-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_8696658-8905875 -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_24-snap.1836-T1 Valid prediction for snap_scaffold_24-snap.1822-T1 Valid prediction for HiQ_model.g35335.t1 Valid prediction for Augustus_model.g35333.t1 Valid prediction for GlimmerHMM_glimmerT_53058-T1 Valid prediction for HiQ_model.g35329.t1 Couldn't classify 161629, 161668 Sorry, prediction pasa_asmbl_32637.p1 fails validation. (ATG) GG 161084-161352 GT CTG (GGA) AG 161629-161668 CG CTC -recovered pasa_asmbl_32637.p1, initial, 161084, 161352 Valid prediction for GlimmerHMM_glimmerT_53053-T1 Valid prediction for snap_scaffold_24-snap.1826-T1 Valid prediction for CodingQuarry_transcript_37387-T1 Valid prediction for HiQ_model.g35327.t1 Couldn't classify 638, 730 Sorry, prediction pasa_asmbl_32433.p1 fails validation. (GTA) AG 638-730 GT AGG (AGG) AG 2875-2985 GT AGG (GCG) AG 3298-3402 GT AGG (CTG) AG 3608-3691 GT AGG (ATC) AG 3850-3921 GT AGG (AGT) AG 4063-4260 GT AGG (GAA) AG 4538-4681 GG GAG -recovered pasa_asmbl_32433.p1, terminal, 4538, 4681 -recovered pasa_asmbl_32433.p1, internal, 638, 730 -recovered pasa_asmbl_32433.p1, internal, 2875, 2985 -recovered pasa_asmbl_32433.p1, internal, 3298, 3402 -recovered pasa_asmbl_32433.p1, internal, 3608, 3691 -recovered pasa_asmbl_32433.p1, internal, 3850, 3921 -recovered pasa_asmbl_32433.p1, internal, 4063, 4260 Valid prediction for CodingQuarry_transcript_37384-T1 Valid prediction for snap_scaffold_24-snap.1842-T1 Valid prediction for snap_scaffold_24-snap.1825-T1 Valid prediction for snap_scaffold_24-snap.1819-T1 Valid prediction for GlimmerHMM_glimmerT_53050-T1 Valid prediction for snap_scaffold_24-snap.1829-T1 Valid prediction for GlimmerHMM_glimmerT_53045-T1 Couldn't classify 169603, 169947 Sorry, prediction pasa_asmbl_32450.p1 fails validation. (ATG) AG 163817-163831 GT AGG (TTT) AG 166062-166155 GT AGG (AAA) AG 167174-167346 GT AGG (GAA) AG 167522-167620 GT AGG (GAG) AG 167928-168092 GT AGG (GCA) AG 168291-168390 GT CAG (ACT) AG 168479-168633 GT TGG (GTG) AG 168826-168948 GT AGG (GTG) AG 169198-169380 GT AGG (GTC) AG 169603-169947 AC AGA -recovered pasa_asmbl_32450.p1, initial, 163817, 163831 add_exon() Sorry, pasa_asmbl_32450.p1 166062-166155-terminal-3 is invalid. -recovered pasa_asmbl_32450.p1, terminal, 166062, 166155 -recovered pasa_asmbl_32450.p1, internal, 163817, 163831 -recovered pasa_asmbl_32450.p1, internal, 166062, 166155 -recovered pasa_asmbl_32450.p1, internal, 167174, 167346 -recovered pasa_asmbl_32450.p1, internal, 167522, 167620 -recovered pasa_asmbl_32450.p1, internal, 167928, 168092 -recovered pasa_asmbl_32450.p1, internal, 168291, 168390 -recovered pasa_asmbl_32450.p1, internal, 168479, 168633 -recovered pasa_asmbl_32450.p1, internal, 168826, 168948 -recovered pasa_asmbl_32450.p1, internal, 169198, 169380 Valid prediction for GlimmerHMM_glimmerT_53049-T1 Valid prediction for snap_scaffold_24-snap.1828-T1 Valid prediction for Augustus_model.g35337.t1 Valid prediction for Augustus_model.g35339.t1 Valid prediction for pasa_asmbl_32445.p1 Valid prediction for CodingQuarry_transcript_37389-T1 Valid prediction for snap_scaffold_24-snap.1848-T1 Valid