-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_14571267-14740504 -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 snap_scaffold_6-snap.3073-T1 Valid prediction for Augustus_model.g10730.t1 Valid prediction for snap_scaffold_6-snap.3061-T1 Valid prediction for snap_scaffold_6-snap.3076-T1 Valid prediction for Augustus_model.g10738.t1 Valid prediction for GlimmerHMM_glimmerT_15983-T1 Valid prediction for snap_scaffold_6-snap.3081-T1 Valid prediction for Augustus_model.g10741.t1 Valid prediction for snap_scaffold_6-snap.3072-T1 Valid prediction for GlimmerHMM_glimmerT_15970-T1 Valid prediction for Augustus_model.g10737.t1 Valid prediction for Augustus_model.g10731.t1 Valid prediction for snap_scaffold_6-snap.3063-T1 Valid prediction for GlimmerHMM_glimmerT_15986-T1 Valid prediction for Augustus_model.g10732.t1 Valid prediction for GlimmerHMM_glimmerT_15982-T1 Valid prediction for GlimmerHMM_glimmerT_15981-T1 Valid prediction for snap_scaffold_6-snap.3057-T1 Valid prediction for GlimmerHMM_glimmerT_15978-T1 Valid prediction for Augustus_model.g10743.t1 Valid prediction for GlimmerHMM_glimmerT_15976-T1 Valid prediction for snap_scaffold_6-snap.3084-T1 Couldn't classify 129059, 129208 Couldn't classify 130062, 130286 Sorry, prediction pasa_asmbl_47987.p1 fails validation. (GTG) CA 129059-129208 GT TGG (ATC) AG 130062-130286 AT GGA Valid prediction for snap_scaffold_6-snap.3074-T1 Valid prediction for snap_scaffold_6-snap.3085-T1 Valid prediction for Augustus_model.g10728.t1 Valid prediction for CodingQuarry_transcript_55347-T1 Valid prediction for snap_scaffold_6-snap.3080-T1 Valid prediction for snap_scaffold_6-snap.3070-T1 Valid prediction for GlimmerHMM_glimmerT_15975-T1 Couldn't classify 154417, 154463 Sorry, prediction pasa_asmbl_47639.p1 fails validation. (ATG) AG 152998-153089 GT ACG (GCT) AG 153208-153304 GT AGG (GAG) AG 153532-153617 GT GTG (GCC) AG 153731-153906 GT ACG (CAA) AG 154030-154067 GT AGG (GGT) AG 154197-154272 GT TAG (GTC) AG 154417-154463 GA AGG -recovered pasa_asmbl_47639.p1, initial, 152998, 153089 -recovered pasa_asmbl_47639.p1, internal, 152998, 153089 -recovered pasa_asmbl_47639.p1, internal, 153208, 153304 -recovered pasa_asmbl_47639.p1, internal, 153532, 153617 -recovered pasa_asmbl_47639.p1, internal, 153731, 153906 -recovered pasa_asmbl_47639.p1, internal, 154030, 154067 -recovered pasa_asmbl_47639.p1, internal, 154197, 154272 Valid prediction for snap_scaffold_6-snap.3079-T1 Sorry, intron length (8) is less than minimum required (10) Valid prediction for snap_scaffold_6-snap.3064-T1 Sorry, intron length (3) is less than minimum required (10) Couldn't classify 21315, 21390 Couldn't classify 23154, 23277 Sorry, prediction pasa_asmbl_47630.p1 fails validation. (GGG) CA 21315-21390 GT GAG (CTC) AG 21997-22117 GT AGG (CTC) AG 23154-23277 GA TGG -recovered pasa_asmbl_47630.p1, internal, 21997, 22117 Valid prediction for snap_scaffold_6-snap.3067-T1 Valid prediction for GlimmerHMM_glimmerT_15968-T1 Valid prediction for snap_scaffold_6-snap.3056-T1 Couldn't classify 131414, 131560 Sorry, prediction pasa_asmbl_47886.p1 fails validation. (GAG) CC 131414-131560 GT TTG (GGC) AG 131921-132092 GT AGG (GTA) AG 132853-133010 CC AGC -recovered pasa_asmbl_47886.p1, terminal, 132853, 133010 -recovered pasa_asmbl_47886.p1, internal, 131921, 132092 Valid prediction for snap_scaffold_6-snap.3071-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 