, 183221 Couldn't classify 183684, 184423 Sorry, prediction pasa_asmbl_31621.p1 fails validation. (GGG) GG 183174-183221 GT TTG (GAT) AG 183367-183403 GT GGG (AGA) AG 183498-183581 GT AGG (AAA) AG 183684-184423 GA CTG -recovered pasa_asmbl_31621.p1, internal, 183367, 183403 -recovered pasa_asmbl_31621.p1, internal, 183498, 183581 Valid prediction for snap_scaffold_23-snap.1142-T1 Valid prediction for snap_scaffold_23-snap.1114-T1 Valid prediction for GlimmerHMM_glimmerT_51149-T1 Valid prediction for snap_scaffold_23-snap.1143-T1 Valid prediction for snap_scaffold_23-snap.1139-T1 Valid prediction for snap_scaffold_23-snap.1123-T1 Valid prediction for pasa_asmbl_31613.p1 Valid prediction for GlimmerHMM_glimmerT_51146-T1 Valid prediction for snap_scaffold_23-snap.1122-T1 Valid prediction for snap_scaffold_23-snap.1125-T1 Valid prediction for Augustus_model.g34221.t1 Valid prediction for GlimmerHMM_glimmerT_51139-T1 Valid prediction for Augustus_model.g34218.t1 Couldn't classify 126177, 126431 Sorry, prediction pasa_asmbl_31609.p1 fails validation. (GTC) CA 126177-126431 GT AGG (GGT) AG 126729-126821 GT AGG (ACA) AG 126892-127032 GT CAG (TCC) AG 127148-127285 GT CGG (GAT) AG 127571-127690 GT AGG (CTG) AG 127893-128081 GC GAG -recovered pasa_asmbl_31609.p1, terminal, 127893, 128081 -recovered pasa_asmbl_31609.p1, internal, 126729, 126821 -recovered pasa_asmbl_31609.p1, internal, 126892, 127032 -recovered pasa_asmbl_31609.p1, internal, 127148, 127285 -recovered pasa_asmbl_31609.p1, internal, 127571, 127690 -recovered pasa_asmbl_31609.p1, internal, 127893, 128081 Valid prediction for GlimmerHMM_glimmerT_51129-T1 Valid prediction for GlimmerHMM_glimmerT_51135-T1 Valid prediction for Augustus_model.g34219.t1 Valid prediction for snap_scaffold_23-snap.1133-T1 Valid prediction for snap_scaffold_23-snap.1111-T1 Valid prediction for GlimmerHMM_glimmerT_51144-T1 Valid prediction for snap_scaffold_23-snap.1109-T1 Valid prediction for CodingQuarry_transcript_35686-T1 Valid prediction for snap_scaffold_23-snap.1130-T1 Valid prediction for CodingQuarry_transcript_35685-T1 Valid prediction for Augustus_model.g34205.t1 Valid prediction for pasa_asmbl_31617.p1 Valid prediction for snap_scaffold_23-snap.1105-T1 Couldn't classify 174684, 175321 Couldn't classify 175487, 175672 Sorry, prediction CodingQuarry_transcript_35683-T1 fails validation. (ATG) CC 170430-170577 GT AGG (CAC) AG 170842-170981 GT AGG (GGC) AG 171203-171301 GT GAG (GTG) AG 171478-171609 GT AGG (GCC) AG 171709-171792 GT AGG (GGT) AG 172058-172084 GT AGG (AAT) AG 172167-172214 GT AAG (CCG) AG 172540-172602 GT CAG (GAG) AG 173221-173835 GT AGG (TCT) AG 174461-174587 GC AGG (GCA) AG 174684-175321 AA ACA (GAC) AA 175487-175672 GT TGG (GCT) AG 175780-175851 AT AAA -recovered CodingQuarry_transcript_35683-T1, initial, 170430, 170577 add_exon() Sorry, CodingQuarry_transcript_35683-T1 174461-174587-terminal-3 is invalid. -recovered CodingQuarry_transcript_35683-T1, terminal, 174461, 174587 -recovered CodingQuarry_transcript_35683-T1, terminal, 175780, 175851 -recovered