-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_9145721-9374303 -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_22-snap.1885-T1 Valid prediction for Augustus_model.g33352.t1 Valid prediction for GlimmerHMM_glimmerT_50004-T1 Valid prediction for snap_scaffold_22-snap.1864-T1 Valid prediction for snap_scaffold_22-snap.1883-T1 Couldn't classify 128839, 129174 Sorry, prediction pasa_asmbl_29534.p1 fails validation. (CAC) CA 128839-129174 AG AGA Valid prediction for snap_scaffold_22-snap.1892-T1 Valid prediction for snap_scaffold_22-snap.1867-T1 Valid prediction for Augustus_model.g33361.t1 Couldn't classify 75999, 76087 Couldn't classify 77925, 78086 Sorry, prediction pasa_asmbl_30299.p1 fails validation. (AAC) AG 75999-76087 GT GCG (GGT) AG 76473-76586 GT AGG (TGC) AG 76898-77048 GT AGG (TTG) AG 77352-77517 GT GGG (CTC) AG 77640-77695 GT AGG (CGC) AG 77925-78086 CC CCC -recovered pasa_asmbl_30299.p1, internal, 75999, 76087 -recovered pasa_asmbl_30299.p1, internal, 76473, 76586 -recovered pasa_asmbl_30299.p1, internal, 76898, 77048 -recovered pasa_asmbl_30299.p1, internal, 77352, 77517 -recovered pasa_asmbl_30299.p1, internal, 77640, 77695 Valid prediction for snap_scaffold_22-snap.1887-T1 Valid prediction for snap_scaffold_22-snap.1878-T1 Valid prediction for snap_scaffold_22-snap.1896-T1 Valid prediction for snap_scaffold_22-snap.1871-T1 Valid prediction for CodingQuarry_transcript_34254-T1 Valid prediction for snap_scaffold_22-snap.1859-T1 Valid prediction for GlimmerHMM_glimmerT_50009-T1 Valid prediction for snap_scaffold_22-snap.1876-T1 Valid prediction for snap_scaffold_22-snap.1865-T1 Valid prediction for Augustus_model.g33349.t1 Valid prediction for Augustus_model.g33348.t1 Valid prediction for Augustus_model.g33358.t1 Valid prediction for snap_scaffold_22-snap.1893-T1 Valid prediction for GlimmerHMM_glimmerT_49995-T1 Valid prediction for snap_scaffold_22-snap.1891-T1 Sorry, intron length (5) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_50012-T1 Valid prediction for snap_scaffold_22-snap.1880-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for HiQ_model.g33354.t1 Valid prediction for snap_scaffold_22-snap.1897-T1 Couldn't classify 162784, 162796 Sorry, prediction pasa_asmbl_30305.p1 fails validation. (GAA) CT 162784-162796 GT AGG (GTT) AG 162976-163038 GT AGG (CTG) AG 163687-163858 GT TAG (CTG) AG 164512-164673 GT AGG (AAA) AG 165411-165499 GT AGG (CCA) AG 166080-166276 GT TGG (ACT) AG 166492-166536 CT AAC -recovered pasa_asmbl_30305.p1, terminal, 166492, 166536 -recovered pasa_asmbl_30305.p1, internal, 162976, 163038 -recovered pasa_asmbl_30305.p1, internal, 163687, 163858 -recovered pasa_asmbl_30305.p1, internal, 164512, 164673 -recovered pasa_asmbl_30305.p1, internal, 165411, 165499 -recovered pasa_asmbl_30305.p1, internal, 166080, 166276 Valid prediction for Augustus_model.g33359.t1 Valid prediction for Augustus_model.g33351.t1 Couldn't classify 73587, 73733 Couldn't classify 75489, 75548 Sorry, prediction pasa_asmbl_30298.p1 fails validation. (AGC) CG 73587-73733 GT AGG (AGT) AG 73971-74035 GT AGG (GTT) AG 74198-74303 GT AGG (TCC) AG 74539-74688 GT AGG (TGC) AG 75316-75387 GT GGG (GAT) AG 75489-75548 GT AGG -recovered pasa_asmbl_30298.p1, internal, 73971, 74035 -recovered pasa_asmbl_30298.p1, internal, 74198, 74303 -recovered pasa_asmbl_30298.p1, internal, 74539, 74688 -recovered pasa_asmbl_30298.p1, internal, 75316, 75387 -recovered pasa_asmbl_30298.p1, internal, 75489, 75548 Valid prediction for snap_scaffold_22-snap.1888-T1 Couldn't classify 88587, 88669 Couldn't classify 89923, 89936 Sorry, prediction pasa_asmbl_30301.p1 fails validation. (GCG) CA 88587-88669 GT AGG (GTG) AG 88753-88875 GT GCG (GCT) AG 89614-89720 GT AGG (AGT) AG 89923-89936 CA AGC -recovered pasa_asmbl_30301.p1, internal, 88753, 88875 -recovered pasa_asmbl_30301.p1, internal, 89614, 89720 Valid prediction for GlimmerHMM_glimmerT_49997-T1 Valid prediction for snap_scaffold_22-snap.1860-T1 Valid prediction for GlimmerHMM_glimmerT_50010-T1 Valid prediction for snap_scaffold_22-snap.1881-T1 Couldn't classify 92020, 92108 Sorry, prediction pasa_asmbl_30302.p1 fails validation. (CGT) CC 92020-92108 GT AGG (TTT) AG 92440-92561 GT TGG (GTC) AG 92958-93058 GT AGG (TTT) AG 93556-93726 GT CGG (GTT) AG 94371-94550 AG AGA -recovered pasa_asmbl_30302.p1, terminal, 