-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_10160464-10344468

-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.56221_t
Valid prediction for GlimmerHMM_glimmerT_32957-T1
Valid prediction for GeneMark_model.56243_t
Valid prediction for GlimmerHMM_glimmerT_32969-T1
Valid prediction for GeneMark_model.56223_t
Valid prediction for GeneMark_model.56246_t
Valid prediction for GlimmerHMM_glimmerT_32952-T1
Valid prediction for GlimmerHMM_glimmerT_32950-T1
Valid prediction for snap_scaffold_13-snap.1881-T1
Valid prediction for snap_scaffold_13-snap.1869-T1
Valid prediction for GeneMark_model.56234_t
Valid prediction for snap_scaffold_13-snap.1855-T1
Valid prediction for snap_scaffold_13-snap.1890-T1
Valid prediction for pasa_asmbl_11220.p1
Valid prediction for GeneMark_model.56196_t
Valid prediction for snap_scaffold_13-snap.1892-T1
Valid prediction for GeneMark_model.56237_t
Valid prediction for snap_scaffold_13-snap.1884-T1
Valid prediction for snap_scaffold_13-snap.1858-T1
Valid prediction for GeneMark_model.56245_t
Valid prediction for snap_scaffold_13-snap.1871-T1
Valid prediction for Augustus_model.g22152.t1
Valid prediction for GeneMark_model.56239_t
Valid prediction for GeneMark_model.56226_t
Valid prediction for GeneMark_model.56241_t
Valid prediction for GlimmerHMM_glimmerT_32948-T1
Valid prediction for GlimmerHMM_glimmerT_32955-T1
Valid prediction for snap_scaffold_13-snap.1856-T1
Valid prediction for Augustus_model.g22133.t1
Valid prediction for GeneMark_model.56191_t
Valid prediction for snap_scaffold_13-snap.1896-T1
Valid prediction for snap_scaffold_13-snap.1883-T1
Valid prediction for GeneMark_model.56200_t
Valid prediction for Augustus_model.g22141.t1
Valid prediction for GeneMark_model.56202_t
Valid prediction for GeneMark_model.56229_t
Valid prediction for snap_scaffold_13-snap.1859-T1
Valid prediction for snap_scaffold_13-snap.1863-T1
Valid prediction for snap_scaffold_13-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_32964-T1
Valid prediction for GeneMark_model.56214_t
Valid prediction for GeneMark_model.56231_t
Valid prediction for GlimmerHMM_glimmerT_32945-T1
Valid prediction for GeneMark_model.56206_t
Valid prediction for GlimmerHMM_glimmerT_32962-T1
Valid prediction for GeneMark_model.56194_t
Valid prediction for HiQ_model.g22147.t1
Valid prediction for GeneMark_model.56218_t
Valid prediction for GeneMark_model.56212_t
Valid prediction for snap_scaffold_13-snap.1872-T1
Valid prediction for GeneMark_model.56198_t
Valid prediction for Augustus_model.g22150.t1
Valid prediction for GlimmerHMM_glimmerT_32973-T1
Valid prediction for Augustus_model.g22149.t1
Valid prediction for GlimmerHMM_glimmerT_32959-T1
Valid prediction for Augustus_model.g22138.t1
Valid prediction for snap_scaffold_13-snap.1877-T1
Valid prediction for snap_scaffold_13-snap.1893-T1
Valid prediction for snap_scaffold_13-snap.1878-T1
Valid prediction for snap_scaffold_13-snap.1887-T1
Valid prediction for GeneMark_model.56225_t
Valid prediction for snap_scaffold_13-snap.1886-T1
Valid prediction for GeneMark_model.56189_t
Valid prediction for Augustus_model.g22142.t1
Valid prediction for GeneMark_model.56204_t
Valid prediction for GeneMark_model.56228_t
Valid prediction for GeneMark_model.56233_t
Valid prediction for Augustus_model.g22155.t1
Couldn't classify 83549, 83935
Sorry, prediction pasa_asmbl_11221.p1 fails validation.
(AAT)	 CC	83549-83935	TG	AGT
Valid prediction for GeneMark_model.56208_t
Valid prediction for snap_scaffold_13-snap.1879-T1
Valid prediction for CodingQuarry_transcript_13193-T1
Valid prediction for GeneMark_model.56230_t
Valid prediction for GlimmerHMM_glimmerT_32968-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 GlimmerHMM_glimmerT_32949-T1
Valid prediction for Augustus_model.g22143.t1
Valid prediction for Augustus_model.g22145.t1
Valid prediction for GlimmerHMM_glimmerT_32971-T1
Valid prediction for GeneMark_model.56220_t
Valid prediction for GlimmerHMM_glimmerT_32960-T1
Valid prediction for snap_scaffold_13-snap.1894-T1
Valid prediction for CodingQuarry_transcript_13194-T1
Valid prediction for GlimmerHMM_glimmerT_32966-T1
Valid prediction for GeneMark_model.56190_t
Valid prediction for GeneMark_model.56227_t
Valid prediction for Augustus_model.g22139.t1
Valid prediction for snap_scaffold_13-snap.1891-T1
Valid prediction for snap_scaffold_13-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_32974-T1
Valid prediction for snap_scaffold_13-snap.1897-T1
Valid prediction for CodingQuarry_transcript_13191-T1
Valid prediction for GeneMark_model.56213_t
Valid prediction for CodingQuarry_transcript_13195-T1
Valid prediction for Augustus_model.g22154.t1
Valid prediction for snap_scaffold_13-snap.1857-T1
Valid prediction for GeneMark_model.56188_t
Valid prediction for GeneMark_model.56203_t
Valid prediction for GlimmerHMM_glimmerT_32967-T1
Valid prediction for snap_scaffold_13-snap.1854-T1
Valid prediction for GlimmerHMM_glimmerT_32956-T1
Valid prediction for GlimmerHMM_glimmerT_32970-T1
Valid prediction for GeneMark_model.56197_t
Valid prediction for GeneMark_model.56210_t
Valid prediction for GeneMark_model.56219_t
Valid prediction for GlimmerHMM_glimmerT_32965-T1
Valid prediction for GeneMark_model.56211_t
Valid prediction for snap_scaffold_13-snap.1866-T1
Valid prediction for GeneMark_model.56242_t
Valid prediction for Augustus_model.g22136.t1
Valid prediction for snap_scaffold_13-snap.1888-T1
Couldn't classify 142933, 142974
Sorry, prediction Augustus_model.g22140.t1 fails validation.
(CTG)	 AG	142933-142974	GT	CTG
(CCC)	 AG	143837-143962	GT	AGG
(TGC)	 AG	144081-144172	AT	AAA
-recovered Augustus_model.g22140.t1, terminal, 144081, 144172
