-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_9670394-9901153 -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 GlimmerHMM_glimmerT_27754-T1 Valid prediction for GlimmerHMM_glimmerT_27748-T1 Valid prediction for GlimmerHMM_glimmerT_27746-T1 Valid prediction for pasa_asmbl_6342.p1 Valid prediction for Augustus_model.g18364.t1 Valid prediction for snap_scaffold_11-snap.2192-T1 Valid prediction for GlimmerHMM_glimmerT_27756-T1 Couldn't classify 118131, 118193 Couldn't classify 122943, 123005 Sorry, prediction pasa_asmbl_5897.p1 fails validation. (GAG) CA 118131-118193 GT AGG (GTG) AG 118630-118711 GT AGG (TGA) AG 118894-118974 GT TGG (CCT) AG 119069-119148 GT AGG (GTG) AG 119447-119553 GT AAG (CAT) AG 119738-119775 GT AGG (ACT) AG 119988-120130 GT TGG (TTT) AG 120457-120527 GT AAG (GGC) AG 121684-121772 GT GGG (GTT) AG 121944-122008 GT ATG (AAA) AG 122183-122285 GT AGG (ACT) AG 122668-122798 GT AGG (CAG) AG 122943-123005 GG TGG -recovered pasa_asmbl_5897.p1, internal, 118630, 118711 -recovered pasa_asmbl_5897.p1, internal, 118894, 118974 -recovered pasa_asmbl_5897.p1, internal, 119069, 119148 -recovered pasa_asmbl_5897.p1, internal, 119447, 119553 -recovered pasa_asmbl_5897.p1, internal, 119738, 119775 -recovered pasa_asmbl_5897.p1, internal, 119988, 120130 -recovered pasa_asmbl_5897.p1, internal, 120457, 120527 -recovered pasa_asmbl_5897.p1, internal, 121684, 121772 -recovered pasa_asmbl_5897.p1, internal, 121944, 122008 -recovered pasa_asmbl_5897.p1, internal, 122183, 122285 -recovered pasa_asmbl_5897.p1, internal, 122668, 122798 Valid prediction for HiQ_model.g18366.t1 Valid prediction for GlimmerHMM_glimmerT_27753-T1 Couldn't classify 147750, 147877 Sorry, prediction pasa_asmbl_5904.p1 fails validation. (TCG) TA 147750-147877 GT AGG (CTC) AG 148152-148347 GT TGG (GTG) AG 148789-148920 GT GGG (GTT) AG 149218-149292 CC GAC -recovered pasa_asmbl_5904.p1, terminal, 149218, 149292 -recovered pasa_asmbl_5904.p1, internal, 148152, 148347 -recovered pasa_asmbl_5904.p1, internal, 148789, 148920 Couldn't classify 147781, 147809 Couldn't classify 148314, 148347 Sorry, prediction CodingQuarry_transcript_8221-T1 fails validation. (ATG) GG 147781-147809 AA CTA (AGT) AC 148314-148347 GT TGG (GTG) AG 148789-148920 GT GGG (GTT) AG 149218-149292 CC GAC -recovered CodingQuarry_transcript_8221-T1, terminal, 149218, 149292 -recovered CodingQuarry_transcript_8221-T1, internal, 148789, 148920 Valid prediction for Augustus_model.g18376.t1 Valid prediction for Augustus_model.g18368.t1 Valid prediction for CodingQuarry_transcript_8220-T1 Couldn't classify 54522, 54941 Sorry, prediction pasa_asmbl_5892.p2 fails validation. (ATG) AC 54522-54941 GA AGG Valid prediction for CodingQuarry_transcript_8219-T1 Valid prediction for GlimmerHMM_glimmerT_27743-T1 Valid prediction for Augustus_model.g18371.t1 Valid prediction for GlimmerHMM_glimmerT_27755-T1 Valid prediction for snap_scaffold_11-snap.2206-T1 Valid prediction for snap_scaffold_11-snap.2222-T1 Valid prediction for Augustus_model.g18372.t1 Valid prediction for snap_scaffold_11-snap.2212-T1 Valid prediction for CodingQuarry_transcript_8218-T1 Valid prediction for snap_scaffold_11-snap.2223-T1 Valid prediction for GlimmerHMM_glimmerT_27757-T1 Valid prediction for snap_scaffold_11-snap.2185-T1 Valid prediction for