-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_3654898-3839024 -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 148972, 149054 Couldn't classify 154634, 154950 Sorry, prediction pasa_asmbl_39975.p1 fails validation. (CCC) GC 148972-149054 GT GGG (TCA) AG 149660-149841 GT AGG (AGA) AG 150049-150089 GT TGG (AAA) AG 151267-151312 GT CGG (TTC) AG 152068-152139 GT CGG (CTG) AG 152396-152473 GT CGG (GAA) AG 154634-154950 TC AGT -recovered pasa_asmbl_39975.p1, internal, 149660, 149841 -recovered pasa_asmbl_39975.p1, internal, 150049, 150089 -recovered pasa_asmbl_39975.p1, internal, 151267, 151312 -recovered pasa_asmbl_39975.p1, internal, 152068, 152139 -recovered pasa_asmbl_39975.p1, internal, 152396, 152473 Valid prediction for GlimmerHMM_glimmerT_6302-T1 Valid prediction for snap_scaffold_3-snap.813-T1 Valid prediction for snap_scaffold_3-snap.796-T1 Valid prediction for Augustus_model.g4094.t1 Valid prediction for GlimmerHMM_glimmerT_6301-T1 Valid prediction for GlimmerHMM_glimmerT_6319-T1 Valid prediction for snap_scaffold_3-snap.792-T1 Sorry, intron length (8) is less than minimum required (10) Valid prediction for snap_scaffold_3-snap.809-T1 Valid prediction for Augustus_model.g4100.t1 Valid prediction for GlimmerHMM_glimmerT_6324-T1 Valid prediction for Augustus_model.g4091.t1 Valid prediction for snap_scaffold_3-snap.819-T1 Valid prediction for GlimmerHMM_glimmerT_6314-T1 Valid prediction for Augustus_model.g4092.t1 Valid prediction for CodingQuarry_transcript_46121-T1 Valid prediction for snap_scaffold_3-snap.801-T1 Valid prediction for pasa_asmbl_39966.p1 Valid prediction for snap_scaffold_3-snap.811-T1 Valid prediction for snap_scaffold_3-snap.789-T1 Valid prediction for GlimmerHMM_glimmerT_6306-T1 Valid prediction for Augustus_model.g4098.t1 Valid prediction for snap_scaffold_3-snap.807-T1 Valid prediction for pasa_asmbl_39960.p1 Valid prediction for GlimmerHMM_glimmerT_6310-T1 Valid prediction for HiQ_model.g4096.t1 Valid prediction for Augustus_model.g4099.t1 Couldn't classify 95732, 95890 Sorry, prediction pasa_asmbl_39971.p1 fails validation. (CAG) TT 95732-95890 GT AGG (GAG) AG 96146-96276 GC AGG (TCT) AG 96425-96541 GT AAG (GTA) AG 96818-96937 GT ACG (GGC) AG 97182-97274 GT GAG (AGC) AG 97361-97539 GT GGG (GTG) AG 97857-97912 GT TGG (GAC) AG 98034-98077 GT AGG (ACC) AG 98253-98321 GT GAG (GTA) AG 98501-98651 GT AGG (GAT) AG 98875-99027 GA AGG -recovered pasa_asmbl_39971.p1, terminal, 98875, 99027 -recovered pasa_asmbl_39971.p1, internal, 96146, 96276 -recovered pasa_asmbl_39971.p1, internal, 96425, 96541 -recovered pasa_asmbl_39971.p1, internal, 96818, 96937 -recovered pasa_asmbl_39971.p1, internal, 97182, 97274 -recovered pasa_asmbl_39971.p1, internal, 97361, 97539 -recovered pasa_asmbl_39971.p1, internal, 97857, 97912 -recovered pasa_asmbl_39971.p1, internal, 98034, 98077 -recovered pasa_asmbl_39971.p1, internal, 98253, 98321 -recovered pasa_asmbl_39971.p1, internal, 98501, 98651 Valid prediction for snap_scaffold_3-snap.791-T1 Valid prediction for GlimmerHMM_glimmerT_6308-T1 Valid prediction for CodingQuarry_transcript_46120-T1 Couldn't classify 95183, 95557 Sorry, prediction pasa_asmbl_39970.p1 fails validation. (GAC) CA 95183-95557 CA CCC Valid prediction for HiQ_model.g4095.t1 Valid prediction for HiQ_model.g4093.t1 Valid prediction for GlimmerHMM_glimmerT_6313-T1 Valid prediction for snap_scaffold_3-snap.817-T1 Valid prediction for snap_scaffold_3-snap.797-T1 Couldn't classify 59944, 59994 Sorry, prediction pasa_asmbl_39958.p1 fails validation. (TTT) AG 59944-59994 GT AGG (ATT) AG 60070-60229 GT AGG (TGC) AG 60995-61125 GT TGG (ACC) AG 61605-62432 AA GAA -recovered pasa_asmbl_39958.p1, terminal, 61605, 62432 -recovered pasa_asmbl_39958.p1, internal, 59944, 59994 -recovered pasa_asmbl_39958.p1, internal, 60070, 60229 -recovered pasa_asmbl_39958.p1, internal, 60995, 61125 Valid prediction for snap_scaffold_3-snap.812-T1 Valid prediction for snap_scaffold_3-snap.815-T1 Valid prediction for snap_scaffold_3-snap.788-T1 Valid