-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_8912874-9115304 -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 Augustus_model.g939.t1 Valid prediction for GlimmerHMM_glimmerT_1321-T1 Couldn't classify 184558, 184905 Sorry, prediction pasa_asmbl_1946.p1 fails validation. (AGT) CC 184558-184905 CT CTC Valid prediction for GeneMark_model.1721_t Valid prediction for GeneMark_model.1715_t Couldn't classify 110932, 111858 Sorry, prediction pasa_asmbl_1944.p1 fails validation. (ATC) CC 110932-111858 GT AGG (TTG) AG 111948-112074 GT TGG (ATG) AG 112160-112387 GT AAG (GAG) AG 112530-112742 GT GGG (GTT) AG 112870-112987 GT AGG (GGG) AG 113069-113240 GT AGG (ACC) AG 113361-113708 GT AGG (TTT) AG 113844-114065 GT AGG (CCC) AG 114192-114432 GT TGG (GAA) AG 114545-114734 GT AAG (CTC) AG 114840-115023 GT AGG (AAG) AG 115185-115196 GG GAG add_exon() Sorry, pasa_asmbl_1944.p1 112160-112387-initial-1 is invalid. -recovered pasa_asmbl_1944.p1, initial, 112160, 112387 -recovered pasa_asmbl_1944.p1, terminal, 115185, 115196 -recovered pasa_asmbl_1944.p1, internal, 111948, 112074 -recovered pasa_asmbl_1944.p1, internal, 112160, 112387 -recovered pasa_asmbl_1944.p1, internal, 112530, 112742 -recovered pasa_asmbl_1944.p1, internal, 112870, 112987 -recovered pasa_asmbl_1944.p1, internal, 113069, 113240 -recovered pasa_asmbl_1944.p1, internal, 113361, 113708 -recovered pasa_asmbl_1944.p1, internal, 113844, 114065 -recovered pasa_asmbl_1944.p1, internal, 114192, 114432 -recovered pasa_asmbl_1944.p1, internal, 114545, 114734 -recovered pasa_asmbl_1944.p1, internal, 114840, 115023 Valid prediction for snap_scaffold_1-snap.1635-T1 Couldn't classify 109194, 109243 Sorry, prediction pasa_asmbl_1942.p1 fails validation. (ATG) GG 106590-106675 GT GGG (GTG) AG 106890-107050 GT AGG (GAA) AG 108297-108397 GT AGG (GCC) AG 108610-108784 GT AGG (CTC) AG 108873-109058 GT AGG (ACC) AG 109194-109243 AG AGA -recovered pasa_asmbl_1942.p1, initial, 106590, 106675 -recovered pasa_asmbl_1942.p1, internal, 106890, 107050 -recovered pasa_asmbl_1942.p1, internal, 108297, 108397 -recovered pasa_asmbl_1942.p1, internal, 108610, 108784 -recovered pasa_asmbl_1942.p1, internal, 108873, 109058 Valid prediction for snap_scaffold_1-snap.1633-T1 Couldn't classify 56808, 56835 Sorry, prediction pasa_asmbl_2693.p1 fails validation. (ATG) AA 55236-55535 GT AAG (TCA) AG 55666-55731 GT CAG (GCA) AG 55889-55921 GT AAG (AAT) AG 56072-56126 GT TGG (ATT) AG 56204-56282 GT TGG (GTT) AG 56413-56479 GT AGG (GCT) AG 56569-56717 GT AGG (AAA) AG 56808-56835 AG CCA -recovered pasa_asmbl_2693.p1, initial, 55236, 55535 -recovered pasa_asmbl_2693.p1, internal, 55666, 55731 -recovered pasa_asmbl_2693.p1, internal, 55889, 55921 -recovered pasa_asmbl_2693.p1, internal, 56072, 56126 -recovered pasa_asmbl_2693.p1, internal, 56204, 56282 -recovered pasa_asmbl_2693.p1, internal, 56413, 56479 -recovered pasa_asmbl_2693.p1, internal, 56569, 56717 Valid prediction for GeneMark_model.1725_t Valid prediction for GeneMark_model.1727_t Valid prediction for snap_scaffold_1-snap.1645-T1 Valid prediction for snap_scaffold_1-snap.1623-T1 Valid prediction for Augustus_model.g930.t1 Valid prediction for