-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_9036980-9264167 -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_1-snap.1625-T1 Valid prediction for GlimmerHMM_glimmerT_1285-T1 Valid prediction for snap_scaffold_1-snap.1651-T1 Valid prediction for snap_scaffold_1-snap.1638-T1 Valid prediction for snap_scaffold_1-snap.1645-T1 Valid prediction for snap_scaffold_1-snap.1629-T1 Valid prediction for pasa_asmbl_1956.p1 Valid prediction for snap_scaffold_1-snap.1642-T1 Valid prediction for pasa_asmbl_1957.p1 Valid prediction for snap_scaffold_1-snap.1620-T1 Valid prediction for snap_scaffold_1-snap.1640-T1 Valid prediction for HiQ_model.g935.t1 Valid prediction for pasa_asmbl_1960.p1 Valid prediction for snap_scaffold_1-snap.1621-T1 Valid prediction for CodingQuarry_transcript_2722-T1 Valid prediction for CodingQuarry_transcript_2726-T1 Valid prediction for pasa_asmbl_1962.p1 Valid prediction for GlimmerHMM_glimmerT_1269-T1 Valid prediction for GlimmerHMM_glimmerT_1267-T1 Valid prediction for GlimmerHMM_glimmerT_1288-T1 Valid prediction for Augustus_model.g936.t1 Valid prediction for GlimmerHMM_glimmerT_1277-T1 Valid prediction for pasa_asmbl_1968.p1 Valid prediction for GlimmerHMM_glimmerT_1293-T1 Valid prediction for CodingQuarry_transcript_2727-T1 Valid prediction for Augustus_model.g945.t1 Valid prediction for snap_scaffold_1-snap.1648-T1 Valid prediction for snap_scaffold_1-snap.1611-T1 Valid prediction for Augustus_model.g931.t1 Valid prediction for snap_scaffold_1-snap.1646-T1 Valid prediction for snap_scaffold_1-snap.1614-T1 Valid prediction for GlimmerHMM_glimmerT_1291-T1 Valid prediction for GlimmerHMM_glimmerT_1282-T1 Valid prediction for GlimmerHMM_glimmerT_1274-T1 Valid prediction for snap_scaffold_1-snap.1633-T1 Valid prediction for Augustus_model.g934.t1 Valid prediction for snap_scaffold_1-snap.1634-T1 Valid prediction for snap_scaffold_1-snap.1626-T1 Valid prediction for GlimmerHMM_glimmerT_1268-T1 Valid prediction for GlimmerHMM_glimmerT_1284-T1 Valid prediction for HiQ_model.g941.t1 Valid prediction for HiQ_model.g943.t1 Couldn't classify 117591, 117722 Sorry, prediction pasa_asmbl_1958.p1 fails validation. (GTA) AA 117591-117722 GT AGG (CTT) AG 118882-119010 GT AGG (GAA) AG 119120-119236 GT ATG (CTG) AG 119388-119445 GT AAG (TGA) AG 119546-119601 GT GTG (ACG) AG 119839-119967 GT AGG (GAG) AG 120133-120334 GT AGG (TGA) AG 120479-120667 GT AGG (AGT) AG 120817-120959 GT AGG (GTG) AG 121045-121176 GT CAG (GAA) AG 121290-121348 GT GAG (GAA) AG 121432-121617 GT AGG (GTT) AG 121834-121924 GT AGG (CAC) AG 122151-122291 GT AGG (TTC) AG 122412-122523 GT AGG (TGG) AG 122706-122818 GT AGG (GAG) AG 123005-123211 GT ACG (AGC) AG 123392-123529 CT AAC add_exon() Sorry, pasa_asmbl_1958.p1 121290-121348-terminal-2 is invalid. -recovered pasa_asmbl_1958.p1, terminal, 121290, 121348 -recovered pasa_asmbl_1958.p1, terminal, 123392, 123529 -recovered pasa_asmbl_1958.p1, internal, 118882, 119010 -recovered pasa_asmbl_1958.p1, internal, 