-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_9494810-9675079 -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_16-snap.1758-T1 Valid prediction for pasa_asmbl_16500.p1 Valid prediction for snap_scaffold_16-snap.1769-T1 Valid prediction for GlimmerHMM_glimmerT_38819-T1 Valid prediction for snap_scaffold_16-snap.1785-T1 Valid prediction for pasa_asmbl_16491.p1 Valid prediction for Augustus_model.g25921.t1 Valid prediction for GlimmerHMM_glimmerT_38816-T1 Valid prediction for Augustus_model.g25922.t1 Valid prediction for snap_scaffold_16-snap.1773-T1 Valid prediction for GlimmerHMM_glimmerT_38811-T1 Valid prediction for GlimmerHMM_glimmerT_38813-T1 Couldn't classify 76859, 77033 Couldn't classify 77591, 77634 Sorry, prediction pasa_asmbl_16497.p1 fails validation. (ATC) AG 76859-77033 GT CTG (TCC) AG 77146-77284 GT TGG (GAA) AG 77379-77482 GT CGG (GAT) AG 77591-77634 GG AGG -recovered pasa_asmbl_16497.p1, internal, 76859, 77033 -recovered pasa_asmbl_16497.p1, internal, 77146, 77284 -recovered pasa_asmbl_16497.p1, internal, 77379, 77482 Valid prediction for pasa_asmbl_16490.p2 Valid prediction for GlimmerHMM_glimmerT_38807-T1 Valid prediction for snap_scaffold_16-snap.1762-T1 Valid prediction for snap_scaffold_16-snap.1765-T1 Valid prediction for GlimmerHMM_glimmerT_38809-T1 Couldn't classify 65006, 65052 Couldn't classify 68914, 68994 Sorry, prediction pasa_asmbl_16493.p1 fails validation. (CCT) AG 65006-65052 GT AGG (CAG) AG 65224-65414 GT TGG (ATA) AG 65846-66028 GT TGG (GTG) AG 66616-66864 GT TGG (ATG) AG 66993-67111 GT AGG (TTT) AG 67229-67336 GT TGG (ATT) AG 67499-67673 GT CTG (TCC) AG 67786-67924 GT TGG (GAA) AG 68019-68122 GT CGG (GAT) AG 68224-68312 GT AGG (GTT) AG 68416-68569 GT TGG (GCA) AG 68657-68820 GT AGG (GCC) AG 68914-68994 AG TCA add_exon() Sorry, pasa_asmbl_16493.p1 66993-67111-initial-1 is invalid. -recovered pasa_asmbl_16493.p1, initial, 66993, 67111 -recovered pasa_asmbl_16493.p1, internal, 65006, 65052 -recovered pasa_asmbl_16493.p1, internal, 65224, 65414 -recovered pasa_asmbl_16493.p1, internal, 65846, 66028 -recovered pasa_asmbl_16493.p1, internal, 66616, 66864 -recovered pasa_asmbl_16493.p1, internal, 66993, 67111 -recovered pasa_asmbl_16493.p1, internal, 67229, 67336 -recovered pasa_asmbl_16493.p1, internal, 67499, 67673 -recovered pasa_asmbl_16493.p1, internal, 67786, 67924 -recovered pasa_asmbl_16493.p1, internal, 68019, 68122 -recovered pasa_asmbl_16493.p1, internal, 68224, 68312 -recovered pasa_asmbl_16493.p1, internal, 68416, 68569 -recovered pasa_asmbl_16493.p1, internal, 68657, 68820 Valid prediction for snap_scaffold_16-snap.1779-T1 Couldn't classify 78919, 79049 Couldn't classify 79212, 79359 Sorry, prediction CodingQuarry_transcript_20062-T1 fails validation. (ATG) CC 78137-78184 GT AGG (GCC) AG 78278-78371 GT TAG (CTG) AG 78608-78765 GT AGG (GTG) AG 78919-79049 AA CAA (GCA) GT 79212-79359 TT GAT -recovered CodingQuarry_transcript_20062-T1, initial, 78137, 78184 -recovered CodingQuarry_transcript_20062-T1, internal, 78278, 78371 -recovered CodingQuarry_transcript_20062-T1, internal, 78608, 78765 Valid prediction for GlimmerHMM_glimmerT_38818-T1 Valid prediction for snap_scaffold_16-snap.1782-T1 Couldn't classify 109926, 110102 Couldn't classify 111630, 111803 Sorry, prediction pasa_asmbl_16499.p1 fails validation. (GGG) AG 109926-110102 GT AGG (GAT) AG 111270-111359 GT AGG (CAT) AG 111630-111803 AG ATA -recovered pasa_asmbl_16499.p1, internal, 109926, 110102 -recovered pasa_asmbl_16499.p1, internal, 111270, 111359 Valid prediction for GlimmerHMM_glimmerT_38820-T1 Couldn't classify 174311, 174355 Couldn't classify 176431, 176462 Sorry, prediction pasa_asmbl_16502.p1 fails validation. (ACC) AG 174311-174355 GT AGG (GTG) AG 