-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_175132-454218 -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_21-snap.73-T1 Valid prediction for GlimmerHMM_glimmerT_46980-T1 Valid prediction for CodingQuarry_transcript_32410-T1 Valid prediction for snap_scaffold_21-snap.57-T1 Valid prediction for Augustus_model.g31266.t1 Valid prediction for snap_scaffold_21-snap.48-T1 Valid prediction for snap_scaffold_21-snap.43-T1 Valid prediction for HiQ_model.g31264.t1 Valid prediction for snap_scaffold_21-snap.72-T1 Valid prediction for GlimmerHMM_glimmerT_46989-T1 Couldn't classify 96470, 96670 Sorry, prediction pasa_asmbl_28255.p1 fails validation. (AAC) AT 96470-96670 GT AGG (GTG) AG 96747-96913 GT ACG (CCC) AG 97002-97100 GT AGG (ATT) AG 97180-97246 GT AAG (CAA) AG 97341-97403 GT AGG (CCT) AG 97607-97677 GT AGG (CTC) AG 97813-97918 GT AGG (GAT) AG 98008-98038 GT AGG (GAG) AG 98118-98216 GT GAG (AAG) AG 98391-98523 GT AGG (GCA) AG 98735-98825 AT GAA -recovered pasa_asmbl_28255.p1, terminal, 98735, 98825 -recovered pasa_asmbl_28255.p1, internal, 96747, 96913 -recovered pasa_asmbl_28255.p1, internal, 97002, 97100 -recovered pasa_asmbl_28255.p1, internal, 97180, 97246 -recovered pasa_asmbl_28255.p1, internal, 97341, 97403 -recovered pasa_asmbl_28255.p1, internal, 97607, 97677 -recovered pasa_asmbl_28255.p1, internal, 97813, 97918 -recovered pasa_asmbl_28255.p1, internal, 98008, 98038 -recovered pasa_asmbl_28255.p1, internal, 98118, 98216 -recovered pasa_asmbl_28255.p1, internal, 98391, 98523 Valid prediction for Augustus_model.g31287.t1 Valid prediction for Augustus_model.g31261.t1 Valid prediction for snap_scaffold_21-snap.54-T1 Valid prediction for snap_scaffold_21-snap.45-T1 Valid prediction for Augustus_model.g31284.t1 Valid prediction for GlimmerHMM_glimmerT_46978-T1 Valid prediction for snap_scaffold_21-snap.58-T1 Valid prediction for GlimmerHMM_glimmerT_46973-T1 Valid prediction for snap_scaffold_21-snap.40-T1 Valid prediction for snap_scaffold_21-snap.74-T1 Valid prediction for GlimmerHMM_glimmerT_46996-T1 Valid prediction for snap_scaffold_21-snap.53-T1 Valid prediction for HiQ_model.g31271.t1 Valid prediction for Augustus_model.g31275.t1 Valid prediction for HiQ_model.g31269.t1 Valid prediction for GlimmerHMM_glimmerT_46966-T1 Valid prediction for GlimmerHMM_glimmerT_46984-T1 Valid prediction for GlimmerHMM_glimmerT_46990-T1 Valid prediction for CodingQuarry_transcript_32409-T1 Valid prediction for snap_scaffold_21-snap.77-T1 Valid prediction for snap_scaffold_21-snap.47-T1 Valid prediction for snap_scaffold_21-snap.69-T1 Valid prediction for snap_scaffold_21-snap.70-T1 Valid prediction for Augustus_model.g31257.t1 Valid prediction for snap_scaffold_21-snap.56-T1 Valid prediction for GlimmerHMM_glimmerT_46975-T1 Valid prediction for snap_scaffold_21-snap.46-T1 Valid prediction for Augustus_model.g31285.t1 Valid prediction for Augustus_model.g31288.t1 Couldn't classify 267010, 268026 Sorry, prediction pasa_asmbl_28260.p1 fails validation. (ATG) GC 267010-268026 TG GGT Valid prediction for GlimmerHMM_glimmerT_46993-T1 Couldn't