119120, 119236 -recovered pasa_asmbl_1958.p1, internal, 119388, 119445 -recovered pasa_asmbl_1958.p1, internal, 119546, 119601 -recovered pasa_asmbl_1958.p1, internal, 119839, 119967 -recovered pasa_asmbl_1958.p1, internal, 120133, 120334 -recovered pasa_asmbl_1958.p1, internal, 120479, 120667 -recovered pasa_asmbl_1958.p1, internal, 120817, 120959 -recovered pasa_asmbl_1958.p1, internal, 121045, 121176 -recovered pasa_asmbl_1958.p1, internal, 121290, 121348 -recovered pasa_asmbl_1958.p1, internal, 121432, 121617 -recovered pasa_asmbl_1958.p1, internal, 121834, 121924 -recovered pasa_asmbl_1958.p1, internal, 122151, 122291 -recovered pasa_asmbl_1958.p1, internal, 122412, 122523 -recovered pasa_asmbl_1958.p1, internal, 122706, 122818 -recovered pasa_asmbl_1958.p1, internal, 123005, 123211 Valid prediction for Augustus_model.g942.t1 Valid prediction for GlimmerHMM_glimmerT_1278-T1 Valid prediction for snap_scaffold_1-snap.1622-T1 Valid prediction for snap_scaffold_1-snap.1623-T1 Valid prediction for snap_scaffold_1-snap.1618-T1 Valid prediction for HiQ_model.g947.t1 Valid prediction for CodingQuarry_transcript_2724-T1 Valid prediction for GlimmerHMM_glimmerT_1280-T1 Valid prediction for GlimmerHMM_glimmerT_1294-T1 Valid prediction for GlimmerHMM_glimmerT_1289-T1 Valid prediction for CodingQuarry_transcript_2720-T1 Valid prediction for pasa_asmbl_1966.p1 Valid prediction for HiQ_model.g932.t1 Valid prediction for GlimmerHMM_glimmerT_1281-T1 Valid prediction for CodingQuarry_transcript_2723-T1 Valid prediction for snap_scaffold_1-snap.1628-T1 Valid prediction for snap_scaffold_1-snap.1616-T1 Valid prediction for HiQ_model.g933.t1 Valid prediction for snap_scaffold_1-snap.1630-T1 Valid prediction for Augustus_model.g927.t1 Valid prediction for HiQ_model.g948.t1 Valid prediction for pasa_asmbl_1953.p1 Couldn't classify 60452, 60799 Sorry, prediction pasa_asmbl_1952.p1 fails validation. (AGT) CC 60452-60799 CT CTC Valid prediction for snap_scaffold_1-snap.1650-T1 Valid prediction for GlimmerHMM_glimmerT_1295-T1 Valid prediction for Augustus_model.g930.t1 Valid prediction for snap_scaffold_1-snap.1619-T1 Valid prediction for GlimmerHMM_glimmerT_1272-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_1-snap.1612-T1 Valid prediction for GlimmerHMM_glimmerT_1283-T1 Valid prediction for snap_scaffold_1-snap.1641-T1 Valid prediction for GlimmerHMM_glimmerT_1287-T1 Valid prediction for snap_scaffold_1-snap.1617-T1 Valid prediction for snap_scaffold_1-snap.1627-T1 Valid prediction for GlimmerHMM_glimmerT_1296-T1 Valid prediction for snap_scaffold_1-snap.1643-T1 Valid prediction for Augustus_model.g944.t1 Valid prediction for GlimmerHMM_glimmerT_1271-T1 Valid prediction for GlimmerHMM_glimmerT_1286-T1 Valid prediction for snap_scaffold_1-snap.1637-T1 Valid prediction for Augustus_model.g937.t1 Valid prediction for GlimmerHMM_glimmerT_1292-T1 Valid prediction for Augustus_model.g949.t1 Couldn't classify 90561, 90657 Couldn't classify 92254, 92433 