174465-174615 GT TGG (ATG) AG 174886-174930 GT GGG (GTA) AG 175030-175234 GT GGG (GAA) AG 175412-175518 GT AGG (ACA) AG 175722-175873 GT AGG (TCC) AG 176086-176332 GT TGG (GTC) AG 176431-176462 AC ACA add_exon() Sorry, pasa_asmbl_16502.p1 174886-174930-initial-1 is invalid. -recovered pasa_asmbl_16502.p1, initial, 174886, 174930 -recovered pasa_asmbl_16502.p1, internal, 174311, 174355 -recovered pasa_asmbl_16502.p1, internal, 174465, 174615 -recovered pasa_asmbl_16502.p1, internal, 174886, 174930 -recovered pasa_asmbl_16502.p1, internal, 175030, 175234 -recovered pasa_asmbl_16502.p1, internal, 175412, 175518 -recovered pasa_asmbl_16502.p1, internal, 175722, 175873 -recovered pasa_asmbl_16502.p1, internal, 176086, 176332 Valid prediction for snap_scaffold_16-snap.1757-T1 Couldn't classify 69227, 69319 Sorry, prediction pasa_asmbl_16496.p1 fails validation. (CTC) AC 69227-69319 GT AGG (GTG) AG 69472-69608 GT AGG (TGT) AG 69770-69911 TT GAT -recovered pasa_asmbl_16496.p1, terminal, 69770, 69911 -recovered pasa_asmbl_16496.p1, internal, 69472, 69608 Valid prediction for snap_scaffold_16-snap.1753-T1 Couldn't classify 78901, 79049 Couldn't classify 79212, 79359 Sorry, prediction CodingQuarry_transcript_20063-T1 fails validation. (ATG) CC 78137-78184 GT AGG (GCC) AG 78278-78371 GT TAG (CTG) AG 78608-78765 GT AGG (TGC) AG 78901-79049 AA CAA (GCA) GT 79212-79359 TT GAT -recovered CodingQuarry_transcript_20063-T1, initial, 78137, 78184 -recovered CodingQuarry_transcript_20063-T1, internal, 78278, 78371 -recovered CodingQuarry_transcript_20063-T1, internal, 78608, 78765 Valid prediction for GlimmerHMM_glimmerT_38817-T1 Valid prediction for snap_scaffold_16-snap.1756-T1 Valid prediction for snap_scaffold_16-snap.1780-T1 Valid prediction for snap_scaffold_16-snap.1755-T1 Valid prediction for GlimmerHMM_glimmerT_38812-T1 Couldn't classify 13377, 13538 Couldn't classify 15360, 15512 Sorry, prediction pasa_asmbl_16732.p1 fails validation. (GCG) CA 13377-13538 GT AGG (CCG) AG 15360-15512 TA AGT Valid prediction for Augustus_model.g25918.t1 Valid prediction for snap_scaffold_16-snap.1766-T1 Valid prediction for snap_scaffold_16-snap.1781-T1 Valid prediction for CodingQuarry_transcript_20061-T1 Valid prediction for GlimmerHMM_glimmerT_38806-T1 Couldn't classify 176629, 176832 Couldn't classify 177309, 177325 Sorry, prediction pasa_asmbl_16503.p1 fails validation. (TTA) AG 176629-176832 GT TAG (ACC) AG 176993-177164 GT GGG (GGG) AG 177309-177325 GT GTG -recovered pasa_asmbl_16503.p1, internal, 176629, 176832 -recovered pasa_asmbl_16503.p1, internal, 176993, 177164 -recovered pasa_asmbl_16503.p1, internal, 177309, 177325 Valid prediction for GlimmerHMM_glimmerT_38805-T1 Valid prediction for snap_scaffold_16-snap.1763-T1 Valid prediction for GlimmerHMM_glimmerT_38814-T1 Valid prediction for snap_scaffold_16-snap.1767-T1 Valid prediction for snap_scaffold_16-snap.1777-T1 Valid prediction for Augustus_model.g25924.t1 Valid prediction for Augustus_model.g25923.t1 Couldn't classify 177816, 177867 Sorry, prediction pasa_asmbl_16761.p1 fails validation. (CCT) AC 177816-177867 GT AGG (ATG) AG 178043-178110 GT AGG (GTG) AG 178229-178345 GT AGG (GGC) AG 178524-178620 GT CTG (CTC) AG 178731-178780 CA AGC add_exon() Sorry, pasa_asmbl_16761.p1 178043-178110-initial-1 is invalid. -recovered pasa_asmbl_16761.p1, initial, 178043, 178110 -recovered pasa_asmbl_16761.p1, terminal, 178731, 178780 -recovered pasa_asmbl_16761.p1, internal, 178043, 178110 -recovered pasa_asmbl_16761.p1, internal, 178229, 178345 -recovered pasa_asmbl_16761.p1, internal, 178524, 178620 Valid prediction for Augustus_model.g25920.t1 Valid prediction for GlimmerHMM_glimmerT_38815-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.g25926.t1 