prediction for GlimmerHMM_glimmerT_6325-T1 Valid prediction for GlimmerHMM_glimmerT_6311-T1 Valid prediction for Augustus_model.g4104.t1 Valid prediction for GlimmerHMM_glimmerT_6309-T1 Valid prediction for Augustus_model.g4103.t1 Valid prediction for pasa_asmbl_39968.p1 Valid prediction for GlimmerHMM_glimmerT_6303-T1 Valid prediction for snap_scaffold_3-snap.800-T1 Valid prediction for snap_scaffold_3-snap.804-T1 Couldn't classify 70541, 70583 Sorry, prediction pasa_asmbl_39963.p1 fails validation. (TCC) TC 70541-70583 GT AAG (CGG) AG 71168-71316 GT AGG (TTC) AG 72251-72410 GT CGG (TGC) AG 73106-73221 GT TGG (TCG) AG 73470-73709 GT GAG -recovered pasa_asmbl_39963.p1, terminal, 73470, 73709 -recovered pasa_asmbl_39963.p1, internal, 71168, 71316 -recovered pasa_asmbl_39963.p1, internal, 72251, 72410 -recovered pasa_asmbl_39963.p1, internal, 73106, 73221 -recovered pasa_asmbl_39963.p1, internal, 73470, 73709 Valid prediction for snap_scaffold_3-snap.794-T1 Valid prediction for snap_scaffold_3-snap.793-T1 Valid prediction for snap_scaffold_3-snap.795-T1 Valid prediction for snap_scaffold_3-snap.803-T1 Valid prediction for snap_scaffold_3-snap.821-T1 Valid prediction for GlimmerHMM_glimmerT_6312-T1 Valid prediction for CodingQuarry_transcript_46122-T1 Valid prediction for Augustus_model.g4097.t1 Valid prediction for GlimmerHMM_glimmerT_6307-T1 Valid prediction for snap_scaffold_3-snap.802-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_6326-T1 Valid prediction for Augustus_model.g4102.t1 Valid prediction for GlimmerHMM_glimmerT_6315-T1 Valid prediction for GlimmerHMM_glimmerT_6318-T1 Valid prediction for snap_scaffold_3-snap.798-T1 Valid prediction for Augustus_model.g4105.t1 Valid prediction for snap_scaffold_3-snap.805-T1 Couldn't classify 8924, 9078 Sorry, prediction pasa_asmbl_38787.p1 fails validation. (ATG) CC 5755-5938 GT GGG (ACG) AG 6245-6328 GT TGG (TTA) AG 8212-8358 GT CGG (ACG) AG 8470-8637 GT AGG (TGC) AG 8924-9078 AC GTA -recovered pasa_asmbl_38787.p1, initial, 5755, 5938 -recovered pasa_asmbl_38787.p1, internal, 6245, 6328 -recovered pasa_asmbl_38787.p1, internal, 8212, 8358 -recovered pasa_asmbl_38787.p1, internal, 8470, 8637 Valid prediction for snap_scaffold_3-snap.816-T1 Valid prediction for snap_scaffold_3-snap.818-T1 Valid prediction for snap_scaffold_3-snap.808-T1 Valid prediction for snap_scaffold_3-snap.822-T1 Valid prediction for GlimmerHMM_glimmerT_6305-T1 Valid prediction for GlimmerHMM_glimmerT_6320-T1 Valid prediction for snap_scaffold_3-snap.820-T1 Valid prediction for snap_scaffold_3-snap.790-T1 Valid prediction for snap_scaffold_3-snap.806-T1 Valid prediction for HiQ_model.g4106.t1 Valid prediction for GlimmerHMM_glimmerT_6327-T1 Valid prediction for snap_scaffold_3-snap.810-T1 Valid prediction for GlimmerHMM_glimmerT_6323-T1 Valid prediction for GlimmerHMM_glimmerT_6316-T1 Valid prediction for snap_scaffold_3-snap.814-T1 Valid prediction for Augustus_model.g4090.t1 Valid prediction for Augustus_model.g4101.t1 Valid prediction for GlimmerHMM_glimmerT_6304-T1 Valid prediction for GlimmerHMM_glimmerT_6317-T1 Valid prediction for GlimmerHMM_glimmerT_6300-T1 Valid prediction for GlimmerHMM_glimmerT_6322-T1 Valid prediction for snap_scaffold_3-snap.799-T1 Valid prediction for GlimmerHMM_glimmerT_6321-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 85072, rend_intergenic: 82909 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99199, rend_intergenic: 88150 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115412, rend_intergenic: 106313 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 124573, rend_intergenic: 117324 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127351, rend_intergenic: 124753 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 141455, rend_intergenic: 129654 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146629, rend_intergenic: 141736 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 150449, rend_intergenic: 148050 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 