Sorry, prediction pasa_asmbl_521.p1 fails validation. (CTC) AT 90561-90657 GT AGG (ACA) AG 90760-90863 GT ATG (CAT) AG 90965-91103 GT AAG (GTG) AG 91188-91306 GT AGG (GTT) AG 91651-91800 GT ATG (CTG) AG 91914-92084 GT AAG (CCT) AG 92254-92433 GT TGG -recovered pasa_asmbl_521.p1, internal, 90760, 90863 -recovered pasa_asmbl_521.p1, internal, 90965, 91103 -recovered pasa_asmbl_521.p1, internal, 91188, 91306 -recovered pasa_asmbl_521.p1, internal, 91651, 91800 -recovered pasa_asmbl_521.p1, internal, 91914, 92084 -recovered pasa_asmbl_521.p1, internal, 92254, 92433 Valid prediction for pasa_asmbl_525.p1 Couldn't classify 5174, 5236 Sorry, prediction pasa_asmbl_529.p1 fails validation. (AGA) GG 5174-5236 GT ACG (GTT) AG 5372-5659 TA GAT -recovered pasa_asmbl_529.p1, terminal, 5372, 5659 Valid prediction for snap_scaffold_1-snap.1647-T1 Valid prediction for GlimmerHMM_glimmerT_1276-T1 Valid prediction for CodingQuarry_transcript_2725-T1 Valid prediction for snap_scaffold_1-snap.1615-T1 Couldn't classify 93275, 93290 Couldn't classify 100447, 100614 Sorry, prediction pasa_asmbl_517.p1 fails validation. (GAG) AT 93275-93290 GT AGG (GGA) AG 93373-93490 GT CGG (ATA) AG 93584-93707 GT AGG (GTG) AG 93797-93933 GT AAG (GGA) AG 95087-95342 GT CTG (GAG) AG 95471-95713 GT AGG (ATT) AG 95950-96126 GT AAG (TTG) AG 96217-96362 GT AAG (GAA) AG 96446-96536 GT AGG (GCT) AG 96675-97064 GT AGG (GCC) AG 97209-97335 GT TGG (CCG) AG 97456-97574 GT AGG (GCT) AG 97688-97884 GT AAG (GAA) AG 97968-98151 GT AGG (GTG) AG 98326-98491 GT GGG (TGG) AG 98597-98721 GT AGG (GGC) AG 98821-98936 GT CGG (CCG) AG 99028-99424 GT ATG (AAC) AG 99526-99651 GT ATG (GCA) AG 99764-99934 GT GAG (GTG) AG 100047-100151 GT AGG (ACT) AG 100240-100335 GT CGG (GAC) AG 100447-100614 TC GGT add_exon() Sorry, pasa_asmbl_517.p1 97688-97884-terminal-2 is invalid. -recovered pasa_asmbl_517.p1, terminal, 97688, 97884 -recovered pasa_asmbl_517.p1, internal, 93373, 93490 -recovered pasa_asmbl_517.p1, internal, 93584, 93707 -recovered pasa_asmbl_517.p1, internal, 93797, 93933 -recovered pasa_asmbl_517.p1, internal, 95087, 95342 -recovered pasa_asmbl_517.p1, internal, 95471, 95713 -recovered pasa_asmbl_517.p1, internal, 95950, 96126 -recovered pasa_asmbl_517.p1, internal, 96217, 96362 -recovered pasa_asmbl_517.p1, internal, 96446, 96536 -recovered pasa_asmbl_517.p1, internal, 96675, 97064 -recovered pasa_asmbl_517.p1, internal, 97209, 97335 -recovered pasa_asmbl_517.p1, internal, 97456, 97574 -recovered pasa_asmbl_517.p1, internal, 97688, 97884 -recovered pasa_asmbl_517.p1, internal, 97968, 98151 -recovered pasa_asmbl_517.p1, internal, 98326, 98491 -recovered pasa_asmbl_517.p1, internal, 98597, 98721 -recovered pasa_asmbl_517.p1, internal, 98821, 98936 -recovered pasa_asmbl_517.p1, internal, 99028, 99424 -recovered pasa_asmbl_517.p1, internal, 99526, 99651 -recovered pasa_asmbl_517.p1, internal, 99764, 99934 -recovered pasa_asmbl_517.p1, internal, 100047, 100151 -recovered pasa_asmbl_517.p1, internal, 