CodingQuarry_transcript_35683-T1, internal, 170842, 170981 -recovered CodingQuarry_transcript_35683-T1, internal, 171203, 171301 -recovered CodingQuarry_transcript_35683-T1, internal, 171478, 171609 -recovered CodingQuarry_transcript_35683-T1, internal, 171709, 171792 -recovered CodingQuarry_transcript_35683-T1, internal, 172058, 172084 -recovered CodingQuarry_transcript_35683-T1, internal, 172167, 172214 -recovered CodingQuarry_transcript_35683-T1, internal, 172540, 172602 -recovered CodingQuarry_transcript_35683-T1, internal, 173221, 173835 -recovered CodingQuarry_transcript_35683-T1, internal, 174461, 174587 Couldn't classify 181630, 181691 Couldn't classify 182389, 182731 Sorry, prediction pasa_asmbl_31620.p1 fails validation. (GAG) AT 181630-181691 GT AGG (CTC) AG 181788-181992 GT AGG (GAG) AG 182123-182250 GT CGG (GTA) AG 182389-182731 AG ACA -recovered pasa_asmbl_31620.p1, internal, 181788, 181992 -recovered pasa_asmbl_31620.p1, internal, 182123, 182250 Valid prediction for CodingQuarry_transcript_35689-T1 Valid prediction for snap_scaffold_23-snap.1110-T1 Valid prediction for pasa_asmbl_31622.p1 Valid prediction for Augustus_model.g34217.t1 Couldn't classify 179622, 179713 Couldn't classify 181628, 181644 Sorry, prediction pasa_asmbl_31618.p1 fails validation. (GAC) AA 179622-179713 GT AGG (TCT) AG 180268-180401 GT AGG (AGA) AG 180674-180768 GT AGG (AAC) AG 180869-180923 GT CAG (GAG) AG 181008-181154 GT AGG (CCA) AG 181312-181521 GT AGG (ATG) AG 181628-181644 GA CTG -recovered pasa_asmbl_31618.p1, internal, 180268, 180401 -recovered pasa_asmbl_31618.p1, internal, 180674, 180768 -recovered pasa_asmbl_31618.p1, internal, 180869, 180923 -recovered pasa_asmbl_31618.p1, internal, 181008, 181154 -recovered pasa_asmbl_31618.p1, internal, 181312, 181521 Valid prediction for Augustus_model.g34214.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_23-snap.1121-T1 Valid prediction for GlimmerHMM_glimmerT_51136-T1 Valid prediction for snap_scaffold_23-snap.1115-T1 Valid prediction for snap_scaffold_23-snap.1116-T1 Valid prediction for GlimmerHMM_glimmerT_51140-T1 Valid prediction for GlimmerHMM_glimmerT_51143-T1 Valid prediction for snap_scaffold_23-snap.1132-T1 Valid prediction for GlimmerHMM_glimmerT_51147-T1 Valid prediction for Augustus_model.g34210.t1 Valid prediction for GlimmerHMM_glimmerT_51132-T1 Valid prediction for snap_scaffold_23-snap.1127-T1 Valid prediction for snap_scaffold_23-snap.1137-T1 Valid prediction for snap_scaffold_23-snap.1144-T1 Valid prediction for Augustus_model.g34213.t1 Valid prediction for GlimmerHMM_glimmerT_51131-T1 Valid prediction for snap_scaffold_23-snap.1134-T1 Valid prediction for GlimmerHMM_glimmerT_51138-T1 Valid prediction for Augustus_model.g34208.t1 Valid prediction for snap_scaffold_23-snap.1113-T1 Valid prediction for GlimmerHMM_glimmerT_51141-T1 Valid prediction for snap_scaffold_23-snap.1126-T1 Valid prediction for HiQ_model.g34216.t1 Valid prediction for Augustus_model.g34207.t1 Valid prediction for Augustus_model.g34220.t1 Valid prediction for