classify 264226, 264291 Couldn't classify 265216, 266073 Sorry, prediction pasa_asmbl_28258.p1 fails validation. (TCT) CC 264226-264291 GT AGG (GTC) AG 264827-264904 GT AGG (ATG) AG 265216-266073 AC GTA -recovered pasa_asmbl_28258.p1, internal, 264827, 264904 Couldn't classify 49991, 50115 Sorry, prediction pasa_asmbl_28250.p1 fails validation. (GTG) AA 49991-50115 GT GGG (GAT) AG 50405-50515 GT AGG (GTT) AG 51114-51196 GT TGG (ATG) AG 52125-52219 GT TAG (GTT) AG 52321-52386 AG AAA -recovered pasa_asmbl_28250.p1, initial, 52125, 52219 -recovered pasa_asmbl_28250.p1, terminal, 52321, 52386 -recovered pasa_asmbl_28250.p1, internal, 50405, 50515 -recovered pasa_asmbl_28250.p1, internal, 51114, 51196 -recovered pasa_asmbl_28250.p1, internal, 52125, 52219 Valid prediction for snap_scaffold_21-snap.76-T1 Valid prediction for GlimmerHMM_glimmerT_46991-T1 Valid prediction for GlimmerHMM_glimmerT_46972-T1 Couldn't classify 261947, 262210 Couldn't classify 262725, 262886 Sorry, prediction pasa_asmbl_28257.p1 fails validation. (GAG) AG 261947-262210 GT AGG (TAC) AG 262725-262886 CC TAC -recovered pasa_asmbl_28257.p1, internal, 261947, 262210 Valid prediction for GlimmerHMM_glimmerT_46967-T1 Valid prediction for snap_scaffold_21-snap.35-T1 Valid prediction for snap_scaffold_21-snap.71-T1 Couldn't classify 272025, 272073 Couldn't classify 273822, 273852 Sorry, prediction pasa_asmbl_28261.p1 fails validation. (AAA) AG 272025-272073 GT GGG (GTT) AG 272627-272716 GT AGG (TGA) AG 273029-273226 GT GGG (AGG) AG 273498-273693 GT AGG (GGG) AG 273822-273852 AT ACA -recovered pasa_asmbl_28261.p1, internal, 272025, 272073 -recovered pasa_asmbl_28261.p1, internal, 272627, 272716 -recovered pasa_asmbl_28261.p1, internal, 273029, 273226 -recovered pasa_asmbl_28261.p1, internal, 273498, 273693 Valid prediction for CodingQuarry_transcript_32408-T1 Valid prediction for Augustus_model.g31267.t1 Valid prediction for pasa_asmbl_28252.p1 Valid prediction for snap_scaffold_21-snap.75-T1 Valid prediction for GlimmerHMM_glimmerT_46979-T1 Valid prediction for GlimmerHMM_glimmerT_46976-T1 Valid prediction for CodingQuarry_transcript_32405-T1 Valid prediction for Augustus_model.g31270.t1 Valid prediction for GlimmerHMM_glimmerT_46977-T1 Valid prediction for Augustus_model.g31290.t1 Valid prediction for GlimmerHMM_glimmerT_46970-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 CodingQuarry_transcript_32413-T1 Valid prediction for Augustus_model.g31283.t1 Valid prediction for snap_scaffold_21-snap.52-T1 Valid prediction for snap_scaffold_21-snap.41-T1 Valid prediction for GlimmerHMM_glimmerT_46974-T1 Valid prediction for Augustus_model.g31279.t1 Valid prediction for snap_scaffold_21-snap.51-T1 Valid prediction for snap_scaffold_21-snap.67-T1 Valid prediction for snap_scaffold_21-snap.37-T1 Valid prediction for snap_scaffold_21-snap.62-T1 Valid prediction for snap_scaffold_21-snap.64-T1 Couldn't classify 37463, 37556 Couldn't classify 41299, 41367 Sorry, prediction pasa_asmbl_27318.p1 fails validation. (CCC) GA 37463-37556 GT AGG (GAG) AG 39358-39699 GT TGG (AGC) AG 39822-40103 GT