snap_scaffold_11-snap.2203-T1 Valid prediction for snap_scaffold_11-snap.2202-T1 Couldn't classify 140913, 140988 Sorry, prediction pasa_asmbl_5899.p1 fails validation. (ATG) AC 137895-138035 GT TGG (GTC) AG 138622-138696 GT AGG (GAG) AG 139275-139324 GT CTG (AAG) AG 139707-139830 GT AGG (TAC) AG 140224-140309 GT AAG (TTT) AG 140913-140988 GT CGG -recovered pasa_asmbl_5899.p1, initial, 137895, 138035 -recovered pasa_asmbl_5899.p1, internal, 138622, 138696 -recovered pasa_asmbl_5899.p1, internal, 139275, 139324 -recovered pasa_asmbl_5899.p1, internal, 139707, 139830 -recovered pasa_asmbl_5899.p1, internal, 140224, 140309 -recovered pasa_asmbl_5899.p1, internal, 140913, 140988 Valid prediction for snap_scaffold_11-snap.2205-T1 Couldn't classify 124793, 124869 Sorry, prediction pasa_asmbl_5898.p1 fails validation. (GTG) AG 124793-124869 GT GGG (CTT) AG 124993-125110 GT AGG (GAT) AG 125330-125467 GT AGG (GGG) AG 125687-125809 AG AGA -recovered pasa_asmbl_5898.p1, terminal, 125687, 125809 -recovered pasa_asmbl_5898.p1, internal, 124793, 124869 -recovered pasa_asmbl_5898.p1, internal, 124993, 125110 -recovered pasa_asmbl_5898.p1, internal, 125330, 125467 Valid prediction for GlimmerHMM_glimmerT_27761-T1 Valid prediction for snap_scaffold_11-snap.2215-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for snap_scaffold_11-snap.2195-T1 Valid prediction for snap_scaffold_11-snap.2225-T1 Couldn't classify 54040, 54213 Couldn't classify 54513, 54941 Sorry, prediction pasa_asmbl_5891.p1 fails validation. (TCC) AT 54040-54213 GT AGG (AGA) AG 54513-54941 GA AGG Valid prediction for GlimmerHMM_glimmerT_27750-T1 Valid prediction for snap_scaffold_11-snap.2199-T1 Valid prediction for snap_scaffold_11-snap.2210-T1 Valid prediction for Augustus_model.g18370.t1 Valid prediction for CodingQuarry_transcript_8222-T1 Valid prediction for snap_scaffold_11-snap.2201-T1 Valid prediction for snap_scaffold_11-snap.2186-T1 Valid prediction for pasa_asmbl_5911.p1 Couldn't classify 145611, 145696 Couldn't classify 147595, 147686 Sorry, prediction pasa_asmbl_5902.p1 fails validation. (GTC) CA 145611-145696 GT ATG (GCA) AG 145784-145958 GT AGG (AGG) AG 146064-146143 GT AGG (CGG) AG 146423-146538 GT AGG (TGA) AG 146717-146784 GT TGG (CTG) AG 146905-147009 GT GGG (GTC) AG 147232-147394 GT AGG (GAC) AG 147595-147686 CC GCC -recovered pasa_asmbl_5902.p1, internal, 145784, 145958 -recovered pasa_asmbl_5902.p1, internal, 146064, 146143 -recovered pasa_asmbl_5902.p1, internal, 146423, 146538 -recovered pasa_asmbl_5902.p1, internal, 146717, 146784 -recovered pasa_asmbl_5902.p1, internal, 146905, 147009 -recovered pasa_asmbl_5902.p1, internal, 147232, 147394 Valid prediction for Augustus_model.g18377.t1 Valid prediction for snap_scaffold_11-snap.2213-T1 Valid prediction for snap_scaffold_11-snap.2197-T1 Valid prediction for GlimmerHMM_glimmerT_27762-T1 Valid prediction for HiQ_model.g18373.