prediction for GlimmerHMM_glimmerT_53051-T1 Valid prediction for GlimmerHMM_glimmerT_53057-T1 Valid prediction for GlimmerHMM_glimmerT_53043-T1 Valid prediction for snap_scaffold_24-snap.1813-T1 Valid prediction for CodingQuarry_transcript_37378-T1 Valid prediction for GlimmerHMM_glimmerT_53054-T1 Valid prediction for snap_scaffold_24-snap.1840-T1 Valid prediction for GlimmerHMM_glimmerT_53037-T1 Valid prediction for snap_scaffold_24-snap.1831-T1 Valid prediction for GlimmerHMM_glimmerT_53039-T1 Valid prediction for snap_scaffold_24-snap.1838-T1 Couldn't classify 114494, 114680 Sorry, prediction pasa_asmbl_32449.p1 fails validation. (ATT) TG 114494-114680 GT AGG (GTC) AG 114784-114945 GT AGG (GGA) AG 115298-115374 GT AGG (GCT) AG 115496-115624 GT GAG (GAT) AG 116055-116159 AA GAA add_exon() Sorry, pasa_asmbl_32449.p1 114784-114945-terminal-1 is invalid. -recovered pasa_asmbl_32449.p1, terminal, 114784, 114945 -recovered pasa_asmbl_32449.p1, terminal, 116055, 116159 -recovered pasa_asmbl_32449.p1, internal, 114784, 114945 -recovered pasa_asmbl_32449.p1, internal, 115298, 115374 -recovered pasa_asmbl_32449.p1, internal, 115496, 115624 Valid prediction for HiQ_model.g35332.t1 Valid prediction for Augustus_model.g35336.t1 Valid prediction for pasa_asmbl_32447.p1 Valid prediction for pasa_asmbl_32441.p1 -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_37385-T1 Valid prediction for GlimmerHMM_glimmerT_53062-T1 Valid prediction for snap_scaffold_24-snap.1847-T1 Valid prediction for snap_scaffold_24-snap.1820-T1 Valid prediction for CodingQuarry_transcript_37380-T1 Valid prediction for GlimmerHMM_glimmerT_53059-T1 Couldn't classify 149966, 150099 Sorry, prediction pasa_asmbl_33104.p1 fails validation. (CAG) TC 149966-150099 GT GGG (GTC) AG 151660-151816 GT AGG (GTG) AG 153867-153980 GT AGG (GAG) AG 154710-154790 GT AGG (GAG) AG 155027-155212 CT AGC -recovered pasa_asmbl_33104.p1, terminal, 155027, 155212 -recovered pasa_asmbl_33104.p1, internal, 151660, 151816 -recovered pasa_asmbl_33104.p1, internal, 153867, 153980 -recovered pasa_asmbl_33104.p1, internal, 154710, 154790 Valid prediction for pasa_asmbl_33112.p1 Valid prediction for snap_scaffold_24-snap.1834-T1 Couldn't classify 144037, 144192 Couldn't classify 145337, 145414 Sorry, prediction pasa_asmbl_33108.p1 fails validation. (GAA) GG 144037-144192 GT AGG (GCT) AG 145060-145191 GT AGG (TTT) AG 145337-145414 AA CCA -recovered pasa_asmbl_33108.p1, internal, 145060, 145191 Valid prediction for snap_scaffold_24-snap.1830-T1 Valid prediction for CodingQuarry_transcript_37386-T1 Valid prediction for snap_scaffold_24-snap.1841-T1 Valid prediction for HiQ_model.g35323.t1 Valid prediction for GlimmerHMM_glimmerT_53046-T1 Valid prediction for Augustus_model.g35334.t1 Valid prediction for snap_scaffold_24-snap.1845-T1 Valid prediction for snap_scaffold_24-snap.1843-T1 Valid prediction for Augustus_model.g35326.t1 Valid prediction for pasa_asmbl_33087.p1 Couldn't classify 124480, 124497 Sorry, prediction pasa_asmbl_33110.p1 fails validation. (GAC) CT 124480-124497 GT AGG (GTG) AG 124684-124802 GT GGG (GCC) AG 125123-125287 GT AGG (CAT) AG 125559-125673 GT TGG (AAT) AG 126162-126305 GT AGG (CTC) AG 