pasa_asmbl_49018.p2 Valid prediction for snap_scaffold_6-snap.3055-T1 Valid prediction for snap_scaffold_6-snap.3062-T1 Valid prediction for GlimmerHMM_glimmerT_15974-T1 Valid prediction for snap_scaffold_6-snap.3075-T1 Valid prediction for Augustus_model.g10729.t1 Valid prediction for Augustus_model.g10739.t1 Valid prediction for Augustus_model.g10733.t1 Valid prediction for GlimmerHMM_glimmerT_15989-T1 Valid prediction for GlimmerHMM_glimmerT_15977-T1 Valid prediction for snap_scaffold_6-snap.3059-T1 Valid prediction for snap_scaffold_6-snap.3087-T1 Valid prediction for snap_scaffold_6-snap.3060-T1 Couldn't classify 7648, 7727 Couldn't classify 11762, 12087 Sorry, prediction pasa_asmbl_49025.p1 fails validation. (TTT) TG 7648-7727 GT CTG (GCT) AG 7882-8049 GT AGG (CTT) AG 8399-8572 GT AGG (ACT) AG 9071-9244 GT AGG (GCT) AG 9792-9965 GT AAG (CGT) AG 10376-10422 GT ATG (ATG) AG 11762-12087 AA AGA add_exon() Sorry, pasa_asmbl_49025.p1 9071-9244-terminal-1 is invalid. -recovered pasa_asmbl_49025.p1, terminal, 9071, 9244 -recovered pasa_asmbl_49025.p1, internal, 7882, 8049 -recovered pasa_asmbl_49025.p1, internal, 8399, 8572 -recovered pasa_asmbl_49025.p1, internal, 9071, 9244 -recovered pasa_asmbl_49025.p1, internal, 9792, 9965 -recovered pasa_asmbl_49025.p1, internal, 10376, 10422 Valid prediction for GlimmerHMM_glimmerT_15980-T1 Valid prediction for CodingQuarry_transcript_55345-T1 Valid prediction for Augustus_model.g10744.t1 Valid prediction for snap_scaffold_6-snap.3086-T1 Valid prediction for GlimmerHMM_glimmerT_15984-T1 Valid prediction for snap_scaffold_6-snap.3066-T1 Valid prediction for snap_scaffold_6-snap.3078-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_15971-T1 Valid prediction for GlimmerHMM_glimmerT_15967-T1 Valid prediction for GlimmerHMM_glimmerT_15972-T1 Valid prediction for HiQ_model.g10735.t1 Couldn't classify 116591, 116687 Sorry, prediction pasa_asmbl_49017.p1 fails validation. (GGT) AG 116591-116687 GT GGG (GAG) AG 116778-116908 GT AGG (CAA) AG 117027-117176 GT GGG (TTA) AG 118001-118114 GA GAG -recovered pasa_asmbl_49017.p1, terminal, 118001, 118114 -recovered pasa_asmbl_49017.p1, internal, 116591, 116687 -recovered pasa_asmbl_49017.p1, internal, 116778, 116908 -recovered pasa_asmbl_49017.p1, internal, 117027, 117176 Couldn't classify 63291, 63349 Couldn't classify 64475, 64847 Sorry, prediction pasa_asmbl_49024.p1 fails validation. (GGG) AG 63291-63349 GT AGG (GCA) AG 64475-64847 GT ACG -recovered pasa_asmbl_49024.p1, internal, 63291, 63349 -recovered pasa_asmbl_49024.p1, internal, 64475, 64847 Valid prediction for Augustus_model.g10745.t1 Valid prediction for Augustus_model.g10742.t1 Valid prediction for snap_scaffold_6-snap.3069-T1 Valid prediction for snap_scaffold_6-snap.3058-T1 Valid prediction for snap_scaffold_6-snap.3082-T1 Couldn't classify 87258, 87281 Couldn't classify 95806, 96051 Sorry, prediction pasa_asmbl_49022.p1 fails validation. (TCT) AA 87258-87281 GC AGG (GGC) AG 89627-89719 GT TTG (GGC) AG 90508-90571 GT TTG (ACC) AG 92102-92200 GT ATG (CTG) AG 92457-92600 GT CTG (GCA) AG 92841-92936 GT AGG (CGG) AG 93091-93209 GT AGG (GCT) AG 93505-93657 GT AGG (CTG) AG 93866-94039 GT CGG (ACC) AG 94463-94636 GT AGG (GTG) AG 95806-96051 GT AGG -recovered pasa_asmbl_49022.p1, internal, 89627, 89719 -recovered pasa_asmbl_49022.p1, internal, 90508, 90571 -recovered pasa_asmbl_49022.p1, internal, 92102, 