-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_9894522-10143804 -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_27766-T1 Valid prediction for snap_scaffold_11-snap.2240-T1 Valid prediction for CodingQuarry_transcript_8224-T1 Valid prediction for snap_scaffold_11-snap.2270-T1 Valid prediction for snap_scaffold_11-snap.2266-T1 Valid prediction for snap_scaffold_11-snap.2230-T1 Couldn't classify 23408, 23465 Couldn't classify 25374, 25393 Sorry, prediction pasa_asmbl_5919.p1 fails validation. (ATC) CT 23408-23465 GT AGG (CGG) AG 23799-23897 GT GGG (GTA) AG 24053-24201 GT AGG (GGT) AG 24321-24400 GT AGG (TGG) AG 24864-24953 GT AGG (GTT) AG 25054-25193 GT GGG (GGT) AG 25374-25393 GG TGG -recovered pasa_asmbl_5919.p1, internal, 23799, 23897 -recovered pasa_asmbl_5919.p1, internal, 24053, 24201 -recovered pasa_asmbl_5919.p1, internal, 24321, 24400 -recovered pasa_asmbl_5919.p1, internal, 24864, 24953 -recovered pasa_asmbl_5919.p1, internal, 25054, 25193 Valid prediction for snap_scaffold_11-snap.2248-T1 Valid prediction for snap_scaffold_11-snap.2246-T1 Valid prediction for HiQ_model.g18384.t1 Valid prediction for snap_scaffold_11-snap.2272-T1 Valid prediction for snap_scaffold_11-snap.2235-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for snap_scaffold_11-snap.2239-T1 Valid prediction for snap_scaffold_11-snap.2260-T1 Valid prediction for Augustus_model.g18388.t1 Valid prediction for GlimmerHMM_glimmerT_27767-T1 Valid prediction for GlimmerHMM_glimmerT_27773-T1 Valid prediction for GlimmerHMM_glimmerT_27784-T1 Valid prediction for snap_scaffold_11-snap.2273-T1 Valid prediction for Augustus_model.g18380.t1 Valid prediction for snap_scaffold_11-snap.2256-T1 Valid prediction for snap_scaffold_11-snap.2265-T1 Valid prediction for GlimmerHMM_glimmerT_27765-T1 Couldn't classify 63867, 63956 Sorry, prediction pasa_asmbl_6234.p1 fails validation. (ATG) GA 57822-58098 GT AGG (GTG) AG 58428-58579 GT AGG (GTA) AG 59148-59216 GT AGG (GTG) AG 59470-59594 GT CGG (CCT) AG 60025-60073 GT AGG (CTG) AG 60583-60719 GT AAG (GTT) AG 61028-61211 GT AGG (CAC) AG 62033-62125 GT AGG (ATC) AG 63867-63956 GT CGG -recovered pasa_asmbl_6234.p1, initial, 57822, 58098 -recovered pasa_asmbl_6234.p1, internal, 58428, 58579 -recovered pasa_asmbl_6234.p1, internal, 59148, 59216 -recovered pasa_asmbl_6234.p1, internal, 59470, 59594 -recovered pasa_asmbl_6234.p1, internal, 60025, 60073 -recovered pasa_asmbl_6234.p1, internal, 60583, 60719 -recovered pasa_asmbl_6234.p1, internal, 61028, 61211 -recovered pasa_asmbl_6234.p1, internal, 62033, 62125 -recovered pasa_asmbl_6234.p1, internal, 63867, 63956 Couldn't classify 25783, 25898 Couldn't classify 27928, 27999 Sorry, prediction pasa_asmbl_5920.p1 fails validation. (GGG) TG 25783-25898 GT AGG (CGA) AG 26012-26094 GT AGG (ATA) AG 26354-26418 GT AGG (GCA) AG 26539-26629 GT AGG (ACC) AG 26755-26876 GT TTG (TCA) AG 27157-27367 GT TGG (GTA) AG 27686-27783 GT TGG (TCT) AG 27928-27999 CT ACC -recovered pasa_asmbl_5920.p1, internal, 26012, 26094 -recovered pasa_asmbl_5920.p1, internal, 26354, 26418 -recovered pasa_asmbl_5920.p1, internal, 26539, 26629 -recovered