126505-126718 GT TGG (CGG) AG 127030-127147 GC AGG (GAC) AG 127257-127413 GT AGG (GAG) AG 127714-127856 GT AGG (GTA) AG 128096-128270 GT CTG (GGA) AG 128369-128450 GT AGG (CAC) AG 128673-128837 GT AGG (GTC) AG 128951-129171 GT AGG (GAC) AG 129370-129489 AG AGA -recovered pasa_asmbl_33110.p1, terminal, 129370, 129489 -recovered pasa_asmbl_33110.p1, internal, 124684, 124802 -recovered pasa_asmbl_33110.p1, internal, 125123, 125287 -recovered pasa_asmbl_33110.p1, internal, 125559, 125673 -recovered pasa_asmbl_33110.p1, internal, 126162, 126305 -recovered pasa_asmbl_33110.p1, internal, 126505, 126718 -recovered pasa_asmbl_33110.p1, internal, 127030, 127147 -recovered pasa_asmbl_33110.p1, internal, 127257, 127413 -recovered pasa_asmbl_33110.p1, internal, 127714, 127856 -recovered pasa_asmbl_33110.p1, internal, 128096, 128270 -recovered pasa_asmbl_33110.p1, internal, 128369, 128450 -recovered pasa_asmbl_33110.p1, internal, 128673, 128837 -recovered pasa_asmbl_33110.p1, internal, 128951, 129171 Valid prediction for GlimmerHMM_glimmerT_53044-T1 Couldn't classify 123101, 123181 Sorry, prediction pasa_asmbl_33111.p1 fails validation. (ATG) AG 120495-120665 GT AGG (GTG) AG 121142-121284 GT AGG (TTA) AG 121535-121624 GT AGG (CCA) AG 121733-121900 GT AGG (GCA) AG 122071-122251 GT AGG (GAC) AG 122615-122776 GT AGG (ACC) AG 123101-123181 TC ACT -recovered pasa_asmbl_33111.p1, initial, 120495, 120665 -recovered pasa_asmbl_33111.p1, internal, 120495, 120665 -recovered pasa_asmbl_33111.p1, internal, 121142, 121284 -recovered pasa_asmbl_33111.p1, internal, 121535, 121624 -recovered pasa_asmbl_33111.p1, internal, 121733, 121900 -recovered pasa_asmbl_33111.p1, internal, 122071, 122251 -recovered pasa_asmbl_33111.p1, internal, 122615, 122776 Valid prediction for GlimmerHMM_glimmerT_53047-T1 Valid prediction for snap_scaffold_24-snap.1814-T1 Valid prediction for Augustus_model.g35325.t1 Valid prediction for snap_scaffold_24-snap.1815-T1 Valid prediction for pasa_asmbl_33097.p1 Valid prediction for GlimmerHMM_glimmerT_53052-T1 Valid prediction for Augustus_model.g35324.t1 Valid prediction for snap_scaffold_24-snap.1823-T1 Valid prediction for Augustus_model.g35330.t1 Valid prediction for GlimmerHMM_glimmerT_53038-T1 Valid prediction for snap_scaffold_24-snap.1832-T1 Valid prediction for snap_scaffold_24-snap.1811-T1 Valid prediction for GlimmerHMM_glimmerT_53042-T1 Valid prediction for CodingQuarry_transcript_37379-T1 Valid prediction for Augustus_model.g35343.t1 Valid prediction for snap_scaffold_24-snap.1844-T1 Valid prediction for snap_scaffold_24-snap.1824-T1 Valid prediction for CodingQuarry_transcript_37382-T1 Couldn't classify 13590, 13715 Sorry, prediction pasa_asmbl_33117.p1 fails validation. (AGC) TC 13590-13715 GT TGG (AGT) AG 13902-14024 GT AGG (AGC) AG 14314-14450 GT AAG (GCG) AG 14788-14972 GT AGG (ACA) AG 15200-16260 CT GAC -recovered pasa_asmbl_33117.p1, terminal, 15200, 16260 -recovered pasa_asmbl_33117.p1, internal, 13902, 14024 -recovered pasa_asmbl_33117.p1, internal, 14314, 14450 -recovered pasa_asmbl_33117.p1, internal, 14788, 14972 Valid prediction for Augustus_model.g35322.t1 Couldn't classify 35100, 35159 Couldn't classify 36075, 36098 