snap_scaffold_1-snap.1646-T1 Valid prediction for GeneMark_model.1706_t Valid prediction for snap_scaffold_1-snap.1637-T1 Valid prediction for GeneMark_model.1719_t Valid prediction for GlimmerHMM_glimmerT_1308-T1 Valid prediction for snap_scaffold_1-snap.1640-T1 Couldn't classify 192799, 194079 Sorry, prediction pasa_asmbl_1947.p1 fails validation. (AAG) GC 192799-194079 GT AGG (GTG) AG 195933-196602 GT GGG (TTA) AG 196790-196882 GT GGG (GCC) AG 198893-198966 GT AGG (GGT) AG 199161-199360 GT AGG (GGT) AG 200077-200168 GT TGG (CCT) AG 200267-200436 GT AGG (GTG) AG 200551-200745 GA AAG -recovered pasa_asmbl_1947.p1, terminal, 200551, 200745 -recovered pasa_asmbl_1947.p1, internal, 195933, 196602 -recovered pasa_asmbl_1947.p1, internal, 196790, 196882 -recovered pasa_asmbl_1947.p1, internal, 198893, 198966 -recovered pasa_asmbl_1947.p1, internal, 199161, 199360 -recovered pasa_asmbl_1947.p1, internal, 200077, 200168 -recovered pasa_asmbl_1947.p1, internal, 200267, 200436 Valid prediction for Augustus_model.g931.t1 Valid prediction for snap_scaffold_1-snap.1632-T1 Valid prediction for snap_scaffold_1-snap.1624-T1 Valid prediction for GlimmerHMM_glimmerT_1303-T1 Valid prediction for snap_scaffold_1-snap.1643-T1 Valid prediction for GlimmerHMM_glimmerT_1318-T1 Valid prediction for GlimmerHMM_glimmerT_1317-T1 Valid prediction for GlimmerHMM_glimmerT_1314-T1 Valid prediction for GeneMark_model.1737_t Valid prediction for snap_scaffold_1-snap.1628-T1 Valid prediction for snap_scaffold_1-snap.1630-T1 Valid prediction for Augustus_model.g934.t1 Valid prediction for Augustus_model.g937.t1 Valid prediction for GlimmerHMM_glimmerT_1309-T1 Valid prediction for snap_scaffold_1-snap.1642-T1 Valid prediction for GeneMark_model.1731_t Couldn't classify 109744, 109865 Couldn't classify 109987, 110527 Sorry, prediction pasa_asmbl_1943.p1 fails validation. (CCG) CG 109744-109865 GT AGG (GGA) AG 109987-110527 CC GTC Valid prediction for Augustus_model.g927.t1 Valid prediction for Augustus_model.g938.t1 Valid prediction for GlimmerHMM_glimmerT_1320-T1 Valid prediction for snap_scaffold_1-snap.1641-T1 Valid prediction for snap_scaffold_1-snap.1626-T1 Valid prediction for Augustus_model.g933.t1 Valid prediction for GlimmerHMM_glimmerT_1304-T1 Valid prediction for GeneMark_model.1739_t Valid prediction for snap_scaffold_1-snap.1639-T1 Valid prediction for GeneMark_model.1733_t Valid prediction for GeneMark_model.1716_t -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 GeneMark_model.1710_t Valid prediction for GeneMark_model.1712_t Valid prediction for GlimmerHMM_glimmerT_1319-T1 Valid prediction for GlimmerHMM_glimmerT_1311-T1 Valid prediction for GeneMark_model.1714_t Valid prediction for snap_scaffold_1-snap.1644-T1 Valid prediction for GeneMark_model.1729_t Valid prediction for snap_scaffold_1-snap.1636-T1 Valid prediction for GlimmerHMM_glimmerT_1307-T1 Valid prediction for GeneMark_model.1735_t Valid prediction for snap_scaffold_1-snap.1619-T1 Valid prediction for GeneMark_model.1728_t Valid prediction for GlimmerHMM_glimmerT_1305-T1 Valid prediction for snap_scaffold_1-snap.1629-T1 Valid prediction for GlimmerHMM_glimmerT_1301-T1 Valid prediction for