-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_8382291-8640580 -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: +)Couldn't classify 15616, 15684 Couldn't classify 16861, 16902 Sorry, prediction pasa_asmbl_21930.p1 fails validation. (AAG) AC 15616-15684 GT AGG (AAC) AG 15794-15968 GT CGG (ATG) AG 16292-16347 GT AGG (ACT) AG 16861-16902 CT GCC add_exon() Sorry, pasa_asmbl_21930.p1 16292-16347-initial-1 is invalid. -recovered pasa_asmbl_21930.p1, initial, 16292, 16347 -recovered pasa_asmbl_21930.p1, internal, 15794, 15968 -recovered pasa_asmbl_21930.p1, internal, 16292, 16347 Valid prediction for Augustus_model.g29509.t1 Valid prediction for GlimmerHMM_glimmerT_44480-T1 Valid prediction for HiQ_model.g29511.t1 Valid prediction for CodingQuarry_transcript_25736-T1 Couldn't classify 244337, 244503 Sorry, prediction pasa_asmbl_21537.p1 fails validation. (GTC) AT 244337-244503 GT AGG (GTA) AG 245759-245934 GT CAG (GTG) AG 246801-247018 TA AAT -recovered pasa_asmbl_21537.p1, terminal, 246801, 247018 -recovered pasa_asmbl_21537.p1, internal, 245759, 245934 Valid prediction for Augustus_model.g29504.t1 Valid prediction for GlimmerHMM_glimmerT_44474-T1 Valid prediction for snap_scaffold_19-snap.1614-T1 Couldn't classify 79993, 80001 Couldn't classify 81061, 81243 Sorry, prediction pasa_asmbl_21528.p1 fails validation. (GAC) CA 79993-80001 GT ATG (CAA) AG 80119-80285 GT AGG (CGG) AG 80405-80473 GT AGG (GAA) AG 80782-80851 GT AGG (AGT) AG 81061-81243 CA AGC -recovered pasa_asmbl_21528.p1, internal, 80119, 80285 -recovered pasa_asmbl_21528.p1, internal, 80405, 80473 -recovered pasa_asmbl_21528.p1, internal, 80782, 80851 Valid prediction for snap_scaffold_19-snap.1630-T1 Valid prediction for snap_scaffold_19-snap.1635-T1 Couldn't classify 86229, 86426 Couldn't classify 88992, 89022 Sorry, prediction pasa_asmbl_21530.p2 fails validation. (GGT) CA 86229-86426 GT AGG (AAG) AG 87075-87164 GT TGG (TCC) AG 88034-88167 GT TGG (GGA) AG 88992-89022 GA GAG -recovered pasa_asmbl_21530.p2, internal, 87075, 87164 -recovered pasa_asmbl_21530.p2, internal, 88034, 88167 Couldn't classify 77419, 77518 Couldn't classify 79906, 79968 Sorry, prediction pasa_asmbl_21527.p1 fails validation. (AGG) CC 77419-77518 GT GTG (CTG) AG 78121-78235 GT GTG (GGG) AG 79193-79340 GT AGG (GGC) AG 79906-79968 AG AGA -recovered pasa_asmbl_21527.p1, internal, 78121, 78235 -recovered pasa_asmbl_21527.p1, internal, 79193, 79340 Valid prediction for GlimmerHMM_glimmerT_44476-T1 Valid prediction for Augustus_model.g29502.t1 Valid prediction for snap_scaffold_19-snap.1638-T1 Valid prediction for snap_scaffold_19-snap.1642-T1 Valid prediction for GlimmerHMM_glimmerT_44478-T1 Valid prediction for snap_scaffold_19-snap.1617-T1 Couldn't classify 18065, 18157 Couldn't classify 23631, 23636 Sorry, prediction pasa_asmbl_21523.p1 fails validation. (GAG) CT 18065-18157 GT AGG (GTG) AG 18282-18364 GT AGG (GCC) AG 18623-18745 GT AAG (ACC) AG 19301-19380 GT CAG (ATT) AG 19501-19688 GT AGG (GCA) AG 19988-20053 GT AGG (TGC) AG 20245-20337 GT AGG (ATT) AG 20453-20564 GT AGG (TGG) AG 20688-20806 GT AGG (CAC) AG 21254-21340 GT AGG (GAT) AG 21510-21599 GT AGG (AGT) AG 21722-21837 GT AGG (GGT) AG 22352-22421 GT AGG (TTT) AG 22650-22775 GT AGG (TAC) AG 22862-22933 GT AGG (CTG) AG 23103-23249 GT AGG (CGC) AG 23389-23472 GT AGG (ACG) AG 23631-23636 TA TGT -recovered pasa_asmbl_21523.p1, internal, 18282, 18364 -recovered