-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_9282039-9556550 -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 52397, 53279 Sorry, prediction pasa_asmbl_33808.p1 fails validation. (TCC) AC 52397-53279 GT AGG (GCT) AG 53724-53830 GT GAG (TCT) AG 53999-54173 GT CCG (TGC) AG 54258-54372 GT CGG (ATG) AG 54457-54612 GT AGG (CGA) AG 55061-55193 GT AGG (TCC) AG 55317-55513 GT TGG (GAA) AG 55709-55773 GT AGG (GCT) AG 55913-56080 GT AGG (GAA) AG 56190-56218 AT GAA add_exon() Sorry, pasa_asmbl_33808.p1 54457-54612-initial-1 is invalid. -recovered pasa_asmbl_33808.p1, initial, 54457, 54612 -recovered pasa_asmbl_33808.p1, terminal, 54457, 54612 -recovered pasa_asmbl_33808.p1, terminal, 56190, 56218 -recovered pasa_asmbl_33808.p1, internal, 53724, 53830 -recovered pasa_asmbl_33808.p1, internal, 53999, 54173 -recovered pasa_asmbl_33808.p1, internal, 54258, 54372 -recovered pasa_asmbl_33808.p1, internal, 54457, 54612 -recovered pasa_asmbl_33808.p1, internal, 55061, 55193 -recovered pasa_asmbl_33808.p1, internal, 55317, 55513 -recovered pasa_asmbl_33808.p1, internal, 55709, 55773 -recovered pasa_asmbl_33808.p1, internal, 55913, 56080 Valid prediction for Augustus_model.g36368.t1 Valid prediction for Augustus_model.g36373.t1 Valid prediction for snap_scaffold_25-snap.2051-T1 Valid prediction for snap_scaffold_25-snap.2044-T1 Valid prediction for snap_scaffold_25-snap.2025-T1 Valid prediction for GlimmerHMM_glimmerT_54782-T1 Valid prediction for GlimmerHMM_glimmerT_54791-T1 Valid prediction for CodingQuarry_transcript_38836-T1 Valid prediction for GlimmerHMM_glimmerT_54809-T1 Valid prediction for snap_scaffold_25-snap.2022-T1 Valid prediction for GlimmerHMM_glimmerT_54783-T1 Valid prediction for GlimmerHMM_glimmerT_54793-T1 Valid prediction for CodingQuarry_transcript_38832-T1 Valid prediction for Augustus_model.g36361.t1 Valid prediction for Augustus_model.g36375.t1 Valid prediction for GlimmerHMM_glimmerT_54795-T1 Valid prediction for snap_scaffold_25-snap.2023-T1 Valid prediction for snap_scaffold_25-snap.2045-T1 Valid prediction for GlimmerHMM_glimmerT_54800-T1 Valid prediction for Augustus_model.g36374.t1 Valid prediction for snap_scaffold_25-snap.2038-T1 Valid prediction for snap_scaffold_25-snap.2053-T1 Valid prediction for GlimmerHMM_glimmerT_54802-T1 Valid prediction for Augustus_model.g36372.t1 Couldn't classify 163657, 163762 Sorry, prediction pasa_asmbl_33817.p1 fails validation. (CGT) GG 163657-163762 GT AGG (ATG) AG 166234-166315 GT AGG (AGA) AG 167744-167879 GT AGG (GTG) AG 167972-168176 GT TTG (GTA) AG 168311-168411 GT AGG (GAG) AG 168707-168844 TG AGT add_exon() Sorry, pasa_asmbl_33817.p1 166234-166315-initial-1 is invalid. -recovered pasa_asmbl_33817.p1, initial, 166234, 166315 add_exon() Sorry, pasa_asmbl_33817.p1 166234-166315-terminal-3 is invalid. -recovered pasa_asmbl_33817.p1, terminal, 166234, 166315 -recovered pasa_asmbl_33817.p1, terminal, 168707, 168844 -recovered pasa_asmbl_33817.p1, internal, 166234, 166315 -recovered pasa_asmbl_33817.p1, internal, 167744, 167879 -recovered pasa_asmbl_33817.p1, internal, 167972, 168176 -recovered pasa_asmbl_33817.p1, internal, 168311, 168411 Valid prediction for pasa_asmbl_33802.p1 Valid prediction for snap_scaffold_25-snap.2049-T1 Valid prediction for