-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_9097254-9274177

-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 GeneMark_model.79641_t
Valid prediction for GeneMark_model.79685_t
Valid prediction for Augustus_model.g30445.t1
Valid prediction for GlimmerHMM_glimmerT_45632-T1
Valid prediction for Augustus_model.g30455.t1
Valid prediction for snap_scaffold_19-snap.1817-T1
Valid prediction for snap_scaffold_19-snap.1786-T1
Valid prediction for GeneMark_model.79653_t
Valid prediction for GeneMark_model.79681_t
Valid prediction for snap_scaffold_19-snap.1798-T1
Valid prediction for snap_scaffold_19-snap.1776-T1
Valid prediction for GeneMark_model.79674_t
Valid prediction for GeneMark_model.79646_t
Valid prediction for GlimmerHMM_glimmerT_45630-T1
Valid prediction for snap_scaffold_19-snap.1810-T1
Valid prediction for snap_scaffold_19-snap.1783-T1
Valid prediction for GeneMark_model.79665_t
Valid prediction for snap_scaffold_19-snap.1784-T1
Valid prediction for snap_scaffold_19-snap.1792-T1
Valid prediction for Augustus_model.g30452.t1
Valid prediction for GeneMark_model.79658_t
Valid prediction for snap_scaffold_19-snap.1809-T1
Valid prediction for GlimmerHMM_glimmerT_45619-T1
Valid prediction for GlimmerHMM_glimmerT_45616-T1
Valid prediction for GlimmerHMM_glimmerT_45615-T1
Valid prediction for CodingQuarry_transcript_25709-T1
Valid prediction for Augustus_model.g30450.t1
Valid prediction for Augustus_model.g30448.t1
Valid prediction for Augustus_model.g30438.t1
Valid prediction for Augustus_model.g30440.t1
Valid prediction for Augustus_model.g30439.t1
Valid prediction for GeneMark_model.79673_t
Valid prediction for GlimmerHMM_glimmerT_45644-T1
Valid prediction for GlimmerHMM_glimmerT_45634-T1
Valid prediction for Augustus_model.g30451.t1
Valid prediction for GlimmerHMM_glimmerT_45645-T1
Valid prediction for GeneMark_model.79667_t
Valid prediction for snap_scaffold_19-snap.1790-T1
Valid prediction for GeneMark_model.79643_t
Valid prediction for Augustus_model.g30447.t1
Valid prediction for GlimmerHMM_glimmerT_45637-T1
Valid prediction for snap_scaffold_19-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_45614-T1
Valid prediction for GeneMark_model.79684_t
Valid prediction for snap_scaffold_19-snap.1815-T1
Valid prediction for HiQ_model.g30443.t1
Valid prediction for snap_scaffold_19-snap.1777-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.79678_t
Valid prediction for GeneMark_model.79651_t
Valid prediction for GeneMark_model.79640_t
Valid prediction for GeneMark_model.79642_t
Valid prediction for Augustus_model.g30456.t1
Valid prediction for snap_scaffold_19-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_45620-T1
Valid prediction for GeneMark_model.79633_t
Valid prediction for GeneMark_model.79686_t
Valid prediction for GeneMark_model.79671_t
Valid prediction for snap_scaffold_19-snap.1813-T1
Valid prediction for GeneMark_model.79663_t
Valid prediction for GlimmerHMM_glimmerT_45640-T1
Valid prediction for pasa_asmbl_22376.p1
Valid prediction for GeneMark_model.79635_t
Valid prediction for CodingQuarry_transcript_25707-T1
Valid prediction for GeneMark_model.79638_t
Valid prediction for snap_scaffold_19-snap.1780-T1
Valid prediction for GeneMark_model.79656_t
Valid prediction for GeneMark_model.79680_t
Valid prediction for snap_scaffold_19-snap.1802-T1
Valid prediction for snap_scaffold_19-snap.1806-T1
Valid prediction for Augustus_model.g30454.t1
Valid prediction for Augustus_model.g30442.t1
Valid prediction for pasa_asmbl_22379.p1
Valid prediction for GeneMark_model.79669_t
Valid prediction for snap_scaffold_19-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_45636-T1
Valid prediction for GeneMark_model.79649_t
Valid prediction for GlimmerHMM_glimmerT_45643-T1
Valid prediction for GlimmerHMM_glimmerT_45627-T1
Valid prediction for snap_scaffold_19-snap.1789-T1
Valid prediction for snap_scaffold_19-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_45623-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 snap_scaffold_19-snap.1793-T1
Valid prediction for pasa_asmbl_21532.p1
Valid prediction for GeneMark_model.79650_t
Valid prediction for HiQ_model.g30453.t1
Valid prediction for GeneMark_model.79634_t
Valid prediction for GeneMark_model.79668_t
Valid prediction for GeneMark_model.79645_t
Valid prediction for GlimmerHMM_glimmerT_45638-T1
Valid prediction for GeneMark_model.79657_t
Valid prediction for GlimmerHMM_glimmerT_45631-T1
Valid prediction for GeneMark_model.79637_t
Valid prediction for GlimmerHMM_glimmerT_45633-T1
Valid prediction for snap_scaffold_19-snap.1778-T1
Valid prediction for GeneMark_model.79636_t
Valid prediction for snap_scaffold_19-snap.1812-T1
Valid prediction for GeneMark_model.79683_t
Valid prediction for GeneMark_model.79654_t
Valid prediction for GeneMark_model.79675_t
Valid prediction for snap_scaffold_19-snap.1818-T1
Valid prediction for snap_scaffold_19-snap.1787-T1
Valid prediction for HiQ_model.g30444.t1
Valid prediction for CodingQuarry_transcript_25708-T1
Valid prediction for GlimmerHMM_glimmerT_45635-T1
Valid prediction for GeneMark_model.79661_t
Valid prediction for GeneMark_model.79682_t
Valid prediction for snap_scaffold_19-snap.1800-T1
Valid prediction for GeneMark_model.79672_t
Valid prediction for snap_scaffold_19-snap.1781-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.79666_t
Valid prediction for snap_scaffold_19-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_45612-T1
Valid prediction for Augustus_model.g30457.t1