pasa_asmbl_5920.p1, internal, 26755, 26876 -recovered pasa_asmbl_5920.p1, internal, 27157, 27367 -recovered pasa_asmbl_5920.p1, internal, 27686, 27783 Valid prediction for snap_scaffold_11-snap.2250-T1 Valid prediction for HiQ_model.g18382.t1 Valid prediction for snap_scaffold_11-snap.2268-T1 Valid prediction for pasa_asmbl_5922.p1 Valid prediction for snap_scaffold_11-snap.2252-T1 Valid prediction for snap_scaffold_11-snap.2234-T1 Valid prediction for CodingQuarry_transcript_8223-T1 Valid prediction for GlimmerHMM_glimmerT_27770-T1 Valid prediction for snap_scaffold_11-snap.2243-T1 Valid prediction for GlimmerHMM_glimmerT_27780-T1 Valid prediction for GlimmerHMM_glimmerT_27783-T1 Valid prediction for GlimmerHMM_glimmerT_27768-T1 Valid prediction for snap_scaffold_11-snap.2237-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_27782-T1 Valid prediction for snap_scaffold_11-snap.2254-T1 Valid prediction for Augustus_model.g18387.t1 Valid prediction for snap_scaffold_11-snap.2231-T1 Valid prediction for CodingQuarry_transcript_8227-T1 Valid prediction for snap_scaffold_11-snap.2251-T1 Valid prediction for Augustus_model.g18389.t1 Valid prediction for snap_scaffold_11-snap.2264-T1 Valid prediction for GlimmerHMM_glimmerT_27779-T1 Couldn't classify 133381, 133507 Couldn't classify 135221, 135338 Sorry, prediction pasa_asmbl_6976.p2 fails validation. (TTC) AG 133381-133507 GT AGG (TTC) AG 133704-133812 GT GGG (TCA) AG 135221-135338 CA ACC -recovered pasa_asmbl_6976.p2, internal, 133381, 133507 -recovered pasa_asmbl_6976.p2, internal, 133704, 133812 Couldn't classify 205244, 205471 Couldn't classify 206388, 206422 Sorry, prediction pasa_asmbl_6968.p1 fails validation. (GCA) CG 205244-205471 GT GGG (AAA) AG 205645-205767 GT AGG (ATC) AG 205909-206062 GT GGG (CCC) AG 206388-206422 CG AGC -recovered pasa_asmbl_6968.p1, internal, 205645, 205767 -recovered pasa_asmbl_6968.p1, internal, 205909, 206062 Valid prediction for Augustus_model.g18385.t1 Valid prediction for GlimmerHMM_glimmerT_27771-T1 Valid prediction for snap_scaffold_11-snap.2247-T1 Valid prediction for snap_scaffold_11-snap.2263-T1 Valid prediction for snap_scaffold_11-snap.2244-T1 Valid prediction for snap_scaffold_11-snap.2261-T1 Valid prediction for CodingQuarry_transcript_8226-T1 Valid prediction for pasa_asmbl_7367.p1 Valid prediction for GlimmerHMM_glimmerT_27774-T1 Valid prediction for snap_scaffold_11-snap.2236-T1 Valid prediction for snap_scaffold_11-snap.2267-T1 Valid prediction for snap_scaffold_11-snap.2227-T1 Couldn't classify 177516, 177553 Sorry, prediction pasa_asmbl_6972.p1 fails validation. (CCA) TC 177516-177553 GT GTG (CTG) AG 178275-178401 GT TGG (GGT) AG 178492-178527 GT AGG (GCT) AG 179419-179588 GT CTG (CTG) AG 179732-179858 GT CGG (AAT) AG 180027-180172 GT GTG (ATG) AG 181027-181153 GT AGG (GAA) AG 181309-181338 GT AGG (GTA) AG 181576-181688 GT AGG (CTG) AG 181949-182081 GT ATG (GAG) AG 182264-182403 GT ATG (GTG) AG 182667-182790 GT AGG (AAG) AG 182940-183098 GT AGG (CTG) AG 183453-183615 GT AGG (GTG) AG 183923-184011 TG AAT add_exon() Sorry, pasa_asmbl_6972.p1 181027-181153-initial-1 is invalid. -recovered pasa_asmbl_6972.p1, initial, 