-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_9611326-9770783 -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_17-snap.1916-T1 Valid prediction for GlimmerHMM_glimmerT_40865-T1 Valid prediction for snap_scaffold_17-snap.1918-T1 Valid prediction for CodingQuarry_transcript_22133-T1 Valid prediction for snap_scaffold_17-snap.1897-T1 Valid prediction for snap_scaffold_17-snap.1896-T1 Valid prediction for snap_scaffold_17-snap.1892-T1 Valid prediction for Augustus_model.g27266.t1 Valid prediction for snap_scaffold_17-snap.1930-T1 Valid prediction for GlimmerHMM_glimmerT_40870-T1 Valid prediction for snap_scaffold_17-snap.1923-T1 Valid prediction for snap_scaffold_17-snap.1891-T1 Valid prediction for Augustus_model.g27269.t1 Valid prediction for snap_scaffold_17-snap.1912-T1 Valid prediction for snap_scaffold_17-snap.1901-T1 Valid prediction for snap_scaffold_17-snap.1921-T1 Valid prediction for snap_scaffold_17-snap.1911-T1 Valid prediction for snap_scaffold_17-snap.1928-T1 Valid prediction for snap_scaffold_17-snap.1920-T1 Valid prediction for snap_scaffold_17-snap.1925-T1 Valid prediction for snap_scaffold_17-snap.1929-T1 Valid prediction for Augustus_model.g27274.t1 Valid prediction for snap_scaffold_17-snap.1924-T1 Valid prediction for GlimmerHMM_glimmerT_40861-T1 Valid prediction for snap_scaffold_17-snap.1894-T1 Valid prediction for snap_scaffold_17-snap.1906-T1 Couldn't classify 83662, 83688 Couldn't classify 85763, 85828 Sorry, prediction pasa_asmbl_19475.p2 fails validation. (AAA) AA 83662-83688 GT AAG (GCT) AG 84543-84669 GT GGG (GTG) AG 84931-85076 GT AAG (CTG) AG 85329-85415 GT AGG (GGT) AG 85763-85828 GA TGG -recovered pasa_asmbl_19475.p2, internal, 84543, 84669 -recovered pasa_asmbl_19475.p2, internal, 84931, 85076 -recovered pasa_asmbl_19475.p2, internal, 85329, 85415 Valid prediction for snap_scaffold_17-snap.1927-T1 Couldn't classify 86063, 86226 Sorry, prediction pasa_asmbl_19124.p1 fails validation. (TTC) AG 86063-86226 GT AAG (ATT) AG 86513-86616 GT TGG (TGA) AG 86709-86834 GT AGG (GGG) AG 86952-87085 GT AGG (ACC) AG 87242-87450 GT CCG (GAA) AG 87787-87913 GT AGG (GGC) AG 88044-88154 GT AGG (GGG) AG 88280-88423 GT AGG (ATC) AG 88625-88739 GT ACG (GTG) AG 88878-88908 GT GGG (GAA) AG 89018-89081 GT AGG (AGT) AG 89193-89277 GT GGG (ATC) AG 89506-89699 GA AGG -recovered pasa_asmbl_19124.p1, terminal, 89506, 89699 -recovered pasa_asmbl_19124.p1, internal, 86063, 86226 -recovered pasa_asmbl_19124.p1, internal, 86513, 86616 -recovered pasa_asmbl_19124.p1, internal, 86709, 86834 -recovered pasa_asmbl_19124.p1, internal, 86952, 87085 -recovered pasa_asmbl_19124.p1, internal, 87242, 87450 -recovered pasa_asmbl_19124.p1, internal, 87787, 87913 -recovered pasa_asmbl_19124.p1, internal, 88044, 88154 -recovered pasa_asmbl_19124.p1, internal, 88280, 88423 -recovered pasa_asmbl_19124.p1, internal, 88625, 88739 -recovered pasa_asmbl_19124.p1, internal, 88878, 88908 -recovered pasa_asmbl_19124.p1, internal, 89018, 89081 -recovered pasa_asmbl_19124.p1, internal, 89193, 89277 Valid prediction for snap_scaffold_17-snap.1900-T1 Valid prediction for snap_scaffold_17-snap.1910-T1 Valid prediction for snap_scaffold_17-snap.1907-T1 Valid prediction for snap_scaffold_17-snap.1919-T1 Valid prediction for Augustus_model.g27276.t1 Valid prediction for GlimmerHMM_glimmerT_40864-T1 Valid prediction for Augustus_model.g27267.t1 Valid prediction for HiQ_model.g27268.