Augustus_model.g36349.t1 Valid prediction for snap_scaffold_25-snap.2029-T1 Valid prediction for GlimmerHMM_glimmerT_54807-T1 Couldn't classify 246644, 246887 Sorry, prediction pasa_asmbl_33826.p1 fails validation. (ATC) AG 246644-246887 GT AGG (GGT) AG 248736-248902 GT AGG (GCA) AG 249008-249085 GT AGG (GCA) AG 250691-250882 GT CCG (ATT) AG 251434-251505 GT AGG (ATC) AG 251955-252122 AC AAA -recovered pasa_asmbl_33826.p1, terminal, 251955, 252122 -recovered pasa_asmbl_33826.p1, internal, 246644, 246887 -recovered pasa_asmbl_33826.p1, internal, 248736, 248902 -recovered pasa_asmbl_33826.p1, internal, 249008, 249085 -recovered pasa_asmbl_33826.p1, internal, 250691, 250882 -recovered pasa_asmbl_33826.p1, internal, 251434, 251505 Valid prediction for snap_scaffold_25-snap.2030-T1 Valid prediction for GlimmerHMM_glimmerT_54785-T1 Valid prediction for GlimmerHMM_glimmerT_54790-T1 Valid prediction for Augustus_model.g36364.t1 Valid prediction for snap_scaffold_25-snap.2017-T1 Valid prediction for Augustus_model.g36352.t1 Valid prediction for HiQ_model.g36376.t1 Valid prediction for snap_scaffold_25-snap.2052-T1 Couldn't classify 146991, 147054 Couldn't classify 152207, 152399 Sorry, prediction pasa_asmbl_33812.p1 fails validation. (ACC) CA 146991-147054 GT TAG (ATC) AG 149966-149997 GT TGG (CAT) AG 150125-150235 GT AGG (AGA) AG 151987-152111 GT TGG (GGA) AG 152207-152399 TC AGT -recovered pasa_asmbl_33812.p1, internal, 149966, 149997 -recovered pasa_asmbl_33812.p1, internal, 150125, 150235 -recovered pasa_asmbl_33812.p1, internal, 151987, 152111 Valid prediction for GlimmerHMM_glimmerT_54806-T1 Valid prediction for snap_scaffold_25-snap.2032-T1 Valid prediction for snap_scaffold_25-snap.2027-T1 Valid prediction for snap_scaffold_25-snap.2021-T1 Valid prediction for Augustus_model.g36350.t1 Valid prediction for Augustus_model.g36353.t1 Valid prediction for Augustus_model.g36366.t1 Valid prediction for GlimmerHMM_glimmerT_54810-T1 Valid prediction for Augustus_model.g36355.t1 Valid prediction for GlimmerHMM_glimmerT_54799-T1 Valid prediction for GlimmerHMM_glimmerT_54787-T1 Couldn't classify 237707, 237834 Sorry, prediction pasa_asmbl_33824.p1 fails validation. (ATG) CA 234195-234252 GT TGG (CTG) AG 234350-234425 GT TGG (GTA) AG 236573-236754 GT AGG (AGG) AG 237707-237834 GT ATG -recovered pasa_asmbl_33824.p1, initial, 234195, 234252 -recovered pasa_asmbl_33824.p1, internal, 234350, 234425 -recovered pasa_asmbl_33824.p1, internal, 236573, 236754 -recovered pasa_asmbl_33824.p1, internal, 237707, 237834 Valid prediction for Augustus_model.g36351.t1 Valid prediction for snap_scaffold_25-snap.2031-T1 Valid prediction for Augustus_model.g36367.t1 Valid prediction for snap_scaffold_25-snap.2042-T1 Valid prediction for GlimmerHMM_glimmerT_54786-T1 Couldn't classify 5349, 5525 Sorry, prediction pasa_asmbl_33803.p1 fails validation. (GGT) AG 5349-5525 GT CCG (GAG) AG 5877-5954 GT GGG (TGC) AG 6038-6141 GT TGG (GTG) AG 6285-6381 GT CGG (TCC) AG 6469-6535 GT TGG (TGG) AG 6825-6991 GT GGG (ATG) AG 7315-7411 GT CAG (AGA) AG 7673-7897 GT TGG (ACA) AG 8187-8332 GT AGG (GTG) AG 8486-8600 GT CGG (CTG) AG 8911-9072 GT AGG (GCT) AG 9189-9277 GT AGG (GAG) AG 9371-9555 GT AGG (GCT) AG 9635-9695 AC AAA -recovered pasa_asmbl_33803.p1, initial, 7315, 