pasa_asmbl_21523.p1, internal, 18623, 18745 -recovered pasa_asmbl_21523.p1, internal, 19301, 19380 -recovered pasa_asmbl_21523.p1, internal, 19501, 19688 -recovered pasa_asmbl_21523.p1, internal, 19988, 20053 -recovered pasa_asmbl_21523.p1, internal, 20245, 20337 -recovered pasa_asmbl_21523.p1, internal, 20453, 20564 -recovered pasa_asmbl_21523.p1, internal, 20688, 20806 -recovered pasa_asmbl_21523.p1, internal, 21254, 21340 -recovered pasa_asmbl_21523.p1, internal, 21510, 21599 -recovered pasa_asmbl_21523.p1, internal, 21722, 21837 -recovered pasa_asmbl_21523.p1, internal, 22352, 22421 -recovered pasa_asmbl_21523.p1, internal, 22650, 22775 -recovered pasa_asmbl_21523.p1, internal, 22862, 22933 -recovered pasa_asmbl_21523.p1, internal, 23103, 23249 -recovered pasa_asmbl_21523.p1, internal, 23389, 23472 Valid prediction for GlimmerHMM_glimmerT_44471-T1 Valid prediction for snap_scaffold_19-snap.1622-T1 Valid prediction for snap_scaffold_19-snap.1625-T1 Valid prediction for GlimmerHMM_glimmerT_44488-T1 Valid prediction for snap_scaffold_19-snap.1615-T1 Valid prediction for snap_scaffold_19-snap.1640-T1 Valid prediction for snap_scaffold_19-snap.1628-T1 Couldn't classify 25856, 25970 Sorry, prediction pasa_asmbl_21526.p1 fails validation. (AAC) AG 25856-25970 GT TGG (ATG) AG 26074-26140 GT GAG (AGT) AG 26234-26281 GT AGG (GAG) AG 27052-27188 GT CAG (CAT) AG 27373-27488 GT AGG (ACC) AG 27766-27903 GT AGG (TTC) AG 28151-28333 GT AGG (GTG) AG 28490-28603 GT AAG (CAC) AG 28730-28945 GT AGG (GCA) AG 29141-29198 GT AGG (GTA) AG 30263-30369 GT AGG (GAG) AG 31231-31353 GT AGG (AAA) AG 31680-31793 GT AGG (GGC) AG 33333-33479 GT GGG (GTG) AG 33741-33951 GT CAG (CCA) AG 34553-34743 GT AGG (GTG) AG 35946-36046 GT AGG (GCA) AG 36281-36419 GT AGG (ATC) AG 36735-36860 TT GAT -recovered pasa_asmbl_21526.p1, initial, 26074, 26140 -recovered pasa_asmbl_21526.p1, terminal, 36735, 36860 -recovered pasa_asmbl_21526.p1, internal, 25856, 25970 -recovered pasa_asmbl_21526.p1, internal, 26074, 26140 -recovered pasa_asmbl_21526.p1, internal, 26234, 26281 -recovered pasa_asmbl_21526.p1, internal, 27052, 27188 -recovered pasa_asmbl_21526.p1, internal, 27373, 27488 -recovered pasa_asmbl_21526.p1, internal, 27766, 27903 -recovered pasa_asmbl_21526.p1, internal, 28151, 28333 -recovered pasa_asmbl_21526.p1, internal, 28490, 28603 -recovered pasa_asmbl_21526.p1, internal, 28730, 28945 -recovered pasa_asmbl_21526.p1, internal, 29141, 29198 -recovered pasa_asmbl_21526.p1, internal, 30263, 30369 -recovered pasa_asmbl_21526.p1, internal, 31231, 31353 -recovered pasa_asmbl_21526.p1, internal, 31680, 31793 -recovered pasa_asmbl_21526.p1, internal, 33333, 33479 -recovered pasa_asmbl_21526.p1, internal, 33741, 33951 -recovered pasa_asmbl_21526.p1, internal, 34553, 34743 -recovered pasa_asmbl_21526.p1, internal, 35946, 36046 -recovered pasa_asmbl_21526.p1, internal, 36281, 36419 Valid prediction for GlimmerHMM_glimmerT_44487-T1 Valid prediction for snap_scaffold_19-snap.1639-T1 Valid prediction for GlimmerHMM_glimmerT_44470-T1 Valid prediction for GlimmerHMM_glimmerT_44484-T1 Valid prediction for snap_scaffold_19-snap.1637-T1 Valid prediction for Augustus_model.g29505.t1 Valid prediction for pasa_asmbl_21525.p1 Valid prediction for GlimmerHMM_glimmerT_44492-T1 Valid prediction for GlimmerHMM_glimmerT_44481-T1 Valid prediction for snap_scaffold_19-snap.1634-T1 Couldn't classify 23946, 24032 