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 GlimmerHMM_glimmerT_40866-T1 Valid prediction for Augustus_model.g27270.t1 Valid prediction for snap_scaffold_17-snap.1899-T1 Valid prediction for Augustus_model.g27271.t1 Valid prediction for GlimmerHMM_glimmerT_40857-T1 Valid prediction for GlimmerHMM_glimmerT_40860-T1 Valid prediction for snap_scaffold_17-snap.1915-T1 Valid prediction for snap_scaffold_17-snap.1905-T1 Valid prediction for GlimmerHMM_glimmerT_40867-T1 Couldn't classify 14967, 15148 Couldn't classify 21823, 21944 Sorry, prediction pasa_asmbl_18193.p1 fails validation. (CTC) CT 14967-15148 GT GGG (ATG) AG 15390-15504 GT ATG (ATG) AG 17573-17699 GT TGG (CTG) AG 18080-18230 GT GGG (CGT) AG 18502-18688 GT ACG (GAG) AG 19703-19748 GT AGG (CCA) AG 21823-21944 GG CAG add_exon() Sorry, pasa_asmbl_18193.p1 15390-15504-initial-1 is invalid. -recovered pasa_asmbl_18193.p1, initial, 15390, 15504 -recovered pasa_asmbl_18193.p1, initial, 17573, 17699 -recovered pasa_asmbl_18193.p1, internal, 15390, 15504 -recovered pasa_asmbl_18193.p1, internal, 17573, 17699 -recovered pasa_asmbl_18193.p1, internal, 18080, 18230 -recovered pasa_asmbl_18193.p1, internal, 18502, 18688 -recovered pasa_asmbl_18193.p1, internal, 19703, 19748 Valid prediction for CodingQuarry_transcript_22132-T1 Valid prediction for GlimmerHMM_glimmerT_40859-T1 Valid prediction for GlimmerHMM_glimmerT_40869-T1 Couldn't classify 35925, 36083 Sorry, prediction pasa_asmbl_18191.p1 fails validation. (AGC) CT 35925-36083 GT AGG (TTT) AG 37509-37660 GT AAG (GGC) AG 37901-38058 GT GAG (CTG) AG 38665-38927 GT AGG (ACC) AG 39207-39365 GT AGG (TTT) AG 39502-39736 GT CGG (GGA) AG 39951-40090 GT AGG (GTA) AG 40282-40365 GT AGG (ATG) AG 40461-40576 GT GGG (CTT) AG 40867-41050 GT CGG (ACC) AG 41318-41464 AG AAA -recovered pasa_asmbl_18191.p1, initial, 40461, 40576 -recovered pasa_asmbl_18191.p1, terminal, 37901, 38058 -recovered pasa_asmbl_18191.p1, terminal, 41318, 41464 -recovered pasa_asmbl_18191.p1, internal, 37509, 37660 -recovered pasa_asmbl_18191.p1, internal, 37901, 38058 -recovered pasa_asmbl_18191.p1, internal, 38665, 38927 -recovered pasa_asmbl_18191.p1, internal, 39207, 39365 -recovered pasa_asmbl_18191.p1, internal, 39502, 39736 -recovered pasa_asmbl_18191.p1, internal, 39951, 40090 -recovered pasa_asmbl_18191.p1, internal, 40282, 40365 -recovered pasa_asmbl_18191.p1, internal, 40461, 40576 -recovered pasa_asmbl_18191.p1, internal, 40867, 41050 Couldn't classify 150394, 150453 Couldn't classify 153870, 153937 Sorry, prediction pasa_asmbl_18186.p1 fails validation. (TCC) TC 150394-150453 GT AGG (GGG) AG 150670-150842 GT ATG (CCG) AG 150976-151118 GT CTG (TGA) AG 151340-151446 GT AGG (AAC) AG 152038-152123 GT TGG (TGC) AG 152546-152817 GT AGG (ATG) AG 153297-153359 GT AGG (GCC) AG 153870-153937 AC CCA add_exon() Sorry, pasa_asmbl_18186.p1 153297-153359-initial-1 is invalid. -recovered pasa_asmbl_18186.p1, initial, 153297, 153359 -recovered pasa_asmbl_18186.p1, internal, 150670, 150842 -recovered pasa_asmbl_18186.p1, internal, 150976, 151118 -recovered pasa_asmbl_18186.p1, internal, 151340, 151446 -recovered pasa_asmbl_18186.p1, internal, 152038, 152123 -recovered pasa_asmbl_18186.p1, internal, 152546, 152817 -recovered pasa_asmbl_18186.p1, internal, 153297, 153359 Valid prediction for snap_scaffold_17-snap.1898-T1 Couldn't classify 7936, 8251 Couldn't classify 10364, 10428 Sorry, prediction pasa_asmbl_18460.p1 fails validation. (AGG) AA 7936-8251 GT TGG (GCA) AG 10364-10428 TG TAT Couldn't classify 17575, 17616 Sorry, prediction CodingQuarry_transcript_22136-T1 fails validation. (ATG) TG 15105-15148 GT GGG (ATG) AG 15390-15504 GT ATG (GAA) AT 17575-17616 TG AAT -recovered CodingQuarry_transcript_22136-T1, initial, 15105, 