-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_7204302-7338019 -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 GlimmerHMM_glimmerT_52808-T1 Valid prediction for snap_scaffold_24-snap.1490-T1 Valid prediction for snap_scaffold_24-snap.1486-T1 Valid prediction for snap_scaffold_24-snap.1468-T1 Valid prediction for snap_scaffold_24-snap.1460-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_52793-T1 Valid prediction for GlimmerHMM_glimmerT_52810-T1 Valid prediction for snap_scaffold_24-snap.1478-T1 Valid prediction for Augustus_model.g35178.t1 Valid prediction for pasa_asmbl_32381.p1 Valid prediction for snap_scaffold_24-snap.1458-T1 Valid prediction for snap_scaffold_24-snap.1484-T1 Valid prediction for GlimmerHMM_glimmerT_52786-T1 Valid prediction for GlimmerHMM_glimmerT_52799-T1 Valid prediction for CodingQuarry_transcript_37361-T1 Valid prediction for snap_scaffold_24-snap.1480-T1 Valid prediction for GlimmerHMM_glimmerT_52788-T1 Valid prediction for pasa_asmbl_32383.p1 Valid prediction for Augustus_model.g35175.t1 Valid prediction for Augustus_model.g35171.t1 Valid prediction for snap_scaffold_24-snap.1462-T1 Valid prediction for snap_scaffold_24-snap.1482-T1 Couldn't classify 90846, 90982 Sorry, prediction pasa_asmbl_32656.p1 fails validation. (ATG) CA 89819-89998 GT AGG (ATT) AG 90118-90300 GT AGG (GTG) AG 90420-90531 GT AGG (GGA) AG 90846-90982 GT GGG -recovered pasa_asmbl_32656.p1, initial, 89819, 89998 -recovered pasa_asmbl_32656.p1, internal, 90118, 90300 -recovered pasa_asmbl_32656.p1, internal, 90420, 90531 -recovered pasa_asmbl_32656.p1, internal, 90846, 90982 Valid prediction for HiQ_model.g35173.t1 Valid prediction for snap_scaffold_24-snap.1472-T1 Valid prediction for GlimmerHMM_glimmerT_52792-T1 Couldn't classify 41774, 42106 Sorry, prediction pasa_asmbl_33021.p2 fails validation. (ATG) GT 41774-42106 AC ATA Valid prediction for snap_scaffold_24-snap.1488-T1 Valid prediction for snap_scaffold_24-snap.1465-T1 Valid prediction for Augustus_model.g35165.t1 Valid prediction for snap_scaffold_24-snap.1464-T1 Valid prediction for snap_scaffold_24-snap.1459-T1 Valid prediction for snap_scaffold_24-snap.1475-T1 Valid prediction for GlimmerHMM_glimmerT_52805-T1 Valid prediction for Augustus_model.g35164.t1 Valid prediction for snap_scaffold_24-snap.1487-T1 Valid prediction for GlimmerHMM_glimmerT_52809-T1 Valid prediction for snap_scaffold_24-snap.1485-T1 Valid prediction for GlimmerHMM_glimmerT_52803-T1 Valid prediction for Augustus_model.g35177.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_24-snap.1481-T1 Valid prediction for GlimmerHMM_glimmerT_52787-T1 Valid prediction for snap_scaffold_24-snap.1469-T1 Couldn't classify 125778, 125921 Couldn't classify 126275, 126398 Sorry, prediction pasa_asmbl_33019.p1 fails validation. (ATG) GT 122890-122991 GT GGG (ATC) AG 123170-123296 GT AGG (AAA) AG 123397-123517 GT CGG (ACC) AG 123741-123827 GT TTG (GCT) AG 123996-124082 GT AGG (CGA) AG 124235-124295 GT TGG (GAG) AG 124521-124697 GT AGG (GGC) AG 125088-125432 GT TGG (GTG) AG 125586-125687 GT AGG (ACG) AG 125778-125921 AT TCA (GTG) AC 126275-126398 GT ATG (ACA) AG 126910-126989 GT GCG (GGG) AG 127086-127256 GT AGG (GAG) AG 127579-127761 AC GAA -recovered pasa_asmbl_33019.p1, initial, 122890, 122991 -recovered pasa_asmbl_33019.p1, terminal, 127579, 127761 -recovered pasa_asmbl_33019.p1, internal, 123170, 123296 -recovered pasa_asmbl_33019.p1, internal, 123397, 123517 -recovered pasa_asmbl_33019.p1, internal, 123741, 123827 -recovered