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_27741-T1 Valid prediction for HiQ_model.g18365.t1 Valid prediction for GlimmerHMM_glimmerT_27742-T1 Valid prediction for Augustus_model.g18374.t1 Valid prediction for Augustus_model.g18362.t1 Valid prediction for snap_scaffold_11-snap.2226-T1 Valid prediction for snap_scaffold_11-snap.2187-T1 Valid prediction for snap_scaffold_11-snap.2214-T1 Valid prediction for snap_scaffold_11-snap.2217-T1 Valid prediction for snap_scaffold_11-snap.2220-T1 Valid prediction for CodingQuarry_transcript_8212-T1 Couldn't classify 12447, 12662 Couldn't classify 15457, 15936 Sorry, prediction pasa_asmbl_6966.p1 fails validation. (TCG) TC 12447-12662 GT AGG (GTT) AG 15040-15246 GT TGG (GTG) AG 15457-15936 GA AGG -recovered pasa_asmbl_6966.p1, internal, 15040, 15246 Valid prediction for GlimmerHMM_glimmerT_27739-T1 Couldn't classify 204894, 204968 Sorry, prediction pasa_asmbl_6955.p1 fails validation. (CCG) CC 204894-204968 GT AGG (ACC) AG 205267-205373 GT AGG (CAG) AG 205490-205644 GT CGG (AGA) AG 205877-206021 GT AGG (GTA) AG 206534-206643 GT AGG (GCC) AG 206759-206886 GT ATG (CCT) AG 206982-207137 GC AGG (ACC) AG 207228-207575 AT GAA -recovered pasa_asmbl_6955.p1, terminal, 207228, 207575 -recovered pasa_asmbl_6955.p1, internal, 205267, 205373 -recovered pasa_asmbl_6955.p1, internal, 205490, 205644 -recovered pasa_asmbl_6955.p1, internal, 205877, 206021 -recovered pasa_asmbl_6955.p1, internal, 206534, 206643 -recovered pasa_asmbl_6955.p1, internal, 206759, 206886 -recovered pasa_asmbl_6955.p1, internal, 206982, 207137 Valid prediction for CodingQuarry_transcript_8211-T1 Valid prediction for HiQ_model.g18361.t1 Valid prediction for snap_scaffold_11-snap.2190-T1 Valid prediction for GlimmerHMM_glimmerT_27744-T1 Valid prediction for snap_scaffold_11-snap.2194-T1 Valid prediction for pasa_asmbl_6947.p1 Valid prediction for snap_scaffold_11-snap.2193-T1 Valid prediction for snap_scaffold_11-snap.2224-T1 Valid prediction for Augustus_model.g18378.t1 Valid prediction for Augustus_model.g18360.t1 Valid prediction for pasa_asmbl_6959.p1 Valid prediction for GlimmerHMM_glimmerT_27759-T1 Valid prediction for snap_scaffold_11-snap.2200-T1 Valid prediction for CodingQuarry_transcript_8216-T1 Valid prediction for CodingQuarry_transcript_8217-T1 Valid prediction for GlimmerHMM_glimmerT_27760-T1 Valid prediction for GlimmerHMM_glimmerT_27745-T1 Valid prediction for CodingQuarry_transcript_8214-T1 Couldn't classify 209198, 209555 Sorry, prediction pasa_asmbl_6951.p1 fails validation. (GTG) AG 209198-209555 GT AGG (ACG) AG 210618-210773 GT GGG (AGA) AG 210875-210972 GC GAG -recovered pasa_asmbl_6951.p1, terminal, 210875, 210972 -recovered pasa_asmbl_6951.p1, internal, 209198, 209555 -recovered pasa_asmbl_6951.p1, internal, 210618, 210773 -recovered pasa_asmbl_6951.p1, internal, 210875, 210972 Couldn't classify 206982, 207199 Couldn't classify 207320, 207575 Sorry, prediction CodingQuarry_transcript_8213-T1 fails validation. (ATG) CC 194059-194431 GT AGG (AGC) AG 195430-195491 GT AGG (TCT) AG 196242-196298 GT AGG (GGG) AG 196432-196606 GT AGG (GCT) AG 197455-197562 GT AGG (GCC) AG 197806-197917 GT ATG (AGA) AG 199984-200128 GT TGG (GCC) AG 200482-200659 GT TGG (GTC) AG 200883-201043 GT AGG (GAG) AG 201638-201994 GT AGG (CAG) AG 204481-204598 GT AGG (AGG) AG 204778-204968 GT AGG (ACC) AG 205267-205373 GT AGG (CAG) AG 205490-205644 GT CGG (AGA) AG 205877-206021 GT AGG (GTA) AG 206534-206643 GT AGG (GCC) AG 206759-206886 GT ATG (CCT) AG 206982-207199 CT ACC (CTC) AC 207320-207575 AT GAA -recovered CodingQuarry_transcript_8213-T1, initial, 194059, 194431 -recovered CodingQuarry_transcript_8213-T1, internal, 195430, 195491 -recovered CodingQuarry_transcript_8213-T1, internal, 