181027, 181153 -recovered pasa_asmbl_6972.p1, terminal, 183923, 184011 -recovered pasa_asmbl_6972.p1, internal, 178275, 178401 -recovered pasa_asmbl_6972.p1, internal, 178492, 178527 -recovered pasa_asmbl_6972.p1, internal, 179419, 179588 -recovered pasa_asmbl_6972.p1, internal, 179732, 179858 -recovered pasa_asmbl_6972.p1, internal, 180027, 180172 -recovered pasa_asmbl_6972.p1, internal, 181027, 181153 -recovered pasa_asmbl_6972.p1, internal, 181309, 181338 -recovered pasa_asmbl_6972.p1, internal, 181576, 181688 -recovered pasa_asmbl_6972.p1, internal, 181949, 182081 -recovered pasa_asmbl_6972.p1, internal, 182264, 182403 -recovered pasa_asmbl_6972.p1, internal, 182667, 182790 -recovered pasa_asmbl_6972.p1, internal, 182940, 183098 -recovered pasa_asmbl_6972.p1, internal, 183453, 183615 Valid prediction for HiQ_model.g18381.t1 Valid prediction for Augustus_model.g18390.t1 Valid prediction for snap_scaffold_11-snap.2233-T1 Valid prediction for Augustus_model.g18379.t1 Valid prediction for snap_scaffold_11-snap.2271-T1 Valid prediction for GlimmerHMM_glimmerT_27781-T1 Valid prediction for HiQ_model.g18383.t1 Valid prediction for snap_scaffold_11-snap.2262-T1 Valid prediction for snap_scaffold_11-snap.2245-T1 Valid prediction for snap_scaffold_11-snap.2274-T1 Valid prediction for GlimmerHMM_glimmerT_27772-T1 Valid prediction for snap_scaffold_11-snap.2238-T1 Valid prediction for snap_scaffold_11-snap.2229-T1 Valid prediction for snap_scaffold_11-snap.2255-T1 Valid prediction for Augustus_model.g18392.t1 Valid prediction for GlimmerHMM_glimmerT_27777-T1 Valid prediction for snap_scaffold_11-snap.2269-T1 Couldn't classify 123936, 124006 Couldn't classify 128165, 128243 Sorry, prediction pasa_asmbl_6978.p1 fails validation. (TTT) GT 123936-124006 GT CTG (GCG) AG 125217-125386 GT TGG (AGG) AG 127623-127740 GT AAG (TAA) AG 128165-128243 AC AGA -recovered pasa_asmbl_6978.p1, internal, 125217, 125386 -recovered pasa_asmbl_6978.p1, internal, 127623, 127740 Valid prediction for snap_scaffold_11-snap.2258-T1 Valid prediction for snap_scaffold_11-snap.2232-T1 Valid prediction for GlimmerHMM_glimmerT_27778-T1 Valid prediction for snap_scaffold_11-snap.2228-T1 Valid prediction for snap_scaffold_11-snap.2249-T1 Valid prediction for GlimmerHMM_glimmerT_27775-T1 Valid prediction for Augustus_model.g18386.t1 Valid prediction for snap_scaffold_11-snap.2242-T1 Couldn't classify 137729, 137803 Sorry, prediction pasa_asmbl_6973.p1 fails validation. (ACC) AT 137729-137803 GT AGG (GTG) AG 137948-138444 GT AGG (GCT) AG 138630-138764 GT CGG (GTT) AG 138898-139106 GT AGG (ACT) AG 141934-142063 GT AGG (CCC) AG 142164-142296 GT AGG (ATT) AG 142503-142616 GT AAG (GAT) AG 142768-142932 TC AAT -recovered pasa_asmbl_6973.p1, terminal, 142768, 142932 -recovered pasa_asmbl_6973.p1, internal, 137948, 138444 -recovered pasa_asmbl_6973.p1, internal, 138630, 138764 -recovered pasa_asmbl_6973.p1, internal, 138898, 139106 -recovered pasa_asmbl_6973.p1, internal, 141934, 142063 -recovered pasa_asmbl_6973.p1, internal, 142164, 142296 -recovered pasa_asmbl_6973.p1, internal, 142503, 142616 Valid prediction for