pasa_asmbl_33019.p1, internal, 123996, 124082 -recovered pasa_asmbl_33019.p1, internal, 124235, 124295 -recovered pasa_asmbl_33019.p1, internal, 124521, 124697 -recovered pasa_asmbl_33019.p1, internal, 125088, 125432 -recovered pasa_asmbl_33019.p1, internal, 125586, 125687 -recovered pasa_asmbl_33019.p1, internal, 126910, 126989 -recovered pasa_asmbl_33019.p1, internal, 127086, 127256 Valid prediction for Augustus_model.g35174.t1 Couldn't classify 30032, 30130 Sorry, prediction pasa_asmbl_33026.p1 fails validation. (CCC) GG 30032-30130 GT AGG (CCC) AG 30456-30566 GT AGG (CTG) AG 30783-30917 GT CAG (GCG) AG 31038-31142 GT AGG (ATA) AG 31311-31397 GT CGG (GGA) AG 31767-31919 GT AGG (GTA) AG 32043-32118 GT GTG (CGG) AG 32323-32437 GT GAG (GAT) AG 32547-32685 GT CTG (GAG) AG 32787-32896 GT AGG (GTT) AG 33026-33098 GT TGG (AAC) AG 33256-33407 GT AGG (GAA) AG 33640-33782 GT GAG (AGT) AG 34421-34607 GT TTG (GTT) AG 35793-35978 GT AGG (CTC) AG 36538-36693 GT AAG (CTT) AG 36913-37376 GT AGG (TGC) AG 37599-37783 GT AGG (GAG) AG 37868-37998 GT AGG (TTC) AG 38103-38227 GT CTG (TGC) AG 38313-38468 GT TCG (AGG) AG 38690-38837 GT AGG (TGA) AG 39130-39245 GT AGG (GTG) AG 39540-39621 GT AGG (CTC) AG 39750-39853 GT AGG (TCT) AG 40044-40189 GT CGG (TCC) AG 40332-40601 GA AAG add_exon() Sorry, pasa_asmbl_33026.p1 39540-39621-terminal-3 is invalid. -recovered pasa_asmbl_33026.p1, terminal, 39540, 39621 -recovered pasa_asmbl_33026.p1, terminal, 40332, 40601 -recovered pasa_asmbl_33026.p1, internal, 30456, 30566 -recovered pasa_asmbl_33026.p1, internal, 30783, 30917 -recovered pasa_asmbl_33026.p1, internal, 31038, 31142 -recovered pasa_asmbl_33026.p1, internal, 31311, 31397 -recovered pasa_asmbl_33026.p1, internal, 31767, 31919 -recovered pasa_asmbl_33026.p1, internal, 32043, 32118 -recovered pasa_asmbl_33026.p1, internal, 32323, 32437 -recovered pasa_asmbl_33026.p1, internal, 32547, 32685 -recovered pasa_asmbl_33026.p1, internal, 32787, 32896 -recovered pasa_asmbl_33026.p1, internal, 33026, 33098 -recovered pasa_asmbl_33026.p1, internal, 33256, 33407 -recovered pasa_asmbl_33026.p1, internal, 33640, 33782 -recovered pasa_asmbl_33026.p1, internal, 34421, 34607 -recovered pasa_asmbl_33026.p1, internal, 35793, 35978 -recovered pasa_asmbl_33026.p1, internal, 36538, 36693 -recovered pasa_asmbl_33026.p1, internal, 36913, 37376 -recovered pasa_asmbl_33026.p1, internal, 37599, 37783 -recovered pasa_asmbl_33026.p1, internal, 37868, 37998 -recovered pasa_asmbl_33026.p1, internal, 38103, 38227 -recovered pasa_asmbl_33026.p1, internal, 38313, 38468 -recovered pasa_asmbl_33026.p1, internal, 38690, 38837 -recovered pasa_asmbl_33026.p1, internal, 39130, 39245 -recovered pasa_asmbl_33026.p1, internal, 39540, 39621 -recovered pasa_asmbl_33026.p1, internal, 39750, 39853 -recovered pasa_asmbl_33026.p1, internal, 40044, 40189 Valid prediction for Augustus_model.g35170.t1 Valid prediction for snap_scaffold_24-snap.1477-T1 Valid prediction for GlimmerHMM_glimmerT_52795-T1 Valid prediction for GlimmerHMM_glimmerT_52806-T1 Valid prediction for GlimmerHMM_glimmerT_52797-T1 Valid prediction for Augustus_model.g35167.t1 Valid prediction for GlimmerHMM_glimmerT_52796-T1 Valid prediction for GlimmerHMM_glimmerT_52785-T1 Valid prediction for snap_scaffold_24-snap.1479-T1 Valid prediction for GlimmerHMM_glimmerT_52798-T1 Valid prediction for Augustus_model.g35166.t1 Valid prediction for GlimmerHMM_glimmerT_52794-T1 Valid prediction for GlimmerHMM_glimmerT_52790-T1 Valid prediction for