92200 -recovered pasa_asmbl_49022.p1, internal, 92457, 92600 -recovered pasa_asmbl_49022.p1, internal, 92841, 92936 -recovered pasa_asmbl_49022.p1, internal, 93091, 93209 -recovered pasa_asmbl_49022.p1, internal, 93505, 93657 -recovered pasa_asmbl_49022.p1, internal, 93866, 94039 -recovered pasa_asmbl_49022.p1, internal, 94463, 94636 -recovered pasa_asmbl_49022.p1, internal, 95806, 96051 Valid prediction for GlimmerHMM_glimmerT_15987-T1 Valid prediction for Augustus_model.g10740.t1 Valid prediction for snap_scaffold_6-snap.3077-T1 Valid prediction for snap_scaffold_6-snap.3065-T1 Valid prediction for GlimmerHMM_glimmerT_15988-T1 Valid prediction for HiQ_model.g10736.t1 Valid prediction for snap_scaffold_6-snap.3083-T1 Valid prediction for snap_scaffold_6-snap.3054-T1 Valid prediction for snap_scaffold_6-snap.3068-T1 Valid prediction for GlimmerHMM_glimmerT_15969-T1 Valid prediction for Augustus_model.g10734.t1 Couldn't classify 111189, 111315 Sorry, prediction pasa_asmbl_49021.p1 fails validation. (ATG) AG 100848-100940 GT AGG (CTG) AG 101247-101591 GT AGG (GAG) AG 101849-101972 GT AGG (AGC) AG 102344-102515 GT AGG (GGG) AG 103290-103502 GT AGG (GAC) AG 104002-104146 GT GGG (TTC) AG 104421-104627 GT AGG (GCA) AG 104943-105047 GT AGG (GAG) AG 105167-105319 GT AGG (CTG) AG 105709-105957 GT AGG (ATG) AG 106196-106408 GT ACG (GTC) AG 106774-106986 GT AGG (GTG) AG 107950-108111 GT AGG (GCC) AG 108319-108447 GT AGG (GAC) AG 108549-108637 GT AAG (GTC) AG 108801-108924 GT AGG (GTG) AG 109280-109488 GT AAG (GGA) AG 110162-110270 GT AGG (ATG) AG 110441-110613 GT AGG (ACG) AG 111189-111315 GA ACG -recovered pasa_asmbl_49021.p1, initial, 100848, 100940 -recovered pasa_asmbl_49021.p1, initial, 106196, 106408 -recovered pasa_asmbl_49021.p1, initial, 110441, 110613 -recovered pasa_asmbl_49021.p1, internal, 100848, 100940 -recovered pasa_asmbl_49021.p1, internal, 101247, 101591 -recovered pasa_asmbl_49021.p1, internal, 101849, 101972 -recovered pasa_asmbl_49021.p1, internal, 102344, 102515 -recovered pasa_asmbl_49021.p1, internal, 103290, 103502 -recovered pasa_asmbl_49021.p1, internal, 104002, 104146 -recovered pasa_asmbl_49021.p1, internal, 104421, 104627 -recovered pasa_asmbl_49021.p1, internal, 104943, 105047 -recovered pasa_asmbl_49021.p1, internal, 105167, 105319 -recovered pasa_asmbl_49021.p1, internal, 105709, 105957 -recovered pasa_asmbl_49021.p1, internal, 106196, 106408 -recovered pasa_asmbl_49021.p1, internal, 106774, 106986 -recovered pasa_asmbl_49021.p1, internal, 107950, 108111 -recovered pasa_asmbl_49021.p1, internal, 108319, 108447 -recovered pasa_asmbl_49021.p1, internal, 108549, 108637 -recovered pasa_asmbl_49021.p1, internal, 108801, 108924 -recovered pasa_asmbl_49021.p1, internal, 109280, 109488 -recovered pasa_asmbl_49021.p1, internal, 110162, 110270 -recovered pasa_asmbl_49021.p1, internal, 110441, 110613 Valid prediction for GlimmerHMM_glimmerT_15985-T1 Valid prediction for GlimmerHMM_glimmerT_15973-T1 Valid prediction for GlimmerHMM_glimmerT_15979-T1 Valid prediction for CodingQuarry_transcript_55346-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22163, rend_intergenic: 15762 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33758, rend_intergenic: 22341 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35788, rend_intergenic: 33850 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 54299, rend_intergenic: 51849 