94371, 94550 -recovered pasa_asmbl_30302.p1, internal, 92440, 92561 -recovered pasa_asmbl_30302.p1, internal, 92958, 93058 -recovered pasa_asmbl_30302.p1, internal, 93556, 93726 Valid prediction for pasa_asmbl_30303.p1 Valid prediction for snap_scaffold_22-snap.1861-T1 Valid prediction for GlimmerHMM_glimmerT_50008-T1 Valid prediction for snap_scaffold_22-snap.1862-T1 Sorry, intron length (9) is less than minimum required (10) Valid prediction for CodingQuarry_transcript_34253-T1 Couldn't classify 80470, 82131 Sorry, prediction pasa_asmbl_30300.p1 fails validation. (CCT) CC 80470-82131 GT AGG Valid prediction for GlimmerHMM_glimmerT_49999-T1 Valid prediction for GlimmerHMM_glimmerT_50011-T1 Valid prediction for snap_scaffold_22-snap.1890-T1 Valid prediction for snap_scaffold_22-snap.1889-T1 Valid prediction for GlimmerHMM_glimmerT_50014-T1 Valid prediction for GlimmerHMM_glimmerT_50000-T1 Valid prediction for GlimmerHMM_glimmerT_50002-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 Augustus_model.g33356.t1 Valid prediction for snap_scaffold_22-snap.1874-T1 Valid prediction for Augustus_model.g33355.t1 Valid prediction for snap_scaffold_22-snap.1894-T1 Valid prediction for snap_scaffold_22-snap.1882-T1 Valid prediction for snap_scaffold_22-snap.1895-T1 Valid prediction for snap_scaffold_22-snap.1858-T1 Valid prediction for GlimmerHMM_glimmerT_49993-T1 Valid prediction for Augustus_model.g33347.t1 Valid prediction for pasa_asmbl_29530.p1 Valid prediction for snap_scaffold_22-snap.1884-T1 Valid prediction for snap_scaffold_22-snap.1870-T1 Valid prediction for snap_scaffold_22-snap.1868-T1 Valid prediction for Augustus_model.g33357.t1 Couldn't classify 218522, 218593 Sorry, prediction pasa_asmbl_29519.p1 fails validation. (ATG) AC 212254-212378 GT AGG (TCC) AG 213387-213492 GT AGG (GTG) AG 214374-214397 GT TGG (CAG) AG 216659-216734 GT GGG (TGA) AG 216998-217092 GT GAG (GAG) AG 217302-217409 GT AGG (GAT) AG 217864-217965 GT TGG (CCC) AG 218129-218212 GT AGG (GGT) AG 218522-218593 CT CCC -recovered pasa_asmbl_29519.p1, initial, 212254, 212378 -recovered pasa_asmbl_29519.p1, internal, 213387, 213492 -recovered pasa_asmbl_29519.p1, internal, 214374, 214397 -recovered pasa_asmbl_29519.p1, internal, 216659, 216734 -recovered pasa_asmbl_29519.p1, internal, 216998, 217092 -recovered pasa_asmbl_29519.p1, internal, 217302, 217409 -recovered pasa_asmbl_29519.p1, internal, 217864, 217965 -recovered pasa_asmbl_29519.p1, internal, 218129, 218212 Valid prediction for GlimmerHMM_glimmerT_50013-T1 Valid prediction for GlimmerHMM_glimmerT_49996-T1 Valid prediction for Augustus_model.g33345.t1 Valid prediction for pasa_asmbl_29533.p1 Valid prediction for GlimmerHMM_glimmerT_50005-T1 Valid prediction for Augustus_model.g33360.t1 Valid prediction for snap_scaffold_22-snap.1873-T1 Valid prediction for snap_scaffold_22-snap.1877-T1 Valid prediction for GlimmerHMM_glimmerT_49992-T1 Valid prediction for CodingQuarry_transcript_34255-T1 Valid prediction for snap_scaffold_22-snap.1898-T1 Valid prediction for pasa_asmbl_29532.p1 Valid prediction for snap_scaffold_22-snap.1879-T1 Valid prediction for snap_scaffold_22-snap.1869-T1 Valid prediction for snap_scaffold_22-snap.1875-T1 Valid prediction for Augustus_model.g33344.t1 Valid prediction for pasa_asmbl_29529.p1 Valid prediction for HiQ_model.g33350.t1 Valid prediction for HiQ_model.g33353.t1 Valid prediction for snap_scaffold_22-snap.1866-T1 Valid prediction for CodingQuarry_transcript_34252-T1 Valid prediction for GlimmerHMM_glimmerT_49998-T1 Valid prediction for GlimmerHMM_glimmerT_50006-T1 Valid prediction for GlimmerHMM_glimmerT_49994-T1 Couldn't classify 196052, 196147 Couldn't classify 198679, 198864 Sorry, prediction pasa_asmbl_29525.p1 fails validation. (GAC) CA 196052-196147 GT CTG (GAC) AG 196355-196465 GT AGG (GAC) AG 196614-196715 GT AGG (CCT) AG 197034-197117 GT AGG (GGC) AG 197835-197984 GT CGG (GTT) AG 198679-198864 GT AGG -recovered pasa_asmbl_29525.p1, internal, 196355, 196465 -recovered pasa_asmbl_29525.p1, internal, 196614, 196715 -recovered pasa_asmbl_29525.p1, internal, 197034, 197117 -recovered pasa_asmbl_29525.p1, internal, 197835, 197984 -recovered pasa_asmbl_29525.p1, internal, 198679, 198864 Valid prediction for GlimmerHMM_glimmerT_50003-T1 Valid prediction for snap_scaffold_22-snap.1863-T1 Valid