196242, 196298 -recovered CodingQuarry_transcript_8213-T1, internal, 196432, 196606 -recovered CodingQuarry_transcript_8213-T1, internal, 197455, 197562 -recovered CodingQuarry_transcript_8213-T1, internal, 197806, 197917 -recovered CodingQuarry_transcript_8213-T1, internal, 199984, 200128 -recovered CodingQuarry_transcript_8213-T1, internal, 200482, 200659 -recovered CodingQuarry_transcript_8213-T1, internal, 200883, 201043 -recovered CodingQuarry_transcript_8213-T1, internal, 201638, 201994 -recovered CodingQuarry_transcript_8213-T1, internal, 204481, 204598 -recovered CodingQuarry_transcript_8213-T1, internal, 204778, 204968 -recovered CodingQuarry_transcript_8213-T1, internal, 205267, 205373 -recovered CodingQuarry_transcript_8213-T1, internal, 205490, 205644 -recovered CodingQuarry_transcript_8213-T1, internal, 205877, 206021 -recovered CodingQuarry_transcript_8213-T1, internal, 206534, 206643 -recovered CodingQuarry_transcript_8213-T1, internal, 206759, 206886 Valid prediction for snap_scaffold_11-snap.2191-T1 Valid prediction for pasa_asmbl_6952.p1 Valid prediction for Augustus_model.g18375.t1 Valid prediction for snap_scaffold_11-snap.2204-T1 Valid prediction for CodingQuarry_transcript_8215-T1 Valid prediction for GlimmerHMM_glimmerT_27752-T1 Valid prediction for snap_scaffold_11-snap.2207-T1 Couldn't classify 62401, 63105 Sorry, prediction pasa_asmbl_6963.p1 fails validation. (CTG) CC 62401-63105 AA AGA Valid prediction for GlimmerHMM_glimmerT_27749-T1 Valid prediction for Augustus_model.g18363.t1 Valid prediction for GlimmerHMM_glimmerT_27763-T1 Valid prediction for snap_scaffold_11-snap.2208-T1 Valid prediction for snap_scaffold_11-snap.2219-T1 Valid prediction for GlimmerHMM_glimmerT_27738-T1 Valid prediction for snap_scaffold_11-snap.2184-T1 Valid prediction for snap_scaffold_11-snap.2211-T1 Valid prediction for GlimmerHMM_glimmerT_27764-T1 Valid prediction for snap_scaffold_11-snap.2209-T1 Valid prediction for snap_scaffold_11-snap.2216-T1 Valid prediction for GlimmerHMM_glimmerT_27740-T1 Valid prediction for GlimmerHMM_glimmerT_27751-T1 Valid prediction for snap_scaffold_11-snap.2189-T1 Valid prediction for snap_scaffold_11-snap.2196-T1 Valid prediction for snap_scaffold_11-snap.2218-T1 Valid prediction for Augustus_model.g18367.t1 Valid prediction for GlimmerHMM_glimmerT_27758-T1 Valid prediction for Augustus_model.g18369.t1 Valid prediction for snap_scaffold_11-snap.2198-T1 Valid prediction for snap_scaffold_11-snap.2188-T1 Valid prediction for GlimmerHMM_glimmerT_27747-T1 Valid prediction for snap_scaffold_11-snap.2221-T1 Valid prediction for pasa_asmbl_6961.p1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4945, rend_intergenic: 3221 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 10787, rend_intergenic: 8056 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34672, rend_intergenic: 30637 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91821, rend_intergenic: 83428 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110928, rend_intergenic: 103836 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120097, rend_intergenic: 116045 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149862, rend_intergenic: 136727 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 221142, rend_intergenic: 218264 