7411 -recovered pasa_asmbl_33803.p1, terminal, 9635, 9695 -recovered pasa_asmbl_33803.p1, internal, 5349, 5525 -recovered pasa_asmbl_33803.p1, internal, 5877, 5954 -recovered pasa_asmbl_33803.p1, internal, 6038, 6141 -recovered pasa_asmbl_33803.p1, internal, 6285, 6381 -recovered pasa_asmbl_33803.p1, internal, 6469, 6535 -recovered pasa_asmbl_33803.p1, internal, 6825, 6991 -recovered pasa_asmbl_33803.p1, internal, 7315, 7411 -recovered pasa_asmbl_33803.p1, internal, 7673, 7897 -recovered pasa_asmbl_33803.p1, internal, 8187, 8332 -recovered pasa_asmbl_33803.p1, internal, 8486, 8600 -recovered pasa_asmbl_33803.p1, internal, 8911, 9072 -recovered pasa_asmbl_33803.p1, internal, 9189, 9277 -recovered pasa_asmbl_33803.p1, internal, 9371, 9555 Valid prediction for GlimmerHMM_glimmerT_54803-T1 Valid prediction for snap_scaffold_25-snap.2050-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_25-snap.2046-T1 Valid prediction for Augustus_model.g36359.t1 Valid prediction for snap_scaffold_25-snap.2016-T1 Valid prediction for GlimmerHMM_glimmerT_54796-T1 Couldn't classify 249748, 249749 Sorry, prediction CodingQuarry_transcript_38833-T1 fails validation. (ATG) AC 248616-248687 GT AGG (ATG) AG 248820-248993 GT AGG (AAC) AG 249167-249248 GT AGG (TGC) AG 249456-249539 GT CTG (GAC) AG 249748-249749 CT GAC -recovered CodingQuarry_transcript_38833-T1, initial, 248616, 248687 -recovered CodingQuarry_transcript_38833-T1, initial, 248820, 248993 -recovered CodingQuarry_transcript_38833-T1, internal, 248820, 248993 -recovered CodingQuarry_transcript_38833-T1, internal, 249167, 249248 -recovered CodingQuarry_transcript_38833-T1, internal, 249456, 249539 Valid prediction for GlimmerHMM_glimmerT_54788-T1 Couldn't classify 248511, 248687 Sorry, prediction pasa_asmbl_34489.p1 fails validation. (GGG) CC 248511-248687 GT AGG (ATG) AG 248820-248993 GT AGG (AAC) AG 249167-249248 GT AGG (GCT) AG 249391-249539 GT CTG (GAC) AG 249748-250014 AC GAA -recovered pasa_asmbl_34489.p1, initial, 248820, 248993 -recovered pasa_asmbl_34489.p1, terminal, 249748, 250014 -recovered pasa_asmbl_34489.p1, internal, 248820, 248993 -recovered pasa_asmbl_34489.p1, internal, 249167, 249248 -recovered pasa_asmbl_34489.p1, internal, 249391, 249539 Valid prediction for GlimmerHMM_glimmerT_54797-T1 Valid prediction for snap_scaffold_25-snap.2043-T1 Valid prediction for GlimmerHMM_glimmerT_54808-T1 Valid prediction for snap_scaffold_25-snap.2036-T1 Valid prediction for GlimmerHMM_glimmerT_54789-T1 Valid prediction for snap_scaffold_25-snap.2040-T1 Valid prediction for snap_scaffold_25-snap.2019-T1 Valid prediction for Augustus_model.g36348.t1 Valid prediction for snap_scaffold_25-snap.2018-T1 Valid prediction for snap_scaffold_25-snap.2055-T1 Couldn't classify 132576, 132745 Sorry, prediction pasa_asmbl_34501.p1 fails validation. (ATG) TA 131743-131881 GT AGG (ATG) AG 132026-132133 GT AGG (GGT) AG 132576-132745 GT TGG -recovered pasa_asmbl_34501.p1, initial, 131743, 131881 add_exon() Sorry, pasa_asmbl_34501.p1 132026-132133-initial-1 is invalid. -recovered pasa_asmbl_34501.p1, initial, 132026, 132133 -recovered pasa_asmbl_34501.p1, internal, 132026, 132133 -recovered pasa_asmbl_34501.p1, internal, 132576, 132745 Valid prediction for Augustus_model.g36365.t1 Valid prediction