snap_scaffold_23-snap.1135-T1 Valid prediction for Augustus_model.g34209.t1 Valid prediction for snap_scaffold_23-snap.1140-T1 Valid prediction for Augustus_model.g34215.t1 Valid prediction for snap_scaffold_23-snap.1107-T1 Valid prediction for Augustus_model.g34211.t1 Valid prediction for snap_scaffold_23-snap.1118-T1 Valid prediction for CodingQuarry_transcript_35680-T1 Valid prediction for snap_scaffold_23-snap.1138-T1 Valid prediction for GlimmerHMM_glimmerT_51134-T1 Valid prediction for snap_scaffold_23-snap.1120-T1 Valid prediction for GlimmerHMM_glimmerT_51130-T1 Valid prediction for pasa_asmbl_30968.p1 Valid prediction for snap_scaffold_23-snap.1128-T1 Valid prediction for GlimmerHMM_glimmerT_51142-T1 Valid prediction for snap_scaffold_23-snap.1124-T1 Valid prediction for CodingQuarry_transcript_35682-T1 Valid prediction for GlimmerHMM_glimmerT_51148-T1 Valid prediction for snap_scaffold_23-snap.1129-T1 Valid prediction for snap_scaffold_23-snap.1117-T1 Couldn't classify 58503, 58621 Sorry, prediction pasa_asmbl_30976.p1 fails validation. (CTG) GA 58503-58621 GT ATG (CCC) AG 58945-59044 GT AGG (CGC) AG 59293-59443 GT AGG (GTT) AG 59599-59743 GT GGG (AAT) AG 59877-60015 GT AGG (ACT) AG 60235-60468 GT AGG (AAA) AG 60724-60964 GT AAG (AAA) AG 61081-61212 GT AGG (ACT) AG 61319-61494 GT AGG (CCG) AG 61803-62025 GT GCG (GTC) AG 62244-62401 AC AAA -recovered pasa_asmbl_30976.p1, terminal, 62244, 62401 -recovered pasa_asmbl_30976.p1, internal, 58945, 59044 -recovered pasa_asmbl_30976.p1, internal, 59293, 59443 -recovered pasa_asmbl_30976.p1, internal, 59599, 59743 -recovered pasa_asmbl_30976.p1, internal, 59877, 60015 -recovered pasa_asmbl_30976.p1, internal, 60235, 60468 -recovered pasa_asmbl_30976.p1, internal, 60724, 60964 -recovered pasa_asmbl_30976.p1, internal, 61081, 61212 -recovered pasa_asmbl_30976.p1, internal, 61319, 61494 -recovered pasa_asmbl_30976.p1, internal, 61803, 62025 Valid prediction for snap_scaffold_23-snap.1108-T1 Valid prediction for snap_scaffold_23-snap.1145-T1 Valid prediction for GlimmerHMM_glimmerT_51137-T1 Valid prediction for Augustus_model.g34212.t1 Valid prediction for snap_scaffold_23-snap.1112-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14670, rend_intergenic: 9159 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 17856, rend_intergenic: 14940 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40877, rend_intergenic: 39857 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51334, rend_intergenic: 41408 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68202, rend_intergenic: 67436 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 84162, rend_intergenic: 81935 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 86663, rend_intergenic: 85146 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 111507, rend_intergenic: 108482 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128081, rend_intergenic: 126367 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140330, rend_intergenic: 139011 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 