100240, 100335 Valid prediction for snap_scaffold_1-snap.1632-T1 Valid prediction for snap_scaffold_1-snap.1639-T1 Valid prediction for Augustus_model.g946.t1 Valid prediction for Augustus_model.g939.t1 Valid prediction for snap_scaffold_1-snap.1624-T1 Valid prediction for snap_scaffold_1-snap.1613-T1 Couldn't classify 92395, 92433 Couldn't classify 93203, 93280 Sorry, prediction pasa_asmbl_519.p1 fails validation. (TAC) AG 92395-92433 GT TGG (GTC) AG 92542-92674 GT AGG (CAG) AG 92764-92837 GT AGG (GAG) AG 93203-93280 AA CCA -recovered pasa_asmbl_519.p1, internal, 92395, 92433 -recovered pasa_asmbl_519.p1, internal, 92542, 92674 -recovered pasa_asmbl_519.p1, internal, 92764, 92837 Valid prediction for GlimmerHMM_glimmerT_1275-T1 Couldn't classify 90026, 90044 Sorry, prediction pasa_asmbl_522.p1 fails validation. (ATG) CT 87787-87883 GT TGG (GTA) AG 88063-88166 GT AGG (ACC) AG 88387-88530 GT ATG (ACG) AG 88716-88872 GT TAG (ACC) AG 89047-89074 GT ACG (AAT) AG 90026-90044 GG GGG -recovered pasa_asmbl_522.p1, initial, 87787, 87883 -recovered pasa_asmbl_522.p1, internal, 88063, 88166 -recovered pasa_asmbl_522.p1, internal, 88387, 88530 -recovered pasa_asmbl_522.p1, internal, 88716, 88872 -recovered pasa_asmbl_522.p1, internal, 89047, 89074 Valid prediction for snap_scaffold_1-snap.1649-T1 Valid prediction for Augustus_model.g928.t1 Valid prediction for GlimmerHMM_glimmerT_1297-T1 Valid prediction for snap_scaffold_1-snap.1631-T1 Valid prediction for Augustus_model.g929.t1 Valid prediction for GlimmerHMM_glimmerT_1290-T1 Valid prediction for HiQ_model.g940.t1 Valid prediction for snap_scaffold_1-snap.1644-T1 Valid prediction for GlimmerHMM_glimmerT_1270-T1 Valid prediction for snap_scaffold_1-snap.1652-T1 Valid prediction for CodingQuarry_transcript_2721-T1 Valid prediction for pasa_asmbl_526.p1 Valid prediction for snap_scaffold_1-snap.1635-T1 Valid prediction for GlimmerHMM_glimmerT_1273-T1 Valid prediction for snap_scaffold_1-snap.1636-T1 Valid prediction for HiQ_model.g938.t1 Valid prediction for GlimmerHMM_glimmerT_1279-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16589, rend_intergenic: 8577 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 22739, rend_intergenic: 17045 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 25128, rend_intergenic: 22826 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33121, rend_intergenic: 32108 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36872, rend_intergenic: 35683 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67218, rend_intergenic: 65759 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 86485, rend_intergenic: 81282 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 112188, rend_intergenic: 97897 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 148750, rend_intergenic: 146109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 227188 -exon list size: 459 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 3.0 3.3 3.5 3.7 3.9 4.1 4.3 4.6 4.8 5.0 