Valid prediction for GlimmerHMM_glimmerT_45646-T1
Valid prediction for snap_scaffold_19-snap.1785-T1
Valid prediction for snap_scaffold_19-snap.1814-T1
Valid prediction for snap_scaffold_19-snap.1779-T1
Valid prediction for GeneMark_model.79677_t
Valid prediction for GlimmerHMM_glimmerT_45626-T1
Valid prediction for GlimmerHMM_glimmerT_45621-T1
Valid prediction for snap_scaffold_19-snap.1795-T1
Valid prediction for GeneMark_model.79644_t
Valid prediction for GeneMark_model.79664_t
Couldn't classify 11643, 11708
Sorry, prediction pasa_asmbl_21534.p1 fails validation.
(GGC)	 CA	11643-11708	GT	AAG
(GAT)	 AG	12344-12406	GT	AGG
(TAT)	 AG	12613-12713	GT	AGG
(GCA)	 AG	12876-12918	GT	AGG
(GGA)	 AG	13088-13174	GT	AGG
(TGT)	 AG	13255-13334	GT	AGG
(GGT)	 AG	13518-13629	GT	AGG
(AAT)	 AG	13786-13917	AC	GAA
-recovered pasa_asmbl_21534.p1, terminal, 13786, 13917
-recovered pasa_asmbl_21534.p1, internal, 12344, 12406
-recovered pasa_asmbl_21534.p1, internal, 12613, 12713
-recovered pasa_asmbl_21534.p1, internal, 12876, 12918
-recovered pasa_asmbl_21534.p1, internal, 13088, 13174
-recovered pasa_asmbl_21534.p1, internal, 13255, 13334
-recovered pasa_asmbl_21534.p1, internal, 13518, 13629
Valid prediction for snap_scaffold_19-snap.1797-T1
Valid prediction for GeneMark_model.79662_t
Valid prediction for GlimmerHMM_glimmerT_45642-T1
Valid prediction for Augustus_model.g30458.t1
Valid prediction for snap_scaffold_19-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_45622-T1
Valid prediction for snap_scaffold_19-snap.1805-T1
Valid prediction for snap_scaffold_19-snap.1788-T1
Valid prediction for Augustus_model.g30441.t1
Valid prediction for GlimmerHMM_glimmerT_45617-T1
Valid prediction for GlimmerHMM_glimmerT_45613-T1
Valid prediction for GlimmerHMM_glimmerT_45628-T1
Valid prediction for GlimmerHMM_glimmerT_45624-T1
Valid prediction for GlimmerHMM_glimmerT_45625-T1
Valid prediction for GeneMark_model.79670_t
Valid prediction for GlimmerHMM_glimmerT_45641-T1
Valid prediction for GeneMark_model.79679_t
Valid prediction for GeneMark_model.79647_t
Valid prediction for snap_scaffold_19-snap.1808-T1
Valid prediction for snap_scaffold_19-snap.1811-T1
Valid prediction for GeneMark_model.79652_t
Valid prediction for GeneMark_model.79655_t
Valid prediction for Augustus_model.g30446.t1
Valid prediction for snap_scaffold_19-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_45629-T1
Valid prediction for GeneMark_model.79648_t
Valid prediction for snap_scaffold_19-snap.1819-T1
Valid prediction for snap_scaffold_19-snap.1807-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.79659_t
Valid prediction for Augustus_model.g30437.t1
Valid prediction for snap_scaffold_19-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_45639-T1
Valid prediction for GeneMark_model.79687_t
Valid prediction for Augustus_model.g30449.t1
Valid prediction for GeneMark_model.79639_t
Valid prediction for snap_scaffold_19-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_45618-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20923, rend_intergenic: 7098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32315, rend_intergenic: 23712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33084, rend_intergenic: 32325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41119, rend_intergenic: 36543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51363, rend_intergenic: 47580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58207, rend_intergenic: 52596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62775, rend_intergenic: 58576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65215, rend_intergenic: 63893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69490, rend_intergenic: 68434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100823, rend_intergenic: 100372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116940, rend_intergenic: 107145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137504, rend_intergenic: 129110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140107, rend_intergenic: 138768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149366, rend_intergenic: 144985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176924
-exon list size: 696


building trellis

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95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 20923, rend_intergenic: 7098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32315, rend_intergenic: 23712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33084, rend_intergenic: 32325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41119, rend_intergenic: 36543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51363, rend_intergenic: 47580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58207, rend_intergenic: 52596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62775, rend_intergenic: 58576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65215, rend_intergenic: 63893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69490, rend_intergenic: 68434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100823, rend_intergenic: 100372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116940, rend_intergenic: 107145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137504, rend_intergenic: 129110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140107, rend_intergenic: 138768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149366, rend_intergenic: 144985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support