CAG (GAA) AG 40392-40485 GT AAG (GCC) AG 40788-40861 GT AGG (TTG) AG 40976-41043 GT AAG (GAT) AG 41299-41367 AG CTA -recovered pasa_asmbl_27318.p1, internal, 39358, 39699 -recovered pasa_asmbl_27318.p1, internal, 39822, 40103 -recovered pasa_asmbl_27318.p1, internal, 40392, 40485 -recovered pasa_asmbl_27318.p1, internal, 40788, 40861 -recovered pasa_asmbl_27318.p1, internal, 40976, 41043 Valid prediction for Augustus_model.g31280.t1 Couldn't classify 46372, 46475 Sorry, prediction pasa_asmbl_27313.p1 fails validation. (CGT) AG 46372-46475 GT AGG (GAT) AG 46714-46908 GT AGG (GTA) AG 47280-47428 GT AGG (CCT) AG 47791-47911 GT AAG (GTT) AG 48489-48498 AG GAA -recovered pasa_asmbl_27313.p1, terminal, 48489, 48498 -recovered pasa_asmbl_27313.p1, internal, 46372, 46475 -recovered pasa_asmbl_27313.p1, internal, 46714, 46908 -recovered pasa_asmbl_27313.p1, internal, 47280, 47428 -recovered pasa_asmbl_27313.p1, internal, 47791, 47911 Valid prediction for HiQ_model.g31282.t1 Valid prediction for GlimmerHMM_glimmerT_46969-T1 Valid prediction for Augustus_model.g31273.t1 Valid prediction for Augustus_model.g31289.t1 Valid prediction for GlimmerHMM_glimmerT_46992-T1 Valid prediction for snap_scaffold_21-snap.61-T1 Valid prediction for Augustus_model.g31260.t1 Valid prediction for GlimmerHMM_glimmerT_46985-T1 Valid prediction for snap_scaffold_21-snap.65-T1 Valid prediction for GlimmerHMM_glimmerT_46995-T1 Valid prediction for snap_scaffold_21-snap.63-T1 Valid prediction for snap_scaffold_21-snap.44-T1 Valid prediction for GlimmerHMM_glimmerT_46987-T1 Valid prediction for Augustus_model.g31272.t1 Valid prediction for GlimmerHMM_glimmerT_46965-T1 Valid prediction for snap_scaffold_21-snap.49-T1 Valid prediction for snap_scaffold_21-snap.60-T1 Valid prediction for GlimmerHMM_glimmerT_46968-T1 Valid prediction for snap_scaffold_21-snap.55-T1 Valid prediction for snap_scaffold_21-snap.39-T1 Valid prediction for Augustus_model.g31262.t1 Valid prediction for CodingQuarry_transcript_32411-T1 Valid prediction for Augustus_model.g31263.t1 Valid prediction for GlimmerHMM_glimmerT_46982-T1 Couldn't classify 125611, 125727 Sorry, prediction pasa_asmbl_27298.p1 fails validation. (ATT) TG 125611-125727 GT TGG (TCC) AG 125929-126012 GT AGG (ATT) AG 126184-126294 GT TGG (CTG) AG 126559-126657 GT CGG (AAT) AG 127401-127443 GT GGG (AGC) AG 127573-127678 GT AGG (GCA) AG 127875-128012 GT CTG (CCT) AG 128689-128721 GT TGG (CAC) AG 129744-129858 GT AGG (AAG) AG 130147-130252 GT TAG (TTG) AG 131292-131510 GT GGG (GCC) AG 132104-132254 GT AGG (AGC) AG 132941-132976 GT AGG (GAT) AG 133155-133321 GT TGG (AAC) AG 133410-133556 GT TGG (TGT) AG 133714-133799 GT GGG (TTC) AG 133887-134012 GT AGG (GAA) AG 134394-134508 GT AGG (ATG) AG 134695-134795 GT AGG (AGG) AG 135133-135210 GT AGG (AAT) AG 135428-135503 GT CGG (AAC) AG 136709-136876 GT TGG (ATA) AG 137835-137922 GT ACG (GTG) AG 138011-138088 GT GAG (TGC) AG 138189-138283 GT AGG (AAA) AG 138443-138721 GT CTG (TGG) AG 138909-139214 GT CGG (GTA) AG 139408-139637 GT AGG (GAC) AG 140025-140097 GT AGG (ATC) AG 140551-140561 TG AGT