Couldn't classify 24691, 24776 Sorry, prediction pasa_asmbl_21524.p1 fails validation. (GAG) AG 23946-24032 GT AGG (AGT) AG 24233-24349 GT ATG (AAT) AG 24439-24550 GT AGG (CCT) AG 24691-24776 CT GCC -recovered pasa_asmbl_21524.p1, internal, 23946, 24032 -recovered pasa_asmbl_21524.p1, internal, 24233, 24349 -recovered pasa_asmbl_21524.p1, internal, 24439, 24550 Valid prediction for snap_scaffold_19-snap.1631-T1 Valid prediction for Augustus_model.g29506.t1 Valid prediction for GlimmerHMM_glimmerT_44485-T1 Valid prediction for GlimmerHMM_glimmerT_44472-T1 Valid prediction for snap_scaffold_19-snap.1618-T1 Valid prediction for GlimmerHMM_glimmerT_44491-T1 Valid prediction for snap_scaffold_19-snap.1613-T1 Valid prediction for CodingQuarry_transcript_25739-T1 Couldn't classify 89548, 89677 Sorry, prediction pasa_asmbl_21923.p1 fails validation. (AAG) AG 89548-89677 GT AGG (CTG) AG 89816-89946 GT GGG (GAG) AG 90089-90157 GT TGG (TTC) AG 90624-90713 GT CGG (ATC) AG 90804-90886 GT AGG (CTC) AG 91277-91389 GT CAG (AAT) AG 92164-92327 GT AGG (AAC) AG 93355-93462 GT AGG (GAT) AG 93586-93737 GT AGG (ATG) AG 93842-93917 TG AGT -recovered pasa_asmbl_21923.p1, terminal, 93842, 93917 -recovered pasa_asmbl_21923.p1, internal, 89548, 89677 -recovered pasa_asmbl_21923.p1, internal, 89816, 89946 -recovered pasa_asmbl_21923.p1, internal, 90089, 90157 -recovered pasa_asmbl_21923.p1, internal, 90624, 90713 -recovered pasa_asmbl_21923.p1, internal, 90804, 90886 -recovered pasa_asmbl_21923.p1, internal, 91277, 91389 -recovered pasa_asmbl_21923.p1, internal, 92164, 92327 -recovered pasa_asmbl_21923.p1, internal, 93355, 93462 -recovered pasa_asmbl_21923.p1, internal, 93586, 93737 Valid prediction for snap_scaffold_19-snap.1620-T1 Valid prediction for Augustus_model.g29510.t1 Valid prediction for GlimmerHMM_glimmerT_44473-T1 Valid prediction for snap_scaffold_19-snap.1641-T1 Valid prediction for GlimmerHMM_glimmerT_44483-T1 Valid prediction for snap_scaffold_19-snap.1627-T1 Valid prediction for snap_scaffold_19-snap.1636-T1 Valid prediction for GlimmerHMM_glimmerT_44490-T1 Couldn't classify 13213, 13242 Sorry, prediction pasa_asmbl_21522.p2 fails validation. (ATG) GA 7438-7554 GT GGG (GTG) AG 9605-9721 GT AGG (ATC) AG 12156-12245 GT AGG (TGT) AG 13213-13242 GT ATG -recovered pasa_asmbl_21522.p2, initial, 7438, 7554 -recovered pasa_asmbl_21522.p2, internal, 9605, 9721 -recovered pasa_asmbl_21522.p2, internal, 12156, 12245 -recovered pasa_asmbl_21522.p2, internal, 13213, 13242 Valid prediction for snap_scaffold_19-snap.1629-T1 Valid prediction for Augustus_model.g29501.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: -)Couldn't classify 162088, 162183 Sorry, prediction pasa_asmbl_22302.p1 fails validation. (GAG) GC 162088-162183 GT TGG (ATG) AG 162506-162988 CA AAC -recovered pasa_asmbl_22302.p1, terminal, 162506, 162988 Valid prediction for snap_scaffold_19-snap.1632-T1 Valid prediction for snap_scaffold_19-snap.1643-T1 Valid prediction for snap_scaffold_19-snap.1619-T1 Valid prediction for GlimmerHMM_glimmerT_44482-T1 Valid prediction for CodingQuarry_transcript_25737-T1 Valid prediction for snap_scaffold_19-snap.1616-T1 Valid prediction for GlimmerHMM_glimmerT_44475-T1 Valid prediction for GlimmerHMM_glimmerT_44493-T1 Valid prediction for GlimmerHMM_glimmerT_44479-T1 Valid prediction for GlimmerHMM_glimmerT_44477-T1 Valid prediction for GlimmerHMM_glimmerT_44486-T1 Valid