snap_scaffold_24-snap.1463-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_24-snap.1470-T1 Valid prediction for Augustus_model.g35162.t1 Couldn't classify 125778, 125921 Couldn't classify 126275, 126398 Sorry, prediction CodingQuarry_transcript_37358-T1 fails validation. (ATG) GT 122890-122991 GT GGG (ATC) AG 123170-123296 GT AGG (AAA) AG 123397-123517 GT CGG (ACC) AG 123741-123827 GT TTG (GCT) AG 123996-124082 GT AGG (CGA) AG 124235-124295 GT TGG (GAG) AG 124521-124697 GT AGG (GGC) AG 125088-125432 GT TGG (GTG) AG 125586-125687 GT AGG (ACG) AG 125778-125921 AT TCA (GTG) AC 126275-126398 GT ATG (ACA) AG 126910-126989 GT GCG (GGG) AG 127086-127256 GT AGG (GAG) AG 127579-127761 AC GAA -recovered CodingQuarry_transcript_37358-T1, initial, 122890, 122991 -recovered CodingQuarry_transcript_37358-T1, terminal, 127579, 127761 -recovered CodingQuarry_transcript_37358-T1, internal, 123170, 123296 -recovered CodingQuarry_transcript_37358-T1, internal, 123397, 123517 -recovered CodingQuarry_transcript_37358-T1, internal, 123741, 123827 -recovered CodingQuarry_transcript_37358-T1, internal, 123996, 124082 -recovered CodingQuarry_transcript_37358-T1, internal, 124235, 124295 -recovered CodingQuarry_transcript_37358-T1, internal, 124521, 124697 -recovered CodingQuarry_transcript_37358-T1, internal, 125088, 125432 -recovered CodingQuarry_transcript_37358-T1, internal, 125586, 125687 -recovered CodingQuarry_transcript_37358-T1, internal, 126910, 126989 -recovered CodingQuarry_transcript_37358-T1, internal, 127086, 127256 Valid prediction for snap_scaffold_24-snap.1466-T1 Valid prediction for GlimmerHMM_glimmerT_52807-T1 Couldn't classify 27622, 27651 Couldn't classify 28854, 28880 Sorry, prediction pasa_asmbl_33289.p1 fails validation. (ATC) AC 27622-27651 GT AGG (GTT) AG 27819-27899 GT GGG (GAG) AG 28112-28262 GT AGG (CAC) AG 28498-28554 GT AGG (ATC) AG 28683-28744 GT CGG (AGC) AG 28854-28880 GC AAG -recovered pasa_asmbl_33289.p1, internal, 27819, 27899 -recovered pasa_asmbl_33289.p1, internal, 28112, 28262 -recovered pasa_asmbl_33289.p1, internal, 28498, 28554 -recovered pasa_asmbl_33289.p1, internal, 28683, 28744 -recovered pasa_asmbl_33289.p1, internal, 28854, 28880 Valid prediction for snap_scaffold_24-snap.1471-T1 Valid prediction for GlimmerHMM_glimmerT_52789-T1 Valid prediction for GlimmerHMM_glimmerT_52801-T1 Couldn't classify 54422, 54859 Sorry, prediction pasa_asmbl_33023.p3 fails validation. (CAC) TC 54422-54859 AT ACA Valid prediction for snap_scaffold_24-snap.1489-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_52800-T1 Valid prediction for snap_scaffold_24-snap.1461-T1 Valid prediction for Augustus_model.g35176.t1 Valid prediction for HiQ_model.g35163.t1 Valid prediction for Augustus_model.g35172.t1 Valid prediction for snap_scaffold_24-snap.1467-T1 Valid prediction for GlimmerHMM_glimmerT_52791-T1 Couldn't classify 55103, 55654 Sorry, prediction pasa_asmbl_33022.p1 fails validation. (CCG) CC 55103-55654 AG AGA Valid prediction for snap_scaffold_24-snap.1476-T1 Valid prediction for GlimmerHMM_glimmerT_52804-T1 Valid prediction for snap_scaffold_24-snap.1473-T1 Valid prediction for GlimmerHMM_glimmerT_52802-T1 Valid prediction for Augustus_model.g35168.t1 Valid prediction for snap_scaffold_24-snap.1483-T1 Valid prediction for snap_scaffold_24-snap.1457-T1 Valid prediction for snap_scaffold_24-snap.1474-T1 Valid prediction for pasa_asmbl_33025.p1 Valid prediction for snap_scaffold_24-snap.1456-T1 Valid prediction for Augustus_model.g35169.