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 224128, rend_intergenic: 221710 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 230760 -exon list size: 454 building trellis 0.2 0.4 0.7 0.9 1.1 1.3 1.5 1.8 2.0 2.2 2.4 2.6 2.9 3.1 3.3 3.5 3.7 3.9 4.2 4.4 4.6 4.8 5.0 5.3 5.5 5.7 5.9 6.1 6.4 6.6 6.8 7.0 7.2 7.5 7.7 7.9 8.1 8.3 8.6 8.8 9.0 9.2 9.4 9.6 9.9 10.1 10.3 10.5 10.7 11.0 11.2 11.4 11.6 11.8 12.1 12.3 12.5 12.7 12.9 13.2 13.4 13.6 13.8 14.0 14.3 14.5 14.7 14.9 15.1 15.4 15.6 15.8 16.0 16.2 16.4 16.7 16.9 17.1 17.3 17.5 17.8 18.0 18.2 18.4 18.6 18.9 19.1 19.3 19.5 19.7 20.0 20.2 20.4 20.6 20.8 21.1 21.3 21.5 21.7 21.9 22.1 22.4 22.6 22.8 23.0 23.2 23.5 23.7 23.9 24.1 24.3 24.6 24.8 25.0 25.2 25.4 25.7 25.9 26.1 26.3 26.5 26.8 27.0 27.2 27.4 27.6 27.9 28.1 28.3 28.5 28.7 28.9 29.2 29.4 29.6 29.8 30.0 30.3 30.5 30.7 30.9 31.1 31.4 31.6 31.8 32.0 32.2 32.5 32.7 32.9 33.1 33.3 33.6 33.8 34.0 34.2 34.4 34.6 34.9 35.1 35.3 35.5 35.7 36.0 36.2 36.4 36.6 36.8 37.1 37.3 37.5 37.7 37.9 38.2 38.4 38.6 38.8 39.0 39.3 39.5 39.7 39.9 40.1 40.4 40.6 40.8 41.0 41.2 41.4 41.7 41.9 42.1 42.3 42.5 42.8 43.0 43.2 43.4 43.6 43.9 44.1 44.3 44.5 44.7 45.0 45.2 45.4 45.6 45.8 46.1 46.3 46.5 46.7 46.9 47.1 47.4 47.6 47.8 48.0 48.2 48.5 48.7 48.9 49.1 49.3 49.6 49.8 50.0 50.2 50.4 50.7 50.9 51.1 51.3 51.5 51.8 52.0 52.2 52.4 52.6 52.9 53.1 53.3 53.5 53.7 53.9 54.2 54.4 54.6 54.8 55.0 55.3 55.5 55.7 55.9 56.1 56.4 56.6 56.8 57.0 57.2 57.5 57.7 57.9 58.1 58.3 58.6 58.8 59.0 59.2 59.4 59.6 59.9 60.1 60.3 60.5 60.7 61.0 61.2 61.4 61.6 61.8 62.1 62.3 62.5 62.7 62.9 63.2 63.4 63.6 63.8 64.0 64.3 64.5 64.7 64.9 65.1 65.4 65.6 65.8 66.0 66.2 66.4 66.7 66.9 67.1 67.3 67.5 67.8 68.0 68.2 68.4 68.6 68.9 69.1 69.3 69.5 69.7 70.0 70.2 70.4 70.6 70.8 71.1 71.3 71.5 71.7 71.9 72.1 72.4 72.6 72.8 73.0 73.2 73.5 73.7 73.9 74.1 74.3 74.6 74.8 75.0 75.2 75.4 75.7 75.9 76.1 76.3 76.5 76.8 77.0 77.2 77.4 77.6 77.9 78.1 78.3 78.5 78.7 78.9 79.2 79.4 79.6 79.8 80.0 80.3 80.5 80.7 80.9 81.1 81.4 81.6 81.8 82.0 82.2 82.5 82.7 82.9 83.1 83.3 83.6 83.8 84.0 84.2 84.4 84.6 84.9 85.1 85.3 85.5 85.7 86.0 86.2 86.4 86.6 86.8 87.1 87.3 87.5 87.7 87.9 88.2 88.4 88.6 88.8 89.0 89.3 89.5 89.7 89.9 90.1 90.4 90.6 90.8 91.0 91.2 91.4 91.7 91.9 92.1 92.3 92.5 92.8 93.0 93.2 93.4 93.6 93.9 94.1 94.3 94.5 94.7 95.0 95.2 95.4 95.6 95.8 96.1 96.3 96.5 96.7 96.9 97.1 97.4 97.6 97.8 98.0 98.2 98.5 98.7 98.9 99.1 99.3 99.6 99.8 -found 31 predictions from path traversal Error with prediction: snap lend_intergenic: 4945, rend_intergenic: 3221 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 10787, rend_intergenic: 8056 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34672, rend_intergenic: 30637 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 91821, rend_intergenic: 83428 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110928, rend_intergenic: 103836 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120097, rend_intergenic: 116045 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149862, rend_intergenic: 136727 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 221142, rend_intergenic: 218264 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 224128, rend_intergenic: 221710 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 29 predictions persist after filtering for low support