5.2 5.4 5.6 5.9 6.1 6.3 6.5 6.7 6.9 7.2 7.4 7.6 7.8 8.0 8.2 8.5 8.7 8.9 9.1 9.3 9.5 9.8 10.0 10.2 10.4 10.6 10.8 11.1 11.3 11.5 11.7 11.9 12.1 12.4 12.6 12.8 13.0 13.2 13.4 13.7 13.9 14.1 14.3 14.5 14.8 15.0 15.2 15.4 15.6 15.8 16.1 16.3 16.5 16.7 16.9 17.1 17.4 17.6 17.8 18.0 18.2 18.4 18.7 18.9 19.1 19.3 19.5 19.7 20.0 20.2 20.4 20.6 20.8 21.0 21.3 21.5 21.7 21.9 22.1 22.3 22.6 22.8 23.0 23.2 23.4 23.6 23.9 24.1 24.3 24.5 24.7 24.9 25.2 25.4 25.6 25.8 26.0 26.2 26.5 26.7 26.9 27.1 27.3 27.5 27.8 28.0 28.2 28.4 28.6 28.9 29.1 29.3 29.5 29.7 29.9 30.2 30.4 30.6 30.8 31.0 31.2 31.5 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 35.1 35.4 35.6 35.8 36.0 36.2 36.4 36.7 36.9 37.1 37.3 37.5 37.7 38.0 38.2 38.4 38.6 38.8 39.0 39.3 39.5 39.7 39.9 40.1 40.3 40.6 40.8 41.0 41.2 41.4 41.6 41.9 42.1 42.3 42.5 42.7 43.0 43.2 43.4 43.6 43.8 44.0 44.3 44.5 44.7 44.9 45.1 45.3 45.6 45.8 46.0 46.2 46.4 46.6 46.9 47.1 47.3 47.5 47.7 47.9 48.2 48.4 48.6 48.8 49.0 49.2 49.5 49.7 49.9 50.1 50.3 50.5 50.8 51.0 51.2 51.4 51.6 51.8 52.1 52.3 52.5 52.7 52.9 53.1 53.4 53.6 53.8 54.0 54.2 54.4 54.7 54.9 55.1 55.3 55.5 55.7 56.0 56.2 56.4 56.6 56.8 57.0 57.3 57.5 57.7 57.9 58.1 58.4 58.6 58.8 59.0 59.2 59.4 59.7 59.9 60.1 60.3 60.5 60.7 61.0 61.2 61.4 61.6 61.8 62.0 62.3 62.5 62.7 62.9 63.1 63.3 63.6 63.8 64.0 64.2 64.4 64.6 64.9 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 68.5 68.8 69.0 69.2 69.4 69.6 69.8 70.1 70.3 70.5 70.7 70.9 71.1 71.4 71.6 71.8 72.0 72.2 72.5 72.7 72.9 73.1 73.3 73.5 73.8 74.0 74.2 74.4 74.6 74.8 75.1 75.3 75.5 75.7 75.9 76.1 76.4 76.6 76.8 77.0 77.2 77.4 77.7 77.9 78.1 78.3 78.5 78.7 79.0 79.2 79.4 79.6 79.8 80.0 80.3 80.5 80.7 80.9 81.1 81.3 81.6 81.8 82.0 82.2 82.4 82.6 82.9 83.1 83.3 83.5 83.7 83.9 84.2 84.4 84.6 84.8 85.0 85.2 85.5 85.7 85.9 86.1 86.3 86.6 86.8 87.0 87.2 87.4 87.6 87.9 88.1 88.3 88.5 88.7 88.9 89.2 89.4 89.6 89.8 90.0 90.2 90.5 90.7 90.9 91.1 91.3 91.5 91.8 92.0 92.2 92.4 92.6 92.8 93.1 93.3 93.5 93.7 93.9 94.1 94.4 94.6 94.8 95.0 95.2 95.4 95.7 95.9 96.1 96.3 96.5 96.7 97.0 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 33 predictions from path traversal Error with prediction: snap lend_intergenic: 16589, rend_intergenic: 8577 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 22739, rend_intergenic: 17045 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 25128, rend_intergenic: 22826 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 33121, rend_intergenic: 32108 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36872, rend_intergenic: 35683 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67218, rend_intergenic: 65759 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 86485, rend_intergenic: 81282 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 112188, rend_intergenic: 97897 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 148750, rend_intergenic: 146109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 22 predictions persist after filtering for low support