-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_8929894-9115777 -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 GlimmerHMM_glimmerT_54740-T1 Valid prediction for snap_scaffold_25-snap.1959-T1 Valid prediction for GlimmerHMM_glimmerT_54748-T1 Valid prediction for snap_scaffold_25-snap.1967-T1 Valid prediction for snap_scaffold_25-snap.1964-T1 Valid prediction for snap_scaffold_25-snap.1941-T1 Valid prediction for GlimmerHMM_glimmerT_54753-T1 Valid prediction for snap_scaffold_25-snap.1950-T1 Valid prediction for snap_scaffold_25-snap.1968-T1 Valid prediction for snap_scaffold_25-snap.1949-T1 Valid prediction for snap_scaffold_25-snap.1935-T1 Valid prediction for snap_scaffold_25-snap.1946-T1 Valid prediction for snap_scaffold_25-snap.1962-T1 Valid prediction for snap_scaffold_25-snap.1960-T1 Valid prediction for snap_scaffold_25-snap.1969-T1 Valid prediction for snap_scaffold_25-snap.1943-T1 Couldn't classify 89196, 89318 Couldn't classify 93152, 93215 Sorry, prediction pasa_asmbl_33883.p1 fails validation. (ACG) CC 89196-89318 GT AGG (ACT) AG 89578-89646 GT AAG (AAA) AG 89771-89928 GT AGG (GAT) AG 90183-90304 GT AGG (ATG) AG 92128-92189 GT TTG (CCA) AG 92298-92378 GT ATG (GTG) AG 92686-92745 GT AGG (GTG) AG 92893-92954 GT CAG (TAT) AG 93152-93215 GT AGG add_exon() Sorry, pasa_asmbl_33883.p1 92128-92189-initial-1 is invalid. -recovered pasa_asmbl_33883.p1, initial, 92128, 92189 -recovered pasa_asmbl_33883.p1, internal, 89578, 89646 -recovered pasa_asmbl_33883.p1, internal, 89771, 89928 -recovered pasa_asmbl_33883.p1, internal, 90183, 90304 -recovered pasa_asmbl_33883.p1, internal, 92128, 92189 -recovered pasa_asmbl_33883.p1, internal, 92298, 92378 -recovered pasa_asmbl_33883.p1, internal, 92686, 92745 -recovered pasa_asmbl_33883.p1, internal, 92893, 92954 -recovered pasa_asmbl_33883.p1, internal, 93152, 93215 Valid prediction for GlimmerHMM_glimmerT_54739-T1 Couldn't classify 156464, 159709 Sorry, prediction pasa_asmbl_33778.p1 fails validation. (AAG) TG 156464-159709 GA AAG Valid prediction for GlimmerHMM_glimmerT_54747-T1 Valid prediction for snap_scaffold_25-snap.1937-T1 Valid prediction for GlimmerHMM_glimmerT_54757-T1 Valid prediction for HiQ_model.g36328.t1 Couldn't classify 154732, 155124 Sorry, prediction pasa_asmbl_33777.p1 fails validation. (AAC) AG 154732-155124 AC GGA Valid prediction for snap_scaffold_25-snap.1933-T1 Valid prediction for pasa_asmbl_33772.p2 Valid prediction for Augustus_model.g36322.t1 Valid prediction for Augustus_model.g36316.t1 Valid prediction for snap_scaffold_25-snap.1945-T1 Valid prediction for GlimmerHMM_glimmerT_54728-T1 Valid prediction for GlimmerHMM_glimmerT_54751-T1 Valid prediction for snap_scaffold_25-snap.1963-T1 Valid prediction for Augustus_model.g36318.t1 Valid prediction for GlimmerHMM_glimmerT_54732-T1 Valid prediction for HiQ_model.g36323.t1 Valid prediction for GlimmerHMM_glimmerT_54744-T1 Valid prediction for snap_scaffold_25-snap.1932-T1 Couldn't classify 152866, 152934 Couldn't classify 153847, 154314 Sorry, prediction pasa_asmbl_33776.p1 fails validation. (CAG) CA 152866-152934 GT AGG (GCA) AG 153129-153212 GT AGG (AAC) AG 153318-153425 GT AGG (GCT) AG 153526-153624 GT AGG (ATG) AG 153847-154314 AT GGA -recovered pasa_asmbl_33776.p1, internal, 153129, 153212 -recovered pasa_asmbl_33776.p1, internal, 153318, 153425 -recovered pasa_asmbl_33776.p1, internal, 153526, 153624 Valid prediction for pasa_asmbl_33775.p1 Valid prediction for snap_scaffold_25-snap.1965-T1 Valid prediction for GlimmerHMM_glimmerT_54733-T1 Valid prediction for Augustus_model.g36314.t1 Valid prediction for GlimmerHMM_glimmerT_54726-T1 Couldn't classify 82717, 82860 Couldn't classify 84696, 84813 Sorry, prediction pasa_asmbl_33769.p1 fails validation. (GCG) GA 82717-82860 GT AGG (GGA) AG 83282-83363 GT AGG (TGT) AG 83609-83711 GT AGG (GTA) AG 84696-84813 GG GAG -recovered pasa_asmbl_33769.p1, internal, 83282, 83363 -recovered pasa_asmbl_33769.p1, internal, 83609, 83711 Valid prediction for GlimmerHMM_glimmerT_54754-T1 Valid prediction for Augustus_model.g36317.t1 Valid prediction for