snap_scaffold_1-snap.1638-T1 Valid prediction for CodingQuarry_transcript_2715-T1 Valid prediction for GeneMark_model.1707_t Valid prediction for GeneMark_model.1723_t Valid prediction for GlimmerHMM_glimmerT_1316-T1 Valid prediction for GeneMark_model.1734_t Valid prediction for pasa_asmbl_519.p1 Valid prediction for GlimmerHMM_glimmerT_1293-T1 Couldn't classify 130630, 130893 Sorry, prediction pasa_asmbl_512.p1 fails validation. (CTG) CA 130630-130893 GT AGG (AAG) AG 132089-132373 GT AGG -recovered pasa_asmbl_512.p1, terminal, 132089, 132373 -recovered pasa_asmbl_512.p1, internal, 132089, 132373 Couldn't classify 122699, 122858 Sorry, prediction pasa_asmbl_514.p1 fails validation. (GCA) CT 122699-122858 GT AGG (CTG) AG 122981-123177 GT AAG (ATC) AG 123271-123351 GT AGG (ATT) AG 123442-123520 GT AGG (AGT) AG 123700-123939 GT AGG (CAA) AG 124073-124242 CC AAC add_exon() Sorry, pasa_asmbl_514.p1 123442-123520-terminal-3 is invalid. -recovered pasa_asmbl_514.p1, terminal, 123442, 123520 -recovered pasa_asmbl_514.p1, terminal, 124073, 124242 -recovered pasa_asmbl_514.p1, internal, 122981, 123177 -recovered pasa_asmbl_514.p1, internal, 123271, 123351 -recovered pasa_asmbl_514.p1, internal, 123442, 123520 -recovered pasa_asmbl_514.p1, internal, 123700, 123939 Valid prediction for GeneMark_model.1738_t Valid prediction for GlimmerHMM_glimmerT_1312-T1 Valid prediction for Augustus_model.g935.t1 Valid prediction for GeneMark_model.1705_t Valid prediction for GeneMark_model.1713_t Valid prediction for GlimmerHMM_glimmerT_1297-T1 Valid prediction for GlimmerHMM_glimmerT_1296-T1 Valid prediction for GlimmerHMM_glimmerT_1310-T1 Valid prediction for Augustus_model.g929.t1 Valid prediction for GeneMark_model.1717_t Valid prediction for snap_scaffold_1-snap.1634-T1 Valid prediction for GeneMark_model.1708_t Valid prediction for GlimmerHMM_glimmerT_1299-T1 Valid prediction for GlimmerHMM_glimmerT_1294-T1 Valid prediction for GeneMark_model.1730_t Valid prediction for GeneMark_model.1722_t Couldn't classify 119780, 120014 Sorry, prediction pasa_asmbl_518.p1 fails validation. (ATG) AG 119352-119429 GT GTG (AGT) AG 119542-119657 GC AGG (GGC) AG 119780-120014 GA CGG -recovered pasa_asmbl_518.p1, initial, 119352, 119429 -recovered pasa_asmbl_518.p1, internal, 119352, 119429 -recovered pasa_asmbl_518.p1, internal, 119542, 119657 Valid prediction for GlimmerHMM_glimmerT_1306-T1 Valid prediction for snap_scaffold_1-snap.1627-T1 Valid prediction for snap_scaffold_1-snap.1617-T1 Valid prediction for GeneMark_model.1718_t Valid prediction for GlimmerHMM_glimmerT_1315-T1 Couldn't classify 138107, 138166 Couldn't classify 139536, 139765 Sorry, prediction pasa_asmbl_508.p1 fails validation. (CGG) GC 138107-138166 GT AGG (GAG) AG 138256-138451 GT AGG (GAC) AG 139536-139765 TC GAT -recovered pasa_asmbl_508.p1, internal, 138256, 138451 Valid prediction for GlimmerHMM_glimmerT_1291-T1 Valid prediction for Augustus_model.g926.t1 Valid prediction for GlimmerHMM_glimmerT_1298-T1 Valid prediction for GeneMark_model.1709_t Valid prediction for GlimmerHMM_glimmerT_1313-T1 Valid prediction for snap_scaffold_1-snap.1616-T1 Valid prediction for Augustus_model.g928.t1 Valid