15148 add_exon() Sorry, CodingQuarry_transcript_22136-T1 15390-15504-initial-1 is invalid. -recovered CodingQuarry_transcript_22136-T1, initial, 15390, 15504 -recovered CodingQuarry_transcript_22136-T1, internal, 15390, 15504 Valid prediction for HiQ_model.g27273.t1 Valid prediction for HiQ_model.g27275.t1 Valid prediction for snap_scaffold_17-snap.1903-T1 Valid prediction for snap_scaffold_17-snap.1914-T1 Valid prediction for GlimmerHMM_glimmerT_40862-T1 Valid prediction for CodingQuarry_transcript_22135-T1 Couldn't classify 44723, 44879 Sorry, prediction pasa_asmbl_18190.p1 fails validation. (GAC) AC 44723-44879 GT AGG (AGA) AG 45036-45116 GT AGG (CCA) AG 45229-45356 CC GAC -recovered pasa_asmbl_18190.p1, terminal, 45229, 45356 -recovered pasa_asmbl_18190.p1, internal, 45036, 45116 Valid prediction for snap_scaffold_17-snap.1895-T1 Valid prediction for snap_scaffold_17-snap.1902-T1 Valid prediction for snap_scaffold_17-snap.1890-T1 Valid prediction for GlimmerHMM_glimmerT_40868-T1 Valid prediction for Augustus_model.g27277.t1 Valid prediction for Augustus_model.g27272.t1 Valid prediction for snap_scaffold_17-snap.1904-T1 Valid prediction for snap_scaffold_17-snap.1893-T1 Valid prediction for Augustus_model.g27265.t1 Valid prediction for Augustus_model.g27264.t1 Valid prediction for GlimmerHMM_glimmerT_40871-T1 Couldn't classify 147010, 147127 Couldn't classify 150009, 150095 Sorry, prediction pasa_asmbl_18188.p1 fails validation. (AGG) CC 147010-147127 GT CCG (GAA) AG 148371-148422 GT AGG (GAA) AG 148804-148912 GT AGG (TTG) AG 149004-149093 GT CGG (CAC) AG 149172-149246 GT GGG (AGT) AG 149388-149455 GT ACG (GTT) AG 149605-149707 GT AGG (GGA) AG 150009-150095 AG CCA -recovered pasa_asmbl_18188.p1, internal, 148371, 148422 -recovered pasa_asmbl_18188.p1, internal, 148804, 148912 -recovered pasa_asmbl_18188.p1, internal, 149004, 149093 -recovered pasa_asmbl_18188.p1, internal, 149172, 149246 -recovered pasa_asmbl_18188.p1, internal, 149388, 149455 -recovered pasa_asmbl_18188.p1, internal, 149605, 149707 Valid prediction for GlimmerHMM_glimmerT_40863-T1 Valid prediction for snap_scaffold_17-snap.1922-T1 Valid prediction for snap_scaffold_17-snap.1917-T1 Valid prediction for snap_scaffold_17-snap.1908-T1 Valid prediction for snap_scaffold_17-snap.1913-T1 Valid prediction for snap_scaffold_17-snap.1926-T1 Valid prediction for GlimmerHMM_glimmerT_40858-T1 Couldn't classify 154043, 154075 Sorry, prediction pasa_asmbl_18185.p1 fails validation. (CGC) CG 154043-154075 GT AGG (GAG) AG 154177-154276 GT CGG (GGA) AG 154593-154672 GT AGG (ATC) AG 154756-155007 GT AGG (GTG) AG 155176-155430 GG GAG -recovered pasa_asmbl_18185.p1, terminal, 155176, 155430 -recovered pasa_asmbl_18185.p1, internal, 154177, 154276 -recovered pasa_asmbl_18185.p1, internal, 154593, 154672 -recovered pasa_asmbl_18185.p1, internal, 154756, 155007 Valid prediction for snap_scaffold_17-snap.1909-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14209, rend_intergenic: 5680 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27808, rend_intergenic: 20109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 42118, rend_intergenic: 35950 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 57928, rend_intergenic: 42882 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 61585, rend_intergenic: 59651 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67456, rend_intergenic: 62749 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 73008, rend_intergenic: 70319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 89699, rend_intergenic: 86059 