prediction for Augustus_model.g29512.t1 Valid prediction for HiQ_model.g29507.t1 Valid prediction for snap_scaffold_19-snap.1623-T1 Valid prediction for snap_scaffold_19-snap.1626-T1 Sorry, intron length (5) is less than minimum required (10) Valid prediction for pasa_asmbl_22299.p1 Valid prediction for snap_scaffold_19-snap.1612-T1 Valid prediction for snap_scaffold_19-snap.1621-T1 Valid prediction for Augustus_model.g29508.t1 Valid prediction for HiQ_model.g29503.t1 Valid prediction for GlimmerHMM_glimmerT_44494-T1 Valid prediction for snap_scaffold_19-snap.1633-T1 Valid prediction for snap_scaffold_19-snap.1624-T1 Valid prediction for GlimmerHMM_glimmerT_44489-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7613, rend_intergenic: 3529 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36860, rend_intergenic: 24176 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 82356, rend_intergenic: 71558 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90950, rend_intergenic: 86638 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 147068, rend_intergenic: 141726 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 258290 -exon list size: 339 building trellis 0.3 0.6 0.9 1.2 1.5 1.8 2.1 2.3 2.6 2.9 3.2 3.5 3.8 4.1 4.4 4.7 5.0 5.3 5.6 5.9 6.2 6.5 6.7 7.0 7.3 7.6 7.9 8.2 8.5 8.8 9.1 9.4 9.7 10.0 10.3 10.6 10.9 11.1 11.4 11.7 12.0 12.3 12.6 12.9 13.2 13.5 13.8 14.1 14.4 14.7 15.0 15.2 15.5 15.8 16.1 16.4 16.7 17.0 17.3 17.6 17.9 18.2 18.5 18.8 19.1 19.4 19.6 19.9 20.2 20.5 20.8 21.1 21.4 21.7 22.0 22.3 22.6 22.9 23.2 23.5 23.8 24.0 24.3 24.6 24.9 25.2 25.5 25.8 26.1 26.4 26.7 27.0 27.3 27.6 27.9 28.2 28.4 28.7 29.0 29.3 29.6 29.9 30.2 30.5 30.8 31.1 31.4 31.7 32.0 32.3 32.6 32.8 33.1 33.4 33.7 34.0 34.3 34.6 34.9 35.2 35.5 35.8 36.1 36.4 36.7 37.0 37.2 37.5 37.8 38.1 38.4 38.7 39.0 39.3 39.6 39.9 40.2 40.5 40.8 41.1 41.3 41.6 41.9 42.2 42.5 42.8 43.1 43.4 43.7 44.0 44.3 44.6 44.9 45.2 45.5 45.7 46.0 46.3 46.6 46.9 47.2 47.5 47.8 48.1 48.4 48.7 49.0 49.3 49.6 49.9 50.1 50.4 50.7 51.0 51.3 51.6 51.9 52.2 52.5 52.8 53.1 53.4 53.7 54.0 54.3 54.5 54.8 55.1 55.4 55.7 56.0 56.3 56.6 56.9 57.2 57.5 57.8 58.1 58.4 58.7 58.9 59.2 59.5 59.8 60.1 60.4 60.7 61.0 61.3 61.6 61.9 62.2 62.5 62.8 63.0 63.3 63.6 63.9 64.2 64.5 64.8 65.1 65.4 65.7 66.0 66.3 66.6 66.9 67.2 67.4 67.7 68.0 68.3 68.6 68.9 69.2 69.5 69.8 70.1 70.4 70.7 71.0 71.3 71.6 71.8 72.1 72.4 72.7 73.0 73.3 73.6 73.9 74.2 74.5 74.8 75.1 75.4 75.7 76.0 76.2 76.5 76.8 77.1 77.4 77.7 78.0 78.3 78.6 78.9 79.2 79.5 79.8 80.1 80.4 80.6 80.9 81.2 81.5 81.8 82.1 82.4 82.7 83.0 83.3 83.6 83.9 84.2 84.5 84.8 85.0 85.3 85.6 85.9 86.2 86.5 86.8 87.1 87.4 87.7 88.0 88.3 88.6 88.9 89.1 89.4 89.7 90.0 90.3 90.6 90.9 91.2 91.5 91.8 92.1 92.4 92.7 93.0 93.3 93.5 93.8 94.1 94.4 94.7 95.0 95.3 95.6 95.9 96.2 96.5 96.8 97.1 97.4 97.7 97.9 98.2 98.5 98.8 99.1 99.4 99.7 -found 20 predictions from path traversal Error with prediction: snap lend_intergenic: 7613, rend_intergenic: 3529 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 36860, rend_intergenic: 24176 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 82356, rend_intergenic: 71558 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90950, rend_intergenic: 86638 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 147068, rend_intergenic: 141726 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 17 predictions persist after filtering for low support