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70588, rend_intergenic: 58397 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 104736, rend_intergenic: 75522 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119727, rend_intergenic: 115604 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131602, rend_intergenic: 119872 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 154717, rend_intergenic: 150834 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 169238 -exon list size: 400 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 2.0 2.2 2.5 2.7 3.0 3.2 3.5 3.7 4.0 4.2 4.5 4.7 5.0 5.2 5.5 5.7 6.0 6.2 6.5 6.7 7.0 7.2 7.5 7.7 8.0 8.2 8.5 8.7 9.0 9.2 9.5 9.7 10.0 10.2 10.4 10.7 10.9 11.2 11.4 11.7 11.9 12.2 12.4 12.7 12.9 13.2 13.4 13.7 13.9 14.2 14.4 14.7 14.9 15.2 15.4 15.7 15.9 16.2 16.4 16.7 16.9 17.2 17.4 17.7 17.9 18.2 18.4 18.7 18.9 19.2 19.4 19.7 19.9 20.1 20.4 20.6 20.9 21.1 21.4 21.6 21.9 22.1 22.4 22.6 22.9 23.1 23.4 23.6 23.9 24.1 24.4 24.6 24.9 25.1 25.4 25.6 25.9 26.1 26.4 26.6 26.9 27.1 27.4 27.6 27.9 28.1 28.4 28.6 28.9 29.1 29.4 29.6 29.9 30.1 30.3 30.6 30.8 31.1 31.3 31.6 31.8 32.1 32.3 32.6 32.8 33.1 33.3 33.6 33.8 34.1 34.3 34.6 34.8 35.1 35.3 35.6 35.8 36.1 36.3 36.6 36.8 37.1 37.3 37.6 37.8 38.1 38.3 38.6 38.8 39.1 39.3 39.6 39.8 40.0 40.3 40.5 40.8 41.0 41.3 41.5 41.8 42.0 42.3 42.5 42.8 43.0 43.3 43.5 43.8 44.0 44.3 44.5 44.8 45.0 45.3 45.5 45.8 46.0 46.3 46.5 46.8 47.0 47.3 47.5 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 52.5 52.7 53.0 53.2 53.5 53.7 54.0 54.2 54.5 54.7 55.0 55.2 55.5 55.7 56.0 56.2 56.5 56.7 57.0 57.2 57.5 57.7 58.0 58.2 58.5 58.7 59.0 59.2 59.5 59.7 60.0 60.2 60.4 60.7 60.9 61.2 61.4 61.7 61.9 62.2 62.4 62.7 62.9 63.2 63.4 63.7 63.9 64.2 64.4 64.7 64.9 65.2 65.4 65.7 65.9 66.2 66.4 66.7 66.9 67.2 67.4 67.7 67.9 68.2 68.4 68.7 68.9 69.2 69.4 69.7 69.9 70.1 70.4 70.6 70.9 71.1 71.4 71.6 71.9 72.1 72.4 72.6 72.9 73.1 73.4 73.6 73.9 74.1 74.4 74.6 74.9 75.1 75.4 75.6 75.9 76.1 76.4 76.6 76.9 77.1 77.4 77.6 77.9 78.1 78.4 78.6 78.9 79.1 79.4 79.6 79.9 80.1 80.3 80.6 80.8 81.1 81.3 81.6 81.8 82.1 82.3 82.6 82.8 83.1 83.3 83.6 83.8 84.1 84.3 84.6 84.8 85.1 85.3 85.6 85.8 86.1 86.3 86.6 86.8 87.1 87.3 87.6 87.8 88.1 88.3 88.6 88.8 89.1 89.3 89.6 89.8 90.0 90.3 90.5 90.8 91.0 91.3 91.5 91.8 92.0 92.3 92.5 92.8 93.0 93.3 93.5 93.8 94.0 94.3 94.5 94.8 95.0 95.3 95.5 95.8 96.0 96.3 96.5 96.8 97.0 97.3 97.5 97.8 98.0 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 22163, rend_intergenic: 15762 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33758, rend_intergenic: 22341 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 35788, rend_intergenic: 33850 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 54299, rend_intergenic: 51849 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70588, rend_intergenic: 58397 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 104736, rend_intergenic: 75522 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119727, rend_intergenic: 115604 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131602, rend_intergenic: 119872 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 154717, rend_intergenic: 150834 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 20 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 13291 -exon list size: 7 building trellis 11.1 22.2 33.3 44.4 55.6 66.7 77.8 88.9 -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