158334, rend_intergenic: 153328 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 165467, rend_intergenic: 159942 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 175270, rend_intergenic: 170819 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 178373, rend_intergenic: 176282 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 170822, rend_intergenic: 170819 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 184127 -exon list size: 368 building trellis 0.3 0.5 0.8 1.1 1.4 1.6 1.9 2.2 2.4 2.7 3.0 3.2 3.5 3.8 4.1 4.3 4.6 4.9 5.1 5.4 5.7 5.9 6.2 6.5 6.8 7.0 7.3 7.6 7.8 8.1 8.4 8.6 8.9 9.2 9.5 9.7 10.0 10.3 10.5 10.8 11.1 11.4 11.6 11.9 12.2 12.4 12.7 13.0 13.2 13.5 13.8 14.1 14.3 14.6 14.9 15.1 15.4 15.7 15.9 16.2 16.5 16.8 17.0 17.3 17.6 17.8 18.1 18.4 18.6 18.9 19.2 19.5 19.7 20.0 20.3 20.5 20.8 21.1 21.4 21.6 21.9 22.2 22.4 22.7 23.0 23.2 23.5 23.8 24.1 24.3 24.6 24.9 25.1 25.4 25.7 25.9 26.2 26.5 26.8 27.0 27.3 27.6 27.8 28.1 28.4 28.6 28.9 29.2 29.5 29.7 30.0 30.3 30.5 30.8 31.1 31.4 31.6 31.9 32.2 32.4 32.7 33.0 33.2 33.5 33.8 34.1 34.3 34.6 34.9 35.1 35.4 35.7 35.9 36.2 36.5 36.8 37.0 37.3 37.6 37.8 38.1 38.4 38.6 38.9 39.2 39.5 39.7 40.0 40.3 40.5 40.8 41.1 41.4 41.6 41.9 42.2 42.4 42.7 43.0 43.2 43.5 43.8 44.1 44.3 44.6 44.9 45.1 45.4 45.7 45.9 46.2 46.5 46.8 47.0 47.3 47.6 47.8 48.1 48.4 48.6 48.9 49.2 49.5 49.7 50.0 50.3 50.5 50.8 51.1 51.4 51.6 51.9 52.2 52.4 52.7 53.0 53.2 53.5 53.8 54.1 54.3 54.6 54.9 55.1 55.4 55.7 55.9 56.2 56.5 56.8 57.0 57.3 57.6 57.8 58.1 58.4 58.6 58.9 59.2 59.5 59.7 60.0 60.3 60.5 60.8 61.1 61.4 61.6 61.9 62.2 62.4 62.7 63.0 63.2 63.5 63.8 64.1 64.3 64.6 64.9 65.1 65.4 65.7 65.9 66.2 66.5 66.8 67.0 67.3 67.6 67.8 68.1 68.4 68.6 68.9 69.2 69.5 69.7 70.0 70.3 70.5 70.8 71.1 71.4 71.6 71.9 72.2 72.4 72.7 73.0 73.2 73.5 73.8 74.1 74.3 74.6 74.9 75.1 75.4 75.7 75.9 76.2 76.5 76.8 77.0 77.3 77.6 77.8 78.1 78.4 78.6 78.9 79.2 79.5 79.7 80.0 80.3 80.5 80.8 81.1 81.4 81.6 81.9 82.2 82.4 82.7 83.0 83.2 83.5 83.8 84.1 84.3 84.6 84.9 85.1 85.4 85.7 85.9 86.2 86.5 86.8 87.0 87.3 87.6 87.8 88.1 88.4 88.6 88.9 89.2 89.5 89.7 90.0 90.3 90.5 90.8 91.1 91.4 91.6 91.9 92.2 92.4 92.7 93.0 93.2 93.5 93.8 94.1 94.3 94.6 94.9 95.1 95.4 95.7 95.9 96.2 96.5 96.8 97.0 97.3 97.6 97.8 98.1 98.4 98.6 98.9 99.2 99.5 99.7 -found 22 predictions from path traversal Error with prediction: snap lend_intergenic: 85072, rend_intergenic: 82909 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99199, rend_intergenic: 88150 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115412, rend_intergenic: 106313 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 124573, rend_intergenic: 117324 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 127351, rend_intergenic: 124753 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 141455, rend_intergenic: 129654 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146629, rend_intergenic: 141736 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 150449, rend_intergenic: 148050 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 158334, rend_intergenic: 153328 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 165467, rend_intergenic: 159942 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 175270, rend_intergenic: 170819 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 178373, rend_intergenic: 176282 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 170822, rend_intergenic: 170819 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 18 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 19420 -exon list size: 5 building trellis 14.3 28.6 42.9 57.1 71.4 85.7 -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 - 17583 -exon list size: 3 building trellis 20.0 40.0 60.0 80.0 -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 - 17451 -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 -building DP trellis -building trellis in range 2217 - 17451 -exon list size: 1 building trellis 33.3 66.7 -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 -no exons in range 2217 - 14580