GlimmerHMM_glimmerT_54737-T1 Valid prediction for pasa_asmbl_33779.p1 Valid prediction for snap_scaffold_25-snap.1956-T1 Valid prediction for GlimmerHMM_glimmerT_54752-T1 Valid prediction for GlimmerHMM_glimmerT_54743-T1 Valid prediction for GlimmerHMM_glimmerT_54736-T1 Valid prediction for snap_scaffold_25-snap.1938-T1 Valid prediction for Augustus_model.g36327.t1 Valid prediction for CodingQuarry_transcript_38825-T1 Valid prediction for CodingQuarry_transcript_38826-T1 Valid prediction for CodingQuarry_transcript_38827-T1 Valid prediction for GlimmerHMM_glimmerT_54750-T1 Valid prediction for snap_scaffold_25-snap.1958-T1 Valid prediction for GlimmerHMM_glimmerT_54734-T1 Valid prediction for Augustus_model.g36326.t1 Valid prediction for snap_scaffold_25-snap.1953-T1 Couldn't classify 69209, 69386 Couldn't classify 72901, 73024 Sorry, prediction pasa_asmbl_33877.p1 fails validation. (GGC) CA 69209-69386 GT CGG (GTA) AG 69771-69897 GT AAG (GGG) AG 72583-72696 GT AGG (TTT) AG 72901-73024 GG CAG -recovered pasa_asmbl_33877.p1, internal, 69771, 69897 -recovered pasa_asmbl_33877.p1, internal, 72583, 72696 -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 snap_scaffold_25-snap.1952-T1 Valid prediction for GlimmerHMM_glimmerT_54755-T1 Valid prediction for CodingQuarry_transcript_38824-T1 Valid prediction for snap_scaffold_25-snap.1939-T1 Valid prediction for Augustus_model.g36330.t1 Valid prediction for Augustus_model.g36329.t1 Valid prediction for Augustus_model.g36320.t1 Valid prediction for Augustus_model.g36315.t1 Valid prediction for GlimmerHMM_glimmerT_54758-T1 Valid prediction for GlimmerHMM_glimmerT_54735-T1 Valid prediction for Augustus_model.g36319.t1 Valid prediction for GlimmerHMM_glimmerT_54746-T1 Valid prediction for snap_scaffold_25-snap.1972-T1 Valid prediction for GlimmerHMM_glimmerT_54741-T1 Valid prediction for GlimmerHMM_glimmerT_54730-T1 Valid prediction for GlimmerHMM_glimmerT_54756-T1 Valid prediction for snap_scaffold_25-snap.1942-T1 Valid prediction for pasa_asmbl_34475.p1 Valid prediction for snap_scaffold_25-snap.1955-T1 Valid prediction for snap_scaffold_25-snap.1944-T1 Valid prediction for snap_scaffold_25-snap.1966-T1 Valid prediction for GlimmerHMM_glimmerT_54729-T1 Valid prediction for snap_scaffold_25-snap.1954-T1 Valid prediction for GlimmerHMM_glimmerT_54742-T1 Valid prediction for snap_scaffold_25-snap.1957-T1 Valid prediction for GlimmerHMM_glimmerT_54727-T1 Valid prediction for snap_scaffold_25-snap.1961-T1 Valid prediction for Augustus_model.g36313.t1 Valid prediction for Augustus_model.g36325.t1 Valid prediction for GlimmerHMM_glimmerT_54745-T1 Valid prediction for HiQ_model.g36321.t1 Valid prediction for GlimmerHMM_glimmerT_54749-T1 Valid prediction for snap_scaffold_25-snap.1951-T1 Valid prediction for snap_scaffold_25-snap.1931-T1 Valid prediction for snap_scaffold_25-snap.1934-T1 Valid prediction for Augustus_model.g36324.t1 Valid prediction for snap_scaffold_25-snap.1936-T1 Valid prediction for snap_scaffold_25-snap.1947-T1 Valid prediction for snap_scaffold_25-snap.1971-T1 Valid prediction for snap_scaffold_25-snap.1948-T1 Valid prediction for GlimmerHMM_glimmerT_54731-T1 Valid prediction for snap_scaffold_25-snap.1970-T1 Valid prediction for snap_scaffold_25-snap.1940-T1 Valid prediction for GlimmerHMM_glimmerT_54738-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10287, rend_intergenic: 3285 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 17465, rend_intergenic: 14398 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 18947, rend_intergenic: 18255 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20816, rend_intergenic: 19021 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31918, rend_intergenic: 24626 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41529, rend_intergenic: 37285 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 45020, rend_intergenic: 42925 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48740, rend_intergenic: 45204 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74105, rend_intergenic: 48815 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 