195262, rend_intergenic: 191424 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 218358 -exon list size: 344 building trellis 0.3 0.6 0.9 1.2 1.4 1.7 2.0 2.3 2.6 2.9 3.2 3.5 3.8 4.0 4.3 4.6 4.9 5.2 5.5 5.8 6.1 6.4 6.6 6.9 7.2 7.5 7.8 8.1 8.4 8.7 9.0 9.2 9.5 9.8 10.1 10.4 10.7 11.0 11.3 11.6 11.8 12.1 12.4 12.7 13.0 13.3 13.6 13.9 14.2 14.5 14.7 15.0 15.3 15.6 15.9 16.2 16.5 16.8 17.1 17.3 17.6 17.9 18.2 18.5 18.8 19.1 19.4 19.7 19.9 20.2 20.5 20.8 21.1 21.4 21.7 22.0 22.3 22.5 22.8 23.1 23.4 23.7 24.0 24.3 24.6 24.9 25.1 25.4 25.7 26.0 26.3 26.6 26.9 27.2 27.5 27.7 28.0 28.3 28.6 28.9 29.2 29.5 29.8 30.1 30.3 30.6 30.9 31.2 31.5 31.8 32.1 32.4 32.7 32.9 33.2 33.5 33.8 34.1 34.4 34.7 35.0 35.3 35.5 35.8 36.1 36.4 36.7 37.0 37.3 37.6 37.9 38.2 38.4 38.7 39.0 39.3 39.6 39.9 40.2 40.5 40.8 41.0 41.3 41.6 41.9 42.2 42.5 42.8 43.1 43.4 43.6 43.9 44.2 44.5 44.8 45.1 45.4 45.7 46.0 46.2 46.5 46.8 47.1 47.4 47.7 48.0 48.3 48.6 48.8 49.1 49.4 49.7 50.0 50.3 50.6 50.9 51.2 51.4 51.7 52.0 52.3 52.6 52.9 53.2 53.5 53.8 54.0 54.3 54.6 54.9 55.2 55.5 55.8 56.1 56.4 56.6 56.9 57.2 57.5 57.8 58.1 58.4 58.7 59.0 59.2 59.5 59.8 60.1 60.4 60.7 61.0 61.3 61.6 61.8 62.1 62.4 62.7 63.0 63.3 63.6 63.9 64.2 64.5 64.7 65.0 65.3 65.6 65.9 66.2 66.5 66.8 67.1 67.3 67.6 67.9 68.2 68.5 68.8 69.1 69.4 69.7 69.9 70.2 70.5 70.8 71.1 71.4 71.7 72.0 72.3 72.5 72.8 73.1 73.4 73.7 74.0 74.3 74.6 74.9 75.1 75.4 75.7 76.0 76.3 76.6 76.9 77.2 77.5 77.7 78.0 78.3 78.6 78.9 79.2 79.5 79.8 80.1 80.3 80.6 80.9 81.2 81.5 81.8 82.1 82.4 82.7 82.9 83.2 83.5 83.8 84.1 84.4 84.7 85.0 85.3 85.5 85.8 86.1 86.4 86.7 87.0 87.3 87.6 87.9 88.2 88.4 88.7 89.0 89.3 89.6 89.9 90.2 90.5 90.8 91.0 91.3 91.6 91.9 92.2 92.5 92.8 93.1 93.4 93.6 93.9 94.2 94.5 94.8 95.1 95.4 95.7 96.0 96.2 96.5 96.8 97.1 97.4 97.7 98.0 98.3 98.6 98.8 99.1 99.4 99.7 -found 33 predictions from path traversal Error with prediction: snap lend_intergenic: 14670, rend_intergenic: 9159 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 17856, rend_intergenic: 14940 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 40877, rend_intergenic: 39857 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 51334, rend_intergenic: 41408 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 68202, rend_intergenic: 67436 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 84162, rend_intergenic: 81935 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 86663, rend_intergenic: 85146 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 111507, rend_intergenic: 108482 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 128081, rend_intergenic: 126367 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140330, rend_intergenic: 139011 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 195262, rend_intergenic: 191424 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 24 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 11630 -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 2 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 1 predictions persist after filtering for low support