prediction for GeneMark_model.1720_t Valid prediction for GlimmerHMM_glimmerT_1302-T1 Couldn't classify 120950, 121001 Couldn't classify 121529, 121632 Sorry, prediction pasa_asmbl_517.p1 fails validation. (CCT) CA 120950-121001 GT GGG (ATC) AG 121167-121349 GT AGG (GTA) AG 121529-121632 GA AGG add_exon() Sorry, pasa_asmbl_517.p1 121167-121349-terminal-1 is invalid. -recovered pasa_asmbl_517.p1, terminal, 121167, 121349 -recovered pasa_asmbl_517.p1, internal, 121167, 121349 Couldn't classify 130041, 130380 Sorry, prediction pasa_asmbl_513.p1 fails validation. (ATG) CT 128236-128317 GT AGG (CAA) AG 128650-129667 GT CGG (GTT) AG 130041-130380 AT AGA -recovered pasa_asmbl_513.p1, initial, 128236, 128317 -recovered pasa_asmbl_513.p1, internal, 128650, 129667 Valid prediction for snap_scaffold_1-snap.1625-T1 Valid prediction for GlimmerHMM_glimmerT_1292-T1 Valid prediction for snap_scaffold_1-snap.1620-T1 Valid prediction for snap_scaffold_1-snap.1618-T1 Valid prediction for GeneMark_model.1711_t Valid prediction for snap_scaffold_1-snap.1631-T1 Valid prediction for HiQ_model.g932.t1 Valid prediction for GeneMark_model.1732_t Valid prediction for snap_scaffold_1-snap.1622-T1 Valid prediction for GlimmerHMM_glimmerT_1300-T1 Valid prediction for snap_scaffold_1-snap.1621-T1 Valid prediction for Augustus_model.g936.t1 Valid prediction for GeneMark_model.1726_t Couldn't classify 122328, 122515 Sorry, prediction pasa_asmbl_516.p1 fails validation. (ATG) CC 121768-122059 GT GGG (GTA) AG 122328-122515 CC CCC -recovered pasa_asmbl_516.p1, initial, 121768, 122059 Valid prediction for GeneMark_model.1724_t Valid prediction for GlimmerHMM_glimmerT_1295-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 103750, rend_intergenic: 103352 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107718, rend_intergenic: 106590 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129163, rend_intergenic: 123891 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 135295, rend_intergenic: 132683 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140661, rend_intergenic: 135773 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 144531, rend_intergenic: 142973 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146845, rend_intergenic: 145319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149234, rend_intergenic: 146932 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 157227, rend_intergenic: 156214 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160978, rend_intergenic: 159789 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 191324, rend_intergenic: 189671 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 202431 -exon list size: 521 building trellis 0.2 0.4 0.6 0.8 1.0 1.1 1.3 1.5 1.7 1.9 2.1 2.3 2.5 2.7 2.9 3.1 3.3 3.4 3.6 3.8 4.0 4.2 4.4 4.6 4.8 5.0 5.2 5.4 5.5 5.7 5.9 6.1 6.3 6.5 6.7 6.9 7.1 7.3 7.5 7.6 7.8 8.0 8.2 8.4 8.6 8.8 9.0 9.2 9.4 9.6 9.8 9.9 10.1 10.3 10.5 10.7 10.9 11.1 11.3 11.5 11.7 11.9 12.0 12.2 12.4 12.6 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.1 14.3 14.5 14.7 14.9 15.1 15.3 15.5 15.7 15.9 16.1 16.3 16.4 16.6 16.8 17.0 17.2 17.4 17.6 17.8 18.0 18.2 18.4 18.5 18.7 18.9 19.1 19.3 19.5 19.7 19.9 