add_exon() Sorry, pasa_asmbl_27298.p1 134695-134795-initial-1 is invalid. -recovered pasa_asmbl_27298.p1, initial, 134695, 134795 add_exon() Sorry, pasa_asmbl_27298.p1 132104-132254-terminal-3 is invalid. -recovered pasa_asmbl_27298.p1, terminal, 132104, 132254 -recovered pasa_asmbl_27298.p1, terminal, 140551, 140561 -recovered pasa_asmbl_27298.p1, internal, 125929, 126012 -recovered pasa_asmbl_27298.p1, internal, 126184, 126294 -recovered pasa_asmbl_27298.p1, internal, 126559, 126657 -recovered pasa_asmbl_27298.p1, internal, 127401, 127443 -recovered pasa_asmbl_27298.p1, internal, 127573, 127678 -recovered pasa_asmbl_27298.p1, internal, 127875, 128012 -recovered pasa_asmbl_27298.p1, internal, 128689, 128721 -recovered pasa_asmbl_27298.p1, internal, 129744, 129858 -recovered pasa_asmbl_27298.p1, internal, 130147, 130252 -recovered pasa_asmbl_27298.p1, internal, 131292, 131510 -recovered pasa_asmbl_27298.p1, internal, 132104, 132254 -recovered pasa_asmbl_27298.p1, internal, 132941, 132976 -recovered pasa_asmbl_27298.p1, internal, 133155, 133321 -recovered pasa_asmbl_27298.p1, internal, 133410, 133556 -recovered pasa_asmbl_27298.p1, internal, 133714, 133799 -recovered pasa_asmbl_27298.p1, internal, 133887, 134012 -recovered pasa_asmbl_27298.p1, internal, 134394, 134508 -recovered pasa_asmbl_27298.p1, internal, 134695, 134795 -recovered pasa_asmbl_27298.p1, internal, 135133, 135210 -recovered pasa_asmbl_27298.p1, internal, 135428, 135503 -recovered pasa_asmbl_27298.p1, internal, 136709, 136876 -recovered pasa_asmbl_27298.p1, internal, 137835, 137922 -recovered pasa_asmbl_27298.p1, internal, 138011, 138088 -recovered pasa_asmbl_27298.p1, internal, 138189, 138283 -recovered pasa_asmbl_27298.p1, internal, 138443, 138721 -recovered pasa_asmbl_27298.p1, internal, 138909, 139214 -recovered pasa_asmbl_27298.p1, internal, 139408, 139637 -recovered pasa_asmbl_27298.p1, internal, 140025, 140097 Valid prediction for CodingQuarry_transcript_32406-T1 Valid prediction for snap_scaffold_21-snap.59-T1 Valid prediction for Augustus_model.g31276.t1 Valid prediction for GlimmerHMM_glimmerT_46994-T1 Valid prediction for pasa_asmbl_27306.p1 Valid prediction for Augustus_model.g31259.t1 Valid prediction for Augustus_model.g31274.t1 Valid prediction for Augustus_model.g31278.t1 Valid prediction for Augustus_model.g31286.t1 Valid prediction for GlimmerHMM_glimmerT_46971-T1 Valid prediction for HiQ_model.g31265.t1 Valid prediction for snap_scaffold_21-snap.38-T1 Valid prediction for snap_scaffold_21-snap.66-T1 Valid prediction for pasa_asmbl_27279.p1 Valid prediction for Augustus_model.g31268.t1 Valid prediction for Augustus_model.g31258.t1 Valid prediction for GlimmerHMM_glimmerT_46981-T1 Valid prediction for GlimmerHMM_glimmerT_46988-T1 Valid prediction for snap_scaffold_21-snap.68-T1 Valid prediction for snap_scaffold_21-snap.36-T1 Valid prediction for snap_scaffold_21-snap.42-T1 Valid prediction for Augustus_model.g31277.t1 Valid prediction for GlimmerHMM_glimmerT_46983-T1 Valid prediction for HiQ_model.g31281.t1 Valid prediction for snap_scaffold_21-snap.50-T1 Valid