78970, rend_intergenic: 75998 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 102724, rend_intergenic: 81781 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110053, rend_intergenic: 106302 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 138805, rend_intergenic: 126919 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146130, rend_intergenic: 140951 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 176381, rend_intergenic: 168033 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 185884 -exon list size: 388 building trellis 0.3 0.5 0.8 1.0 1.3 1.5 1.8 2.1 2.3 2.6 2.8 3.1 3.3 3.6 3.8 4.1 4.4 4.6 4.9 5.1 5.4 5.6 5.9 6.2 6.4 6.7 6.9 7.2 7.4 7.7 7.9 8.2 8.5 8.7 9.0 9.2 9.5 9.7 10.0 10.3 10.5 10.8 11.0 11.3 11.5 11.8 12.1 12.3 12.6 12.8 13.1 13.3 13.6 13.8 14.1 14.4 14.6 14.9 15.1 15.4 15.6 15.9 16.2 16.4 16.7 16.9 17.2 17.4 17.7 17.9 18.2 18.5 18.7 19.0 19.2 19.5 19.7 20.0 20.3 20.5 20.8 21.0 21.3 21.5 21.8 22.1 22.3 22.6 22.8 23.1 23.3 23.6 23.8 24.1 24.4 24.6 24.9 25.1 25.4 25.6 25.9 26.2 26.4 26.7 26.9 27.2 27.4 27.7 27.9 28.2 28.5 28.7 29.0 29.2 29.5 29.7 30.0 30.3 30.5 30.8 31.0 31.3 31.5 31.8 32.1 32.3 32.6 32.8 33.1 33.3 33.6 33.8 34.1 34.4 34.6 34.9 35.1 35.4 35.6 35.9 36.2 36.4 36.7 36.9 37.2 37.4 37.7 37.9 38.2 38.5 38.7 39.0 39.2 39.5 39.7 40.0 40.3 40.5 40.8 41.0 41.3 41.5 41.8 42.1 42.3 42.6 42.8 43.1 43.3 43.6 43.8 44.1 44.4 44.6 44.9 45.1 45.4 45.6 45.9 46.2 46.4 46.7 46.9 47.2 47.4 47.7 47.9 48.2 48.5 48.7 49.0 49.2 49.5 49.7 50.0 50.3 50.5 50.8 51.0 51.3 51.5 51.8 52.1 52.3 52.6 52.8 53.1 53.3 53.6 53.8 54.1 54.4 54.6 54.9 55.1 55.4 55.6 55.9 56.2 56.4 56.7 56.9 57.2 57.4 57.7 57.9 58.2 58.5 58.7 59.0 59.2 59.5 59.7 60.0 60.3 60.5 60.8 61.0 61.3 61.5 61.8 62.1 62.3 62.6 62.8 63.1 63.3 63.6 63.8 64.1 64.4 64.6 64.9 65.1 65.4 65.6 65.9 66.2 66.4 66.7 66.9 67.2 67.4 67.7 67.9 68.2 68.5 68.7 69.0 69.2 69.5 69.7 70.0 70.3 70.5 70.8 71.0 71.3 71.5 71.8 72.1 72.3 72.6 72.8 73.1 73.3 73.6 73.8 74.1 74.4 74.6 74.9 75.1 75.4 75.6 75.9 76.2 76.4 76.7 76.9 77.2 77.4 77.7 77.9 78.2 78.5 78.7 79.0 79.2 79.5 79.7 80.0 80.3 80.5 80.8 81.0 81.3 81.5 81.8 82.1 82.3 82.6 82.8 83.1 83.3 83.6 83.8 84.1 84.4 84.6 84.9 85.1 85.4 85.6 85.9 86.2 86.4 86.7 86.9 87.2 87.4 87.7 87.9 88.2 88.5 88.7 89.0 89.2 89.5 89.7 90.0 90.3 90.5 90.8 91.0 91.3 91.5 91.8 92.1 92.3 92.6 92.8 93.1 93.3 93.6 93.8 94.1 94.4 94.6 94.9 95.1 95.4 95.6 95.9 96.2 96.4 96.7 96.9 97.2 97.4 97.7 97.9 98.2 98.5 98.7 99.0 99.2 99.5 99.7 -found 29 predictions from path traversal Error with prediction: snap lend_intergenic: 10287, rend_intergenic: 3285 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 17465, rend_intergenic: 14398 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 18947, rend_intergenic: 18255 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 20816, rend_intergenic: 19021 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 31918, rend_intergenic: 24626 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 41529, rend_intergenic: 37285 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 45020, rend_intergenic: 42925 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 48740, rend_intergenic: 45204 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74105, rend_intergenic: 48815 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 78970, rend_intergenic: 75998 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 102724, rend_intergenic: 81781 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 110053, rend_intergenic: 106302 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 138805, rend_intergenic: 126919 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 146130, rend_intergenic: 140951 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 176381, rend_intergenic: 168033 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 19 predictions persist after filtering for low support -building DP trellis -building trellis in range 1 - 13795 -exon list size: 14 building trellis 6.2 12.5 18.8 25.0 31.2 37.5 43.8 50.0 56.2 62.5 68.8 75.0 81.2 87.5 93.8 -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