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19823, rend_intergenic: 16517 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28498, rend_intergenic: 21836 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34312, rend_intergenic: 33188 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 45881, rend_intergenic: 41939 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 63334, rend_intergenic: 57511 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70096, rend_intergenic: 63349 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 77611, rend_intergenic: 74657 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110690, rend_intergenic: 99220 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 130744, rend_intergenic: 123635 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 133718 -exon list size: 382 building trellis 0.3 0.5 0.8 1.0 1.3 1.6 1.8 2.1 2.3 2.6 2.9 3.1 3.4 3.6 3.9 4.2 4.4 4.7 4.9 5.2 5.5 5.7 6.0 6.2 6.5 6.8 7.0 7.3 7.6 7.8 8.1 8.3 8.6 8.9 9.1 9.4 9.6 9.9 10.2 10.4 10.7 10.9 11.2 11.5 11.7 12.0 12.2 12.5 12.8 13.0 13.3 13.5 13.8 14.1 14.3 14.6 14.8 15.1 15.4 15.6 15.9 16.1 16.4 16.7 16.9 17.2 17.4 17.7 18.0 18.2 18.5 18.8 19.0 19.3 19.5 19.8 20.1 20.3 20.6 20.8 21.1 21.4 21.6 21.9 22.1 22.4 22.7 22.9 23.2 23.4 23.7 24.0 24.2 24.5 24.7 25.0 25.3 25.5 25.8 26.0 26.3 26.6 26.8 27.1 27.3 27.6 27.9 28.1 28.4 28.6 28.9 29.2 29.4 29.7 29.9 30.2 30.5 30.7 31.0 31.2 31.5 31.8 32.0 32.3 32.6 32.8 33.1 33.3 33.6 33.9 34.1 34.4 34.6 34.9 35.2 35.4 35.7 35.9 36.2 36.5 36.7 37.0 37.2 37.5 37.8 38.0 38.3 38.5 38.8 39.1 39.3 39.6 39.8 40.1 40.4 40.6 40.9 41.1 41.4 41.7 41.9 42.2 42.4 42.7 43.0 43.2 43.5 43.8 44.0 44.3 44.5 44.8 45.1 45.3 45.6 45.8 46.1 46.4 46.6 46.9 47.1 47.4 47.7 47.9 48.2 48.4 48.7 49.0 49.2 49.5 49.7 50.0 50.3 50.5 50.8 51.0 51.3 51.6 51.8 52.1 52.3 52.6 52.9 53.1 53.4 53.6 53.9 54.2 54.4 54.7 54.9 55.2 55.5 55.7 56.0 56.2 56.5 56.8 57.0 57.3 57.6 57.8 58.1 58.3 58.6 58.9 59.1 59.4 59.6 59.9 60.2 60.4 60.7 60.9 61.2 61.5 61.7 62.0 62.2 62.5 62.8 63.0 63.3 63.5 63.8 64.1 64.3 64.6 64.8 65.1 65.4 65.6 65.9 66.1 66.4 66.7 66.9 67.2 67.4 67.7 68.0 68.2 68.5 68.8 69.0 69.3 69.5 69.8 70.1 70.3 70.6 70.8 71.1 71.4 71.6 71.9 72.1 72.4 72.7 72.9 73.2 73.4 73.7 74.0 74.2 74.5 74.7 75.0 75.3 75.5 75.8 76.0 76.3 76.6 76.8 77.1 77.3 77.6 77.9 78.1 78.4 78.6 78.9 79.2 79.4 79.7 79.9 80.2 80.5 80.7 81.0 81.2 81.5 81.8 82.0 82.3 82.6 82.8 83.1 83.3 83.6 83.9 84.1 84.4 84.6 84.9 85.2 85.4 85.7 85.9 86.2 86.5 86.7 87.0 87.2 87.5 87.8 88.0 88.3 88.5 88.8 89.1 89.3 89.6 89.8 90.1 90.4 90.6 90.9 91.1 91.4 91.7 91.9 92.2 92.4 92.7 93.0 93.2 93.5 93.8 94.0 94.3 94.5 94.8 95.1 95.3 95.6 95.8 96.1 96.4 96.6 96.9 97.1 97.4 97.7 97.9 98.2 98.4 98.7 99.0 99.2 99.5 99.7 -found 25 predictions from path traversal Error with prediction: snap lend_intergenic: 19823, rend_intergenic: 16517 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 28498, rend_intergenic: 21836 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 34312, rend_intergenic: 33188 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 45881, rend_intergenic: 41939 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 63334, rend_intergenic: 57511 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 70096, rend_intergenic: 63349 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 77611, rend_intergenic: 74657 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110690, rend_intergenic: 99220 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 130744, rend_intergenic: 123635 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