prediction for CodingQuarry_transcript_32412-T1 Valid prediction for GlimmerHMM_glimmerT_46986-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 155898, rend_intergenic: 148998 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 161041, rend_intergenic: 159457 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 279087 -exon list size: 491 building trellis 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.7 3.9 4.1 4.3 4.5 4.7 4.9 5.1 5.3 5.5 5.7 5.9 6.1 6.3 6.5 6.7 6.9 7.1 7.3 7.5 7.7 7.9 8.1 8.3 8.5 8.7 8.9 9.1 9.3 9.5 9.7 9.9 10.1 10.3 10.5 10.8 11.0 11.2 11.4 11.6 11.8 12.0 12.2 12.4 12.6 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.6 15.8 16.0 16.2 16.4 16.6 16.8 17.0 17.2 17.4 17.6 17.8 18.1 18.3 18.5 18.7 18.9 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.5 20.7 20.9 21.1 21.3 21.5 21.7 21.9 22.1 22.3 22.5 22.7 22.9 23.1 23.3 23.5 23.7 23.9 24.1 24.3 24.5 24.7 24.9 25.2 25.4 25.6 25.8 26.0 26.2 26.4 26.6 26.8 27.0 27.2 27.4 27.6 27.8 28.0 28.2 28.4 28.6 28.8 29.0 29.2 29.4 29.6 29.8 30.0 30.2 30.4 30.6 30.8 31.0 31.2 31.4 31.6 31.8 32.0 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.5 34.7 34.9 35.1 35.3 35.5 35.7 35.9 36.1 36.3 36.5 36.7 36.9 37.1 37.3 37.5 37.7 37.9 38.1 38.3 38.5 38.7 38.9 39.1 39.4 39.6 39.8 40.0 40.2 40.4 40.6 40.8 41.0 41.2 41.4 41.6 41.8 42.0 42.2 42.4 42.6 42.8 43.0 43.2 43.4 43.6 43.8 44.0 44.2 44.4 44.6 44.8 45.0 45.2 45.4 45.6 45.8 46.0 46.2 46.5 46.7 46.9 47.1 47.3 47.5 47.7 47.9 48.1 48.3 48.5 48.7 48.9 49.1 49.3 49.5 49.7 49.9 50.1 50.3 50.5 50.7 50.9 51.1 51.3 51.5 51.7 51.9 52.1 52.3 52.5 52.7 52.9 53.1 53.3 53.5 53.8 54.0 54.2 54.4 54.6 54.8 55.0 55.2 55.4 55.6 55.8 56.0 56.2 56.4 56.6 56.8 57.0 57.2 57.4 57.6 57.8 58.0 58.2 58.4 58.6 58.8 59.0 59.2 59.4 59.6 59.8 60.0 60.2 60.4 60.6 60.9 61.1 61.3 61.5 61.7 61.9 62.1 62.3 62.5 62.7 62.9 63.1 63.3 63.5 63.7 63.9 64.1 64.3 64.5 64.7 64.9 65.1 65.3 65.5 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.1 67.3 67.5 67.7 68.0 68.2 68.4 68.6 68.8 69.0 69.2 69.4 69.6 69.8 70.0 70.2 70.4 70.6 70.8 71.0 71.2 71.4 71.6 71.8 72.0 72.2 72.4 72.6 72.8 73.0 73.2 73.4 73.6 73.8 74.0 74.2 74.4 74.6 74.8 75.1 75.3 75.5 75.7 75.9 76.1 76.3 76.5 76.7 76.9 77.1 77.3 77.5 77.7 77.9 78.1 78.3 78.5 78.7 78.9 79.1 79.3 79.5 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.1 81.3 81.5 81.7 81.9 82.2 82.4 82.6 82.8 83.0 83.2 83.4 83.6 83.8 84.0 84.2 84.4 84.6 84.8 85.0 85.2 85.4 85.6 85.8 86.0 86.2 86.4 86.6 86.8 87.0 87.2 87.4 87.6 87.8 88.0 88.2 88.4 88.6 88.8 89.0 89.2 89.5 89.7 89.9 90.1 90.3 90.5 90.7 90.9 91.1 91.3 91.5 91.7 91.9 92.1 92.3 92.5 92.7 92.9 93.1 93.3 93.5 93.7 93.9 94.1 94.3 94.5 94.7 94.9 95.1 95.3 95.5 95.7 95.9 96.1 96.3 96.6 96.8 97.0 97.2 97.4 97.6 97.8 98.0 98.2 98.4 98.6 98.8 99.0 99.2 99.4 99.6 99.8 -found 40 predictions from path traversal Error with prediction: snap lend_intergenic: 155898, rend_intergenic: 148998 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 161041, rend_intergenic: 159457 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 40 predictions persist after filtering for low support