snap_scaffold_11-snap.2241-T1 Couldn't classify 136985, 137590 Sorry, prediction pasa_asmbl_6975.p2 fails validation. (CGG) AA 136985-137590 CC GCC Valid prediction for GlimmerHMM_glimmerT_27776-T1 Valid prediction for GlimmerHMM_glimmerT_27769-T1 Valid prediction for Augustus_model.g18391.t1 Valid prediction for snap_scaffold_11-snap.2257-T1 Valid prediction for snap_scaffold_11-snap.2253-T1 Couldn't classify 191847, 191954 Sorry, prediction pasa_asmbl_6969.p1 fails validation. (CAA) AA 191847-191954 GT AGG (GTC) AG 192340-192499 GT AGG (GTG) AG 192646-192744 GT AGG (ACT) AG 192848-192944 GC GGG (TGC) AG 193034-193195 GT CTG (AGC) AG 193480-193655 GT CGG (GTG) AG 194046-194158 GT AGG (GAG) AG 194534-194726 GT CGG (GCC) AG 194878-194995 GT CAG (GAA) AG 195268-195473 GT AGG (GTC) AG 196574-196791 GA GAG -recovered pasa_asmbl_6969.p1, terminal, 196574, 196791 -recovered pasa_asmbl_6969.p1, internal, 192340, 192499 -recovered pasa_asmbl_6969.p1, internal, 192646, 192744 -recovered pasa_asmbl_6969.p1, internal, 192848, 192944 -recovered pasa_asmbl_6969.p1, internal, 193034, 193195 -recovered pasa_asmbl_6969.p1, internal, 193480, 193655 -recovered pasa_asmbl_6969.p1, internal, 194046, 194158 -recovered pasa_asmbl_6969.p1, internal, 194534, 194726 -recovered pasa_asmbl_6969.p1, internal, 194878, 194995 -recovered pasa_asmbl_6969.p1, internal, 195268, 195473 Couldn't classify 129668, 129938 Couldn't classify 132350, 132390 Sorry, prediction pasa_asmbl_6977.p2 fails validation. (CGG) CT 129668-129938 GT GGG (CCA) AG 130219-130494 GT AGG (TAA) AG 132350-132390 GA TGG -recovered pasa_asmbl_6977.p2, internal, 130219, 130494 Valid prediction for snap_scaffold_11-snap.2259-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33306, rend_intergenic: 22125 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38767, rend_intergenic: 36817 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 111453, rend_intergenic: 106352 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118227, rend_intergenic: 115502 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119536, rend_intergenic: 118755 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125597, rend_intergenic: 121015 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 159411, rend_intergenic: 156053 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160360, rend_intergenic: 159919 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 195086, rend_intergenic: 192305 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 200375, rend_intergenic: 196815 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 203111, rend_intergenic: 201550 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 210155, rend_intergenic: 205895 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 225937, rend_intergenic: 222597 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 249283 -exon list size: 408 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 2.0 2.2 2.4 2.7 2.9 3.2 3.4 3.7 3.9 4.1 4.4 4.6 4.9 5.1 5.4 5.6 5.9 6.1 6.3 6.6 6.8 7.1 7.3 7.6 7.8 8.0 8.3 8.5 8.8 9.0 9.3 9.5 9.8 10.0 10.2 10.5 10.7 11.0 11.2 11.5 11.7 12.0 12.2 12.4 12.7 12.9 13.2 13.4 13.7 13.9 14.1 14.4 