Sorry, prediction pasa_asmbl_33253.p1 fails validation. (GGA) CA 35100-35159 GT AGG (TCC) AG 35342-35431 GT CTG (TGT) AG 35703-35855 GT GGG (GAA) AG 36075-36098 AA ACA -recovered pasa_asmbl_33253.p1, internal, 35342, 35431 -recovered pasa_asmbl_33253.p1, internal, 35703, 35855 Valid prediction for snap_scaffold_24-snap.1821-T1 Valid prediction for snap_scaffold_24-snap.1846-T1 Valid prediction for Augustus_model.g35338.t1 Valid prediction for GlimmerHMM_glimmerT_53036-T1 Valid prediction for snap_scaffold_24-snap.1833-T1 Valid prediction for Augustus_model.g35340.t1 Valid prediction for snap_scaffold_24-snap.1817-T1 Couldn't classify 200181, 200312 Sorry, prediction pasa_asmbl_33088.p1 fails validation. (ATG) AA 198915-199386 GT AGG (AGA) AG 199523-199574 GT GAG (GAA) AG 199741-199936 GT AGG (TTT) AG 200181-200312 CA GTC -recovered pasa_asmbl_33088.p1, initial, 198915, 199386 add_exon() Sorry, pasa_asmbl_33088.p1 199523-199574-terminal-3 is invalid. -recovered pasa_asmbl_33088.p1, terminal, 199523, 199574 -recovered pasa_asmbl_33088.p1, internal, 199523, 199574 -recovered pasa_asmbl_33088.p1, internal, 199741, 199936 Valid prediction for snap_scaffold_24-snap.1827-T1 Couldn't classify 9022, 9229 Couldn't classify 13064, 13140 Sorry, prediction pasa_asmbl_33118.p1 fails validation. (GCT) GA 9022-9229 GT AGG (GTG) AG 10332-10470 GT AAG (CTT) AG 10569-10701 GT AGG (GTG) AG 10932-11097 GT CGG (ACG) AG 11239-11340 GT CGG (GGG) AG 11435-11557 GT CAG (CTC) AG 11813-11925 GT AGG (GTC) AG 12221-12399 GT AGG (CCT) AG 12697-12821 GT AGG (CTG) AG 13064-13140 GA ACG -recovered pasa_asmbl_33118.p1, internal, 10332, 10470 -recovered pasa_asmbl_33118.p1, internal, 10569, 10701 -recovered pasa_asmbl_33118.p1, internal, 10932, 11097 -recovered pasa_asmbl_33118.p1, internal, 11239, 11340 -recovered pasa_asmbl_33118.p1, internal, 11435, 11557 -recovered pasa_asmbl_33118.p1, internal, 11813, 11925 -recovered pasa_asmbl_33118.p1, internal, 12221, 12399 -recovered pasa_asmbl_33118.p1, internal, 12697, 12821 Valid prediction for GlimmerHMM_glimmerT_53048-T1 Valid prediction for snap_scaffold_24-snap.1849-T1 Valid prediction for Augustus_model.g35342.t1 Valid prediction for Augustus_model.g35341.t1 Valid prediction for pasa_asmbl_33089.p1 Valid prediction for snap_scaffold_24-snap.1837-T1 Valid prediction for snap_scaffold_24-snap.1812-T1 Valid prediction for snap_scaffold_24-snap.1839-T1 Valid prediction for Augustus_model.g35328.t1 Valid prediction for GlimmerHMM_glimmerT_53056-T1 Valid prediction for GlimmerHMM_glimmerT_53055-T1 Valid prediction for GlimmerHMM_glimmerT_53060-T1 Valid prediction for GlimmerHMM_glimmerT_53061-T1 Valid prediction for GlimmerHMM_glimmerT_53041-T1 Valid prediction for GlimmerHMM_glimmerT_53040-T1 Valid prediction for snap_scaffold_24-snap.1816-T1 Valid prediction for HiQ_model.g35331.t1 Valid prediction for snap_scaffold_24-snap.1818-T1 Couldn't classify 28246, 28253 Couldn't classify 30841, 30865 Sorry, prediction pasa_asmbl_33116.p1 fails validation. (ATC) AC 28246-28253 GT AGG (AGA) AG 28437-28535 GT AGG (GAA) AG 28990-29170 GT AGG (GAC) AG 29434-29559 GT AGG (GAG) AG 30062-30204 GT AGG (AAT) AG 30304-30480 GT GTG (GTG) AG 30561-30632 