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 113527, rend_intergenic: 98193 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120000, rend_intergenic: 117995 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 122472, rend_intergenic: 120116 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 136159, rend_intergenic: 132872 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 157619, rend_intergenic: 136681 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 159458 -exon list size: 374 building trellis 0.3 0.5 0.8 1.1 1.3 1.6 1.9 2.1 2.4 2.7 2.9 3.2 3.5 3.7 4.0 4.3 4.5 4.8 5.1 5.3 5.6 5.9 6.1 6.4 6.6 6.9 7.2 7.4 7.7 8.0 8.2 8.5 8.8 9.0 9.3 9.6 9.8 10.1 10.4 10.6 10.9 11.2 11.4 11.7 12.0 12.2 12.5 12.8 13.0 13.3 13.6 13.8 14.1 14.4 14.6 14.9 15.2 15.4 15.7 16.0 16.2 16.5 16.8 17.0 17.3 17.6 17.8 18.1 18.4 18.6 18.9 19.1 19.4 19.7 19.9 20.2 20.5 20.7 21.0 21.3 21.5 21.8 22.1 22.3 22.6 22.9 23.1 23.4 23.7 23.9 24.2 24.5 24.7 25.0 25.3 25.5 25.8 26.1 26.3 26.6 26.9 27.1 27.4 27.7 27.9 28.2 28.5 28.7 29.0 29.3 29.5 29.8 30.1 30.3 30.6 30.9 31.1 31.4 31.6 31.9 32.2 32.4 32.7 33.0 33.2 33.5 33.8 34.0 34.3 34.6 34.8 35.1 35.4 35.6 35.9 36.2 36.4 36.7 37.0 37.2 37.5 37.8 38.0 38.3 38.6 38.8 39.1 39.4 39.6 39.9 40.2 40.4 40.7 41.0 41.2 41.5 41.8 42.0 42.3 42.6 42.8 43.1 43.4 43.6 43.9 44.1 44.4 44.7 44.9 45.2 45.5 45.7 46.0 46.3 46.5 46.8 47.1 47.3 47.6 47.9 48.1 48.4 48.7 48.9 49.2 49.5 49.7 50.0 50.3 50.5 50.8 51.1 51.3 51.6 51.9 52.1 52.4 52.7 52.9 53.2 53.5 53.7 54.0 54.3 54.5 54.8 55.1 55.3 55.6 55.9 56.1 56.4 56.6 56.9 57.2 57.4 57.7 58.0 58.2 58.5 58.8 59.0 59.3 59.6 59.8 60.1 60.4 60.6 60.9 61.2 61.4 61.7 62.0 62.2 62.5 62.8 63.0 63.3 63.6 63.8 64.1 64.4 64.6 64.9 65.2 65.4 65.7 66.0 66.2 66.5 66.8 67.0 67.3 67.6 67.8 68.1 68.4 68.6 68.9 69.1 69.4 69.7 69.9 70.2 70.5 70.7 71.0 71.3 71.5 71.8 72.1 72.3 72.6 72.9 73.1 73.4 73.7 73.9 74.2 74.5 74.7 75.0 75.3 75.5 75.8 76.1 76.3 76.6 76.9 77.1 77.4 77.7 77.9 78.2 78.5 78.7 79.0 79.3 79.5 79.8 80.1 80.3 80.6 80.9 81.1 81.4 81.6 81.9 82.2 82.4 82.7 83.0 83.2 83.5 83.8 84.0 84.3 84.6 84.8 85.1 85.4 85.6 85.9 86.2 86.4 86.7 87.0 87.2 87.5 87.8 88.0 88.3 88.6 88.8 89.1 89.4 89.6 89.9 90.2 90.4 90.7 91.0 91.2 91.5 91.8 92.0 92.3 92.6 92.8 93.1 93.4 93.6 93.9 94.1 94.4 94.7 94.9 95.2 95.5 95.7 96.0 96.3 96.5 96.8 97.1 97.3 97.6 97.9 98.1 98.4 98.7 98.9 99.2 99.5 99.7 -found 19 predictions from path traversal Error with prediction: snap lend_intergenic: 14209, rend_intergenic: 5680 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 27808, rend_intergenic: 20109 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 42118, rend_intergenic: 35950 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 57928, rend_intergenic: 42882 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 61585, rend_intergenic: 59651 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 67456, rend_intergenic: 62749 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 73008, rend_intergenic: 70319 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 89699, rend_intergenic: 86059 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 113527, rend_intergenic: 98193 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120000, rend_intergenic: 117995 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 122472, rend_intergenic: 120116 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 136159, rend_intergenic: 132872 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 157619, rend_intergenic: 136681 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 16 predictions persist after filtering for low support