Valid prediction for GlimmerHMM_glimmerT_38823-T1 Valid prediction for snap_scaffold_16-snap.1775-T1 Valid prediction for CodingQuarry_transcript_20065-T1 Valid prediction for snap_scaffold_16-snap.1786-T1 Valid prediction for snap_scaffold_16-snap.1752-T1 Valid prediction for snap_scaffold_16-snap.1784-T1 Valid prediction for pasa_asmbl_17294.p1 Valid prediction for snap_scaffold_16-snap.1754-T1 Valid prediction for GlimmerHMM_glimmerT_38821-T1 Valid prediction for snap_scaffold_16-snap.1771-T1 Valid prediction for snap_scaffold_16-snap.1778-T1 Couldn't classify 41608, 41625 Couldn't classify 43101, 43250 Sorry, prediction pasa_asmbl_17291.p1 fails validation. (CAG) AC 41608-41625 GT CTG (GTG) AG 42298-42393 GC CGG (GTG) AG 42612-42716 GT TGG (GCC) AG 43101-43250 AG ACA -recovered pasa_asmbl_17291.p1, internal, 42298, 42393 -recovered pasa_asmbl_17291.p1, internal, 42612, 42716 Valid prediction for pasa_asmbl_17289.p1 Valid prediction for HiQ_model.g25929.t1 Valid prediction for GlimmerHMM_glimmerT_38824-T1 Valid prediction for snap_scaffold_16-snap.1761-T1 Couldn't classify 39407, 39463 Couldn't classify 40101, 40190 Sorry, prediction pasa_asmbl_17293.p1 fails validation. (GCT) CA 39407-39463 GT AGG (GTG) AG 39603-39710 GT AGG (AGG) AG 39887-39997 GT AGG (AAG) AG 40101-40190 AA CCA -recovered pasa_asmbl_17293.p1, internal, 39603, 39710 -recovered pasa_asmbl_17293.p1, internal, 39887, 39997 Valid prediction for CodingQuarry_transcript_20064-T1 Valid prediction for snap_scaffold_16-snap.1772-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for HiQ_model.g25925.t1 Valid prediction for GlimmerHMM_glimmerT_38808-T1 Valid prediction for Augustus_model.g25919.t1 Valid prediction for GlimmerHMM_glimmerT_38810-T1 Valid prediction for snap_scaffold_16-snap.1770-T1 Valid prediction for snap_scaffold_16-snap.1759-T1 Valid prediction for GlimmerHMM_glimmerT_38822-T1 Valid prediction for snap_scaffold_16-snap.1783-T1 Valid prediction for GlimmerHMM_glimmerT_38825-T1 Valid prediction for snap_scaffold_16-snap.1760-T1 Valid prediction for snap_scaffold_16-snap.1768-T1 Valid prediction for snap_scaffold_16-snap.1774-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for CodingQuarry_transcript_20066-T1 Valid prediction for snap_scaffold_16-snap.1764-T1 Valid prediction for Augustus_model.g25928.t1 Valid prediction for snap_scaffold_16-snap.1776-T1 Valid prediction for Augustus_model.g25927.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13556, rend_intergenic: 11563 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 16583, rend_intergenic: 13575 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24350, rend_intergenic: 17027 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 44372, rend_intergenic: 32879 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 62393, rend_intergenic: 58289 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99952, rend_intergenic: 89215 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100903, rend_intergenic: 100215 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119564, rend_intergenic: 100917 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120268, rend_intergenic: 119641 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 126885, rend_intergenic: 122636 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137537, rend_intergenic: 137100 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 139015, rend_intergenic: 137604 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 159654, rend_intergenic: 139350 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 169663, rend_intergenic: 159813 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179015, rend_intergenic: 173366 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 