20.1 20.3 20.5 20.7 20.8 21.0 21.2 21.4 21.6 21.8 22.0 22.2 22.4 22.6 22.8 22.9 23.1 23.3 23.5 23.7 23.9 24.1 24.3 24.5 24.7 24.9 25.0 25.2 25.4 25.6 25.8 26.0 26.2 26.4 26.6 26.8 27.0 27.2 27.3 27.5 27.7 27.9 28.1 28.3 28.5 28.7 28.9 29.1 29.3 29.4 29.6 29.8 30.0 30.2 30.4 30.6 30.8 31.0 31.2 31.4 31.5 31.7 31.9 32.1 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.7 33.8 34.0 34.2 34.4 34.6 34.8 35.0 35.2 35.4 35.6 35.8 35.9 36.1 36.3 36.5 36.7 36.9 37.1 37.3 37.5 37.7 37.9 38.0 38.2 38.4 38.6 38.8 39.0 39.2 39.4 39.6 39.8 40.0 40.2 40.3 40.5 40.7 40.9 41.1 41.3 41.5 41.7 41.9 42.1 42.3 42.4 42.6 42.8 43.0 43.2 43.4 43.6 43.8 44.0 44.2 44.4 44.6 44.7 44.9 45.1 45.3 45.5 45.7 45.9 46.1 46.3 46.5 46.7 46.8 47.0 47.2 47.4 47.6 47.8 48.0 48.2 48.4 48.6 48.8 48.9 49.1 49.3 49.5 49.7 49.9 50.1 50.3 50.5 50.7 50.9 51.1 51.2 51.4 51.6 51.8 52.0 52.2 52.4 52.6 52.8 53.0 53.2 53.3 53.5 53.7 53.9 54.1 54.3 54.5 54.7 54.9 55.1 55.3 55.4 55.6 55.8 56.0 56.2 56.4 56.6 56.8 57.0 57.2 57.4 57.6 57.7 57.9 58.1 58.3 58.5 58.7 58.9 59.1 59.3 59.5 59.7 59.8 60.0 60.2 60.4 60.6 60.8 61.0 61.2 61.4 61.6 61.8 62.0 62.1 62.3 62.5 62.7 62.9 63.1 63.3 63.5 63.7 63.9 64.1 64.2 64.4 64.6 64.8 65.0 65.2 65.4 65.6 65.8 66.0 66.2 66.3 66.5 66.7 66.9 67.1 67.3 67.5 67.7 67.9 68.1 68.3 68.5 68.6 68.8 69.0 69.2 69.4 69.6 69.8 70.0 70.2 70.4 70.6 70.7 70.9 71.1 71.3 71.5 71.7 71.9 72.1 72.3 72.5 72.7 72.8 73.0 73.2 73.4 73.6 73.8 74.0 74.2 74.4 74.6 74.8 75.0 75.1 75.3 75.5 75.7 75.9 76.1 76.3 76.5 76.7 76.9 77.1 77.2 77.4 77.6 77.8 78.0 78.2 78.4 78.6 78.8 79.0 79.2 79.3 79.5 79.7 79.9 80.1 80.3 80.5 80.7 80.9 81.1 81.3 81.5 81.6 81.8 82.0 82.2 82.4 82.6 82.8 83.0 83.2 83.4 83.6 83.7 83.9 84.1 84.3 84.5 84.7 84.9 85.1 85.3 85.5 85.7 85.9 86.0 86.2 86.4 86.6 86.8 87.0 87.2 87.4 87.6 87.8 88.0 88.1 88.3 88.5 88.7 88.9 89.1 89.3 89.5 89.7 89.9 90.1 90.2 90.4 90.6 90.8 91.0 91.2 91.4 91.6 91.8 92.0 92.2 92.4 92.5 92.7 92.9 93.1 93.3 93.5 93.7 93.9 94.1 94.3 94.5 94.6 94.8 95.0 95.2 95.4 95.6 95.8 96.0 96.2 96.4 96.6 96.7 96.9 97.1 97.3 97.5 97.7 97.9 98.1 98.3 98.5 98.7 98.9 99.0 99.2 99.4 99.6 99.8 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 103750, rend_intergenic: 103352 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 107718, rend_intergenic: 106590 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 129163, rend_intergenic: 123891 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 135295, rend_intergenic: 132683 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 140661, rend_intergenic: 135773 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 144531, rend_intergenic: 142973 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146845, rend_intergenic: 145319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 149234, rend_intergenic: 146932 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 157227, rend_intergenic: 156214 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 160978, rend_intergenic: 159789 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 191324, rend_intergenic: 189671 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 14 predictions persist after filtering for low support -no exons in range 1 - 10277