prediction for snap_scaffold_22-snap.1872-T1 Valid prediction for GlimmerHMM_glimmerT_50001-T1 Valid prediction for snap_scaffold_22-snap.1886-T1 Valid prediction for GlimmerHMM_glimmerT_50007-T1 Couldn't classify 219318, 219524 Couldn't classify 221183, 221278 Sorry, prediction pasa_asmbl_29517.p1 fails validation. (CTC) AG 219318-219524 GT CGG (CGT) AG 220212-220304 GT AGG (TTT) AG 220720-220833 GC AGG (GAG) AG 221183-221278 CT TCC -recovered pasa_asmbl_29517.p1, internal, 219318, 219524 -recovered pasa_asmbl_29517.p1, internal, 220212, 220304 -recovered pasa_asmbl_29517.p1, internal, 220720, 220833 Couldn't classify 93074, 93334 Sorry, prediction pasa_asmbl_29535.p1 fails validation. (ATG) CC 89903-90559 GT AGG (GTG) AG 91698-91902 GT AGG (AGA) AG 92564-92757 GT AGG (GAT) AG 93074-93334 AC ACA -recovered pasa_asmbl_29535.p1, initial, 89903, 90559 -recovered pasa_asmbl_29535.p1, internal, 91698, 91902 -recovered pasa_asmbl_29535.p1, internal, 92564, 92757 Couldn't classify 32497, 32668 Sorry, prediction pasa_asmbl_29537.p1 fails validation. (TCC) CT 32497-32668 GT GGG (AGA) AG 33418-33506 GT AGG (GCA) AG 33764-34222 GC AGG -recovered pasa_asmbl_29537.p1, terminal, 33764, 34222 -recovered pasa_asmbl_29537.p1, internal, 33418, 33506 -recovered pasa_asmbl_29537.p1, internal, 33764, 34222 Valid prediction for Augustus_model.g33346.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15820, rend_intergenic: 7821 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30753, rend_intergenic: 19240 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36860, rend_intergenic: 31119 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 52584, rend_intergenic: 41896 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 69708, rend_intergenic: 53156 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 94550, rend_intergenic: 73965 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 102415, rend_intergenic: 98985 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115794, rend_intergenic: 114955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123549, rend_intergenic: 115841 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 132240, rend_intergenic: 129171 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134563, rend_intergenic: 133614 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 135136, rend_intergenic: 134653 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146435, rend_intergenic: 135305 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 153634, rend_intergenic: 148225 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 212578, rend_intergenic: 203313 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 228583 -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 28 predictions from path traversal Error with prediction: snap lend_intergenic: 15820, rend_intergenic: 7821 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 30753, rend_intergenic: 19240 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36860, rend_intergenic: 31119 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 52584, rend_intergenic: 41896 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 69708, rend_intergenic: 53156 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 94550, rend_intergenic: 73965 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 102415, rend_intergenic: 98985 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 115794, rend_intergenic: 114955 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 123549, rend_intergenic: 115841 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 132240, rend_intergenic: 129171 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 134563, rend_intergenic: 133614 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 135136, rend_intergenic: 134653 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146435, rend_intergenic: 135305 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 153634, rend_intergenic: 148225 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 212578, rend_intergenic: 203313 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 21 predictions persist after filtering for low support -building DP trellis -building trellis in range 217066 - 228583 -exon list size: 5 building trellis 14.3 28.6 42.9 57.1 71.4 85.7 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support