GT GAG (CCC) AG 30841-30865 GA AGG -recovered pasa_asmbl_33116.p1, internal, 28437, 28535 -recovered pasa_asmbl_33116.p1, internal, 28990, 29170 -recovered pasa_asmbl_33116.p1, internal, 29434, 29559 -recovered pasa_asmbl_33116.p1, internal, 30062, 30204 -recovered pasa_asmbl_33116.p1, internal, 30304, 30480 -recovered pasa_asmbl_33116.p1, internal, 30561, 30632 Valid prediction for snap_scaffold_24-snap.1835-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29329, rend_intergenic: 21356 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137749, rend_intergenic: 135494 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 155981, rend_intergenic: 153890 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 166235, rend_intergenic: 162366 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 209218 -exon list size: 385 building trellis 0.3 0.5 0.8 1.0 1.3 1.6 1.8 2.1 2.3 2.6 2.8 3.1 3.4 3.6 3.9 4.1 4.4 4.7 4.9 5.2 5.4 5.7 5.9 6.2 6.5 6.7 7.0 7.2 7.5 7.8 8.0 8.3 8.5 8.8 9.0 9.3 9.6 9.8 10.1 10.3 10.6 10.9 11.1 11.4 11.6 11.9 12.1 12.4 12.7 12.9 13.2 13.4 13.7 14.0 14.2 14.5 14.7 15.0 15.2 15.5 15.8 16.0 16.3 16.5 16.8 17.1 17.3 17.6 17.8 18.1 18.3 18.6 18.9 19.1 19.4 19.6 19.9 20.2 20.4 20.7 20.9 21.2 21.4 21.7 22.0 22.2 22.5 22.7 23.0 23.3 23.5 23.8 24.0 24.3 24.5 24.8 25.1 25.3 25.6 25.8 26.1 26.4 26.6 26.9 27.1 27.4 27.6 27.9 28.2 28.4 28.7 28.9 29.2 29.5 29.7 30.0 30.2 30.5 30.7 31.0 31.3 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 35.1 35.4 35.7 35.9 36.2 36.4 36.7 37.0 37.2 37.5 37.7 38.0 38.2 38.5 38.8 39.0 39.3 39.5 39.8 40.1 40.3 40.6 40.8 41.1 41.3 41.6 41.9 42.1 42.4 42.6 42.9 43.2 43.4 43.7 43.9 44.2 44.4 44.7 45.0 45.2 45.5 45.7 46.0 46.3 46.5 46.8 47.0 47.3 47.5 47.8 48.1 48.3 48.6 48.8 49.1 49.4 49.6 49.9 50.1 50.4 50.6 50.9 51.2 51.4 51.7 51.9 52.2 52.5 52.7 53.0 53.2 53.5 53.7 54.0 54.3 54.5 54.8 55.0 55.3 55.6 55.8 56.1 56.3 56.6 56.8 57.1 57.4 57.6 57.9 58.1 58.4 58.7 58.9 59.2 59.4 59.7 59.9 60.2 60.5 60.7 61.0 61.2 61.5 61.8 62.0 62.3 62.5 62.8 63.0 63.3 63.6 63.8 64.1 64.3 64.6 64.9 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 68.7 69.0 69.3 69.5 69.8 70.0 70.3 70.5 70.8 71.1 71.3 71.6 71.8 72.1 72.4 72.6 72.9 73.1 73.4 73.6 73.9 74.2 74.4 74.7 74.9 75.2 75.5 75.7 76.0 76.2 76.5 76.7 77.0 77.3 77.5 77.8 78.0 78.3 78.6 78.8 79.1 79.3 79.6 79.8 80.1 80.4 80.6 80.9 81.1 81.4 81.7 81.9 82.2 82.4 82.7 82.9 83.2 83.5 83.7 84.0 84.2 84.5 84.8 85.0 85.3 85.5 85.8 86.0 86.3 86.6 86.8 87.1 87.3 87.6 87.9 88.1 88.4 88.6 88.9 89.1 89.4 89.7 89.9 90.2 90.4 90.7 91.0 91.2 91.5 91.7 92.0 92.2 92.5 92.8 93.0 93.3 93.5 93.8 94.1 94.3 94.6 94.8 95.1 95.3 95.6 95.9 96.1 96.4 96.6 96.9 97.2 97.4 97.7 97.9 98.2 98.4 98.7 99.0 99.2 99.5 99.7 -found 30 predictions from path traversal Error with prediction: snap lend_intergenic: 29329, rend_intergenic: 21356 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137749, rend_intergenic: 135494 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 155981, rend_intergenic: 153890 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 166235, rend_intergenic: 162366 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 26 predictions persist after filtering for low support