180270 -exon list size: 416 building trellis 0.2 0.5 0.7 1.0 1.2 1.4 1.7 1.9 2.2 2.4 2.6 2.9 3.1 3.3 3.6 3.8 4.1 4.3 4.5 4.8 5.0 5.3 5.5 5.7 6.0 6.2 6.5 6.7 6.9 7.2 7.4 7.7 7.9 8.1 8.4 8.6 8.9 9.1 9.3 9.6 9.8 10.0 10.3 10.5 10.8 11.0 11.2 11.5 11.7 12.0 12.2 12.4 12.7 12.9 13.2 13.4 13.6 13.9 14.1 14.4 14.6 14.8 15.1 15.3 15.6 15.8 16.0 16.3 16.5 16.7 17.0 17.2 17.5 17.7 17.9 18.2 18.4 18.7 18.9 19.1 19.4 19.6 19.9 20.1 20.3 20.6 20.8 21.1 21.3 21.5 21.8 22.0 22.2 22.5 22.7 23.0 23.2 23.4 23.7 23.9 24.2 24.4 24.6 24.9 25.1 25.4 25.6 25.8 26.1 26.3 26.6 26.8 27.0 27.3 27.5 27.8 28.0 28.2 28.5 28.7 28.9 29.2 29.4 29.7 29.9 30.1 30.4 30.6 30.9 31.1 31.3 31.6 31.8 32.1 32.3 32.5 32.8 33.0 33.3 33.5 33.7 34.0 34.2 34.4 34.7 34.9 35.2 35.4 35.6 35.9 36.1 36.4 36.6 36.8 37.1 37.3 37.6 37.8 38.0 38.3 38.5 38.8 39.0 39.2 39.5 39.7 40.0 40.2 40.4 40.7 40.9 41.1 41.4 41.6 41.9 42.1 42.3 42.6 42.8 43.1 43.3 43.5 43.8 44.0 44.3 44.5 44.7 45.0 45.2 45.5 45.7 45.9 46.2 46.4 46.7 46.9 47.1 47.4 47.6 47.8 48.1 48.3 48.6 48.8 49.0 49.3 49.5 49.8 50.0 50.2 50.5 50.7 51.0 51.2 51.4 51.7 51.9 52.2 52.4 52.6 52.9 53.1 53.3 53.6 53.8 54.1 54.3 54.5 54.8 55.0 55.3 55.5 55.7 56.0 56.2 56.5 56.7 56.9 57.2 57.4 57.7 57.9 58.1 58.4 58.6 58.9 59.1 59.3 59.6 59.8 60.0 60.3 60.5 60.8 61.0 61.2 61.5 61.7 62.0 62.2 62.4 62.7 62.9 63.2 63.4 63.6 63.9 64.1 64.4 64.6 64.8 65.1 65.3 65.6 65.8 66.0 66.3 66.5 66.7 67.0 67.2 67.5 67.7 67.9 68.2 68.4 68.7 68.9 69.1 69.4 69.6 69.9 70.1 70.3 70.6 70.8 71.1 71.3 71.5 71.8 72.0 72.2 72.5 72.7 73.0 73.2 73.4 73.7 73.9 74.2 74.4 74.6 74.9 75.1 75.4 75.6 75.8 76.1 76.3 76.6 76.8 77.0 77.3 77.5 77.8 78.0 78.2 78.5 78.7 78.9 79.2 79.4 79.7 79.9 80.1 80.4 80.6 80.9 81.1 81.3 81.6 81.8 82.1 82.3 82.5 82.8 83.0 83.3 83.5 83.7 84.0 84.2 84.4 84.7 84.9 85.2 85.4 85.6 85.9 86.1 86.4 86.6 86.8 87.1 87.3 87.6 87.8 88.0 88.3 88.5 88.8 89.0 89.2 89.5 89.7 90.0 90.2 90.4 90.7 90.9 91.1 91.4 91.6 91.9 92.1 92.3 92.6 92.8 93.1 93.3 93.5 93.8 94.0 94.3 94.5 94.7 95.0 95.2 95.5 95.7 95.9 96.2 96.4 96.7 96.9 97.1 97.4 97.6 97.8 98.1 98.3 98.6 98.8 99.0 99.3 99.5 99.8 -found 23 predictions from path traversal Error with prediction: snap lend_intergenic: 13556, rend_intergenic: 11563 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 16583, rend_intergenic: 13575 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 24350, rend_intergenic: 17027 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 44372, rend_intergenic: 32879 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 62393, rend_intergenic: 58289 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99952, rend_intergenic: 89215 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 100903, rend_intergenic: 100215 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119564, rend_intergenic: 100917 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 120268, rend_intergenic: 119641 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 126885, rend_intergenic: 122636 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 137537, rend_intergenic: 137100 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 139015, rend_intergenic: 137604 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 159654, rend_intergenic: 139350 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 169663, rend_intergenic: 159813 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 179015, rend_intergenic: 173366 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 -building DP trellis -building trellis in range 1 - 11372 -exon list size: 2 building trellis 25.0 50.0 75.0 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 10538 -exon list size: 1 building trellis 33.3 66.7 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support