for GlimmerHMM_glimmerT_54792-T1 Valid prediction for GlimmerHMM_glimmerT_54794-T1 Valid prediction for CodingQuarry_transcript_38834-T1 Valid prediction for GlimmerHMM_glimmerT_54804-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for Augustus_model.g36370.t1 Valid prediction for GlimmerHMM_glimmerT_54798-T1 Valid prediction for GlimmerHMM_glimmerT_54801-T1 Valid prediction for GlimmerHMM_glimmerT_54805-T1 Valid prediction for Augustus_model.g36362.t1 Valid prediction for Augustus_model.g36358.t1 Valid prediction for snap_scaffold_25-snap.2039-T1 Valid prediction for Augustus_model.g36363.t1 Valid prediction for snap_scaffold_25-snap.2024-T1 Valid prediction for snap_scaffold_25-snap.2048-T1 Sorry, intron length (3) is less than minimum required (10) Couldn't classify 161782, 161852 Sorry, prediction pasa_asmbl_34498.p1 fails validation. (ATG) AA 160552-161551 GT CGG (ATA) AG 161782-161852 CA CCC -recovered pasa_asmbl_34498.p1, initial, 160552, 161551 Couldn't classify 137619, 137765 Couldn't classify 140181, 140326 Sorry, prediction pasa_asmbl_34564.p1 fails validation. (TGT) TG 137619-137765 GT AGG (GTG) AG 139867-139972 GT TGG (TTG) AG 140181-140326 CC GCC -recovered pasa_asmbl_34564.p1, internal, 139867, 139972 Valid prediction for snap_scaffold_25-snap.2041-T1 Valid prediction for snap_scaffold_25-snap.2026-T1 Valid prediction for snap_scaffold_25-snap.2047-T1 Valid prediction for snap_scaffold_25-snap.2037-T1 Couldn't classify 149826, 150036 Sorry, prediction pasa_asmbl_34500.p1 fails validation. (GTG) AG 149826-150036 GT AGG (ACA) AG 150185-150318 GT AGG (GGC) AG 151617-151809 GT CTG (CTA) AG 152579-152792 GT AGG (GAT) AG 154184-154267 GT AGG (GTG) AG 154554-154680 AC GAA add_exon() Sorry, pasa_asmbl_34500.p1 152579-152792-terminal-3 is invalid. -recovered pasa_asmbl_34500.p1, terminal, 152579, 152792 -recovered pasa_asmbl_34500.p1, terminal, 154554, 154680 -recovered pasa_asmbl_34500.p1, internal, 149826, 150036 -recovered pasa_asmbl_34500.p1, internal, 150185, 150318 -recovered pasa_asmbl_34500.p1, internal, 151617, 151809 -recovered pasa_asmbl_34500.p1, internal, 152579, 152792 -recovered pasa_asmbl_34500.p1, internal, 154184, 154267 Valid prediction for Augustus_model.g36357.t1 Valid prediction for HiQ_model.g36371.t1 Valid prediction for snap_scaffold_25-snap.2034-T1 Valid prediction for snap_scaffold_25-snap.2028-T1 Valid prediction for Augustus_model.g36356.t1 Valid prediction for Augustus_model.g36354.t1 Valid prediction for snap_scaffold_25-snap.2033-T1 Valid prediction for GlimmerHMM_glimmerT_54784-T1 Valid prediction for snap_scaffold_25-snap.2054-T1 Valid prediction for Augustus_model.g36369.t1 Valid prediction for Augustus_model.g36360.t1 Couldn't classify 54598, 54717 Sorry, prediction pasa_asmbl_34503.p1 fails validation. (ATG) GA 50802-50834 GT GTG (GGC) AG 50927-51027 GT AGG (ACC) AG 52026-52169 GT GGG (GAG) AG 52267-52390 GT AGG (GTA) AG 53078-53136 GT AGG (GGG) AG 53279-53420 GT AGG (CTG) AG 54598-54717 AT TCA -recovered pasa_asmbl_34503.p1, initial, 50802, 50834 -recovered pasa_asmbl_34503.p1, internal, 50927, 51027 -recovered pasa_asmbl_34503.p1, internal, 52026, 52169 -recovered pasa_asmbl_34503.p1, internal, 52267, 52390 -recovered pasa_asmbl_34503.p1, internal, 53078, 53136 -recovered pasa_asmbl_34503.p1, internal, 53279, 53420 Valid prediction for snap_scaffold_25-snap.2035-T1 Valid prediction for snap_scaffold_25-snap.2020-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22143, rend_intergenic: 12525 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27196, rend_intergenic: 24922 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 37381, rend_intergenic: 35429 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53884, rend_intergenic: 43947 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 274512 -exon list size: 456 building trellis 0.2 0.4 0.7 0.9 1.1 1.3 1.5 1.7 2.0 2.2 2.4 2.6 2.8 3.1 3.3 3.5 3.7 3.9 4.1 4.4 4.6 4.8 5.0 5.2 5.5 5.7 5.9 6.1 6.3 6.6 6.8 7.0 7.2 7.4 7.6 7.9 8.1 8.3 8.5 8.7 9.0 9.2 9.4 9.6 9.8 10.0 10.3 10.5 10.7 10.9 11.1 11.4 11.6 11.8 12.0 12.2 12.4 12.7 12.9 13.1 13.3 13.5 13.8 14.0 14.2 14.4 14.6 14.8 15.1 15.3 15.5 15.7 15.9 16.2 16.4 16.6 16.8 17.0 17.2 17.5 17.7 17.9 18.1 18.3 18.6 18.8 19.0 19.2 19.4 19.7 19.9 20.1 20.3 20.5 20.7 21.0 21.2 21.4 21.6 21.8 22.1 22.3 22.5 22.7 22.9 23.1 23.4 23.6 23.8 24.0 24.2 24.5 24.7 24.9 25.1 25.3 25.5 25.8 26.0 26.2 26.4 26.6 26.9 27.1 27.3 27.5 27.7 27.9 28.2 28.4 28.6 28.8 29.0 29.3 29.5 29.7 29.9 30.1 30.3 30.6 30.8 31.0 31.2 31.4 31.7 31.9 32.1 32.3 32.5 32.8 33.0 33.2 33.4 33.6 33.8 34.1 34.3 34.5 34.7 34.9 35.2 35.4 35.6 35.8 36.0 36.2 36.5 36.7 36.9 37.1 37.3 37.6 37.8 38.0 38.2 38.4 38.6 38.9 39.1 39.3 39.5 39.7 40.0 40.2 40.4 40.6 40.8 41.0 41.3 41.5 41.7 41.9 42.1 42.4 42.6 42.8 43.0 43.2 43.4 43.7 43.9 44.1 44.3 44.5 44.8 45.0 45.2 45.4 45.6 45.9 46.1 46.3 46.5 46.7 46.9 47.2 47.4 47.6 47.8 48.0 48.3 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 51.7 52.0 52.2 52.4 52.6 52.8 53.1 53.3 53.5 53.7 53.9 54.1 54.4 54.6 54.8 55.0 55.2 55.5 55.7 55.9 56.1 56.3 56.6 56.8 57.0 57.2 57.4 57.6 57.9 58.1 58.3 58.5 58.7 59.0 59.2 59.4 59.6 59.8 60.0 60.3 60.5 60.7 60.9 61.1 61.4 61.6 61.8 62.0 62.2 62.4 62.7 62.9 63.1 63.3 63.5 63.8 64.0 64.2 64.4 64.6 64.8 65.1 65.3 65.5 65.7 65.9 66.2 66.4 66.6 66.8 67.0 67.2 67.5 67.7 67.9 68.1 68.3 68.6 68.8 69.0 69.2 69.4 69.7 69.9 70.1 70.3 70.5 70.7 71.0 71.2 71.4 71.6 71.8 72.1 72.3 72.5 72.7 72.9 73.1 73.4 73.6 73.8 74.0 74.2 74.5 74.7 74.9 75.1 75.3 75.5 75.8 76.0 76.2 76.4 76.6 76.9 77.1 77.3 77.5 77.7 77.9 78.2 78.4 78.6 78.8 79.0 79.3 79.5 79.7 79.9 80.1 80.3 80.6 80.8 81.0 81.2 81.4 81.7 81.9 82.1 82.3 82.5 82.8 83.0 83.2 83.4 83.6 83.8 84.1 84.3 84.5 84.7 84.9 85.2 85.4 85.6 85.8 86.0 86.2 86.5 86.7 86.9 87.1 87.3 87.6 87.8 88.0 88.2 88.4 88.6 88.9 89.1 89.3 89.5 89.7 90.0 90.2 90.4 90.6 90.8 91.0 91.3 91.5 91.7 91.9 92.1 92.4 92.6 92.8 93.0 93.2 93.4 93.7 93.9 94.1 94.3 94.5 94.8 95.0 95.2 95.4 95.6 95.9 96.1 96.3 96.5 96.7 96.9 97.2 97.4 97.6 97.8 98.0 98.3 98.5 98.7 98.9 99.1 99.3 99.6 99.8 -found 41 predictions from path traversal Error with prediction: snap lend_intergenic: 22143, rend_intergenic: 12525 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27196, rend_intergenic: 24922 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 37381, rend_intergenic: 35429 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 53884, rend_intergenic: 43947 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 35 predictions persist after filtering for low support