-recovered Augustus_model.g22140.t1, internal, 142933, 142974
-recovered Augustus_model.g22140.t1, internal, 143837, 143962
Valid prediction for snap_scaffold_13-snap.1868-T1
Valid prediction for snap_scaffold_13-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_32953-T1
Valid prediction for snap_scaffold_13-snap.1860-T1
Valid prediction for GeneMark_model.56201_t
Valid prediction for Augustus_model.g22151.t1
Valid prediction for GeneMark_model.56209_t
Valid prediction for GeneMark_model.56224_t
Valid prediction for Augustus_model.g22144.t1
Valid prediction for GlimmerHMM_glimmerT_32954-T1
Valid prediction for GeneMark_model.56244_t
Valid prediction for GlimmerHMM_glimmerT_32961-T1
Valid prediction for HiQ_model.g22148.t1
Valid prediction for GeneMark_model.56207_t
Valid prediction for GlimmerHMM_glimmerT_32958-T1
Valid prediction for snap_scaffold_13-snap.1889-T1
Valid prediction for snap_scaffold_13-snap.1862-T1
Valid prediction for GeneMark_model.56240_t
Valid prediction for snap_scaffold_13-snap.1864-T1
Valid prediction for GeneMark_model.56195_t
Valid prediction for snap_scaffold_13-snap.1895-T1
Valid prediction for GeneMark_model.56192_t
Valid prediction for GeneMark_model.56247_t
Valid prediction for CodingQuarry_transcript_13192-T1
Valid prediction for snap_scaffold_13-snap.1867-T1
Valid prediction for snap_scaffold_13-snap.1885-T1
Valid prediction for GlimmerHMM_glimmerT_32946-T1
Valid prediction for GlimmerHMM_glimmerT_32963-T1
Valid prediction for GeneMark_model.56199_t
Valid prediction for Augustus_model.g22137.t1
Valid prediction for GlimmerHMM_glimmerT_32972-T1
Valid prediction for snap_scaffold_13-snap.1870-T1
Valid prediction for pasa_asmbl_10014.p1
Valid prediction for Augustus_model.g22135.t1
Valid prediction for Augustus_model.g22134.t1
Valid prediction for GeneMark_model.56236_t
Valid prediction for pasa_asmbl_10012.p1
Valid prediction for snap_scaffold_13-snap.1873-T1
Valid prediction for HiQ_model.g22146.t1
Valid prediction for GeneMark_model.56205_t
Valid prediction for snap_scaffold_13-snap.1874-T1
Valid prediction for GeneMark_model.56232_t
Valid prediction for GeneMark_model.56235_t
Valid prediction for GeneMark_model.56216_t
Valid prediction for GeneMark_model.56238_t
Valid prediction for GeneMark_model.56215_t
Valid prediction for snap_scaffold_13-snap.1865-T1
Valid prediction for GlimmerHMM_glimmerT_32951-T1
Valid prediction for snap_scaffold_13-snap.1876-T1
Valid prediction for GeneMark_model.56193_t
Valid prediction for GeneMark_model.56222_t
Valid prediction for snap_scaffold_13-snap.1861-T1
Valid prediction for Augustus_model.g22153.t1
Valid prediction for GlimmerHMM_glimmerT_32947-T1
Valid prediction for snap_scaffold_13-snap.1882-T1
Valid prediction for GeneMark_model.56248_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23101, rend_intergenic: 8843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44919, rend_intergenic: 32538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49503, rend_intergenic: 45998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79201, rend_intergenic: 67879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92611, rend_intergenic: 90929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103213, rend_intergenic: 98326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105079, rend_intergenic: 103707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122067, rend_intergenic: 105099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142252, rend_intergenic: 122369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142825, rend_intergenic: 142480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149173, rend_intergenic: 142934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153031, rend_intergenic: 149243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159854, rend_intergenic: 157579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169124, rend_intergenic: 168811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179511, rend_intergenic: 172507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181472, rend_intergenic: 179865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184005
-exon list size: 752


building trellis

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88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 23101, rend_intergenic: 8843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44919, rend_intergenic: 32538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49503, rend_intergenic: 45998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79201, rend_intergenic: 67879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92611, rend_intergenic: 90929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103213, rend_intergenic: 98326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105079, rend_intergenic: 103707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122067, rend_intergenic: 105099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142252, rend_intergenic: 122369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142825, rend_intergenic: 142480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149173, rend_intergenic: 142934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153031, rend_intergenic: 149243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159854, rend_intergenic: 157579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169124, rend_intergenic: 168811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179511, rend_intergenic: 172507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181472, rend_intergenic: 179865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support