14.6 14.9 15.1 15.4 15.6 15.9 16.1 16.3 16.6 16.8 17.1 17.3 17.6 17.8 18.0 18.3 18.5 18.8 19.0 19.3 19.5 19.8 20.0 20.2 20.5 20.7 21.0 21.2 21.5 21.7 22.0 22.2 22.4 22.7 22.9 23.2 23.4 23.7 23.9 24.1 24.4 24.6 24.9 25.1 25.4 25.6 25.9 26.1 26.3 26.6 26.8 27.1 27.3 27.6 27.8 28.0 28.3 28.5 28.8 29.0 29.3 29.5 29.8 30.0 30.2 30.5 30.7 31.0 31.2 31.5 31.7 32.0 32.2 32.4 32.7 32.9 33.2 33.4 33.7 33.9 34.1 34.4 34.6 34.9 35.1 35.4 35.6 35.9 36.1 36.3 36.6 36.8 37.1 37.3 37.6 37.8 38.0 38.3 38.5 38.8 39.0 39.3 39.5 39.8 40.0 40.2 40.5 40.7 41.0 41.2 41.5 41.7 42.0 42.2 42.4 42.7 42.9 43.2 43.4 43.7 43.9 44.1 44.4 44.6 44.9 45.1 45.4 45.6 45.9 46.1 46.3 46.6 46.8 47.1 47.3 47.6 47.8 48.0 48.3 48.5 48.8 49.0 49.3 49.5 49.8 50.0 50.2 50.5 50.7 51.0 51.2 51.5 51.7 52.0 52.2 52.4 52.7 52.9 53.2 53.4 53.7 53.9 54.1 54.4 54.6 54.9 55.1 55.4 55.6 55.9 56.1 56.3 56.6 56.8 57.1 57.3 57.6 57.8 58.0 58.3 58.5 58.8 59.0 59.3 59.5 59.8 60.0 60.2 60.5 60.7 61.0 61.2 61.5 61.7 62.0 62.2 62.4 62.7 62.9 63.2 63.4 63.7 63.9 64.1 64.4 64.6 64.9 65.1 65.4 65.6 65.9 66.1 66.3 66.6 66.8 67.1 67.3 67.6 67.8 68.0 68.3 68.5 68.8 69.0 69.3 69.5 69.8 70.0 70.2 70.5 70.7 71.0 71.2 71.5 71.7 72.0 72.2 72.4 72.7 72.9 73.2 73.4 73.7 73.9 74.1 74.4 74.6 74.9 75.1 75.4 75.6 75.9 76.1 76.3 76.6 76.8 77.1 77.3 77.6 77.8 78.0 78.3 78.5 78.8 79.0 79.3 79.5 79.8 80.0 80.2 80.5 80.7 81.0 81.2 81.5 81.7 82.0 82.2 82.4 82.7 82.9 83.2 83.4 83.7 83.9 84.1 84.4 84.6 84.9 85.1 85.4 85.6 85.9 86.1 86.3 86.6 86.8 87.1 87.3 87.6 87.8 88.0 88.3 88.5 88.8 89.0 89.3 89.5 89.8 90.0 90.2 90.5 90.7 91.0 91.2 91.5 91.7 92.0 92.2 92.4 92.7 92.9 93.2 93.4 93.7 93.9 94.1 94.4 94.6 94.9 95.1 95.4 95.6 95.9 96.1 96.3 96.6 96.8 97.1 97.3 97.6 97.8 98.0 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 29 predictions from path traversal Error with prediction: snap lend_intergenic: 33306, rend_intergenic: 22125 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 38767, rend_intergenic: 36817 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 111453, rend_intergenic: 106352 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 118227, rend_intergenic: 115502 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119536, rend_intergenic: 118755 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 125597, rend_intergenic: 121015 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 159411, rend_intergenic: 156053 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160360, rend_intergenic: 159919 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 195086, rend_intergenic: 192305 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 200375, rend_intergenic: 196815 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 203111, rend_intergenic: 201550 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 210155, rend_intergenic: 205895 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 225937, rend_intergenic: 222597 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 18 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 17143 -exon list size: 6 building trellis 12.5 25.0 37.5 50.0 62.5 75.0 87.5 -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