-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_10229713-10570653

-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_12821-T1
Valid prediction for pasa_asmbl_44337.p1
Valid prediction for snap_scaffold_5-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_12816-T1
Valid prediction for GeneMark_model.21688_t
Valid prediction for snap_scaffold_5-snap.1952-T1
Valid prediction for HiQ_model.g8535.t1
Valid prediction for GeneMark_model.21671_t
Valid prediction for GlimmerHMM_glimmerT_12834-T1
Valid prediction for pasa_asmbl_44348.p1
Valid prediction for snap_scaffold_5-snap.1975-T1
Valid prediction for Augustus_model.g8532.t1
Valid prediction for CodingQuarry_transcript_52097-T1
Valid prediction for GlimmerHMM_glimmerT_12819-T1
Valid prediction for GeneMark_model.21666_t
Valid prediction for GlimmerHMM_glimmerT_12815-T1
Valid prediction for snap_scaffold_5-snap.1970-T1
Valid prediction for Augustus_model.g8506.t1
Valid prediction for GlimmerHMM_glimmerT_12805-T1
Valid prediction for GlimmerHMM_glimmerT_12831-T1
Valid prediction for GeneMark_model.21673_t
Valid prediction for GeneMark_model.21677_t
Couldn't classify 76673, 76793
Sorry, prediction pasa_asmbl_44338.p1 fails validation.
(GAG)	 CC	76673-76793	GT	AGG
(ACT)	 AG	77044-77125	GT	ATG
(GAT)	 AG	77566-77736	GT	GGG
(GAT)	 AG	77959-78052	GT	AGG
(AAT)	 AG	78445-78482	GT	GAG
(AAA)	 AG	78618-78692	GT	AGG
(AAA)	 AG	78901-79038	GT	GGG
(TGT)	 AG	79156-79424	GT	TAG
(TGC)	 AG	79532-79839	AC	GAA
-recovered pasa_asmbl_44338.p1, terminal, 78445, 78482
-recovered pasa_asmbl_44338.p1, terminal, 79532, 79839
-recovered pasa_asmbl_44338.p1, internal, 77044, 77125
-recovered pasa_asmbl_44338.p1, internal, 77566, 77736
-recovered pasa_asmbl_44338.p1, internal, 77959, 78052
-recovered pasa_asmbl_44338.p1, internal, 78445, 78482
-recovered pasa_asmbl_44338.p1, internal, 78618, 78692
-recovered pasa_asmbl_44338.p1, internal, 78901, 79038
-recovered pasa_asmbl_44338.p1, internal, 79156, 79424
Valid prediction for pasa_asmbl_44344.p1
Valid prediction for CodingQuarry_transcript_52089-T1
Valid prediction for GlimmerHMM_glimmerT_12817-T1
Valid prediction for snap_scaffold_5-snap.1956-T1
Valid prediction for Augustus_model.g8512.t1
Valid prediction for GeneMark_model.21692_t
Valid prediction for Augustus_model.g8513.t1
Valid prediction for snap_scaffold_5-snap.1957-T1
Valid prediction for Augustus_model.g8536.t1
Valid prediction for snap_scaffold_5-snap.1946-T1
Valid prediction for snap_scaffold_5-snap.1953-T1
Valid prediction for snap_scaffold_5-snap.1969-T1
Valid prediction for GeneMark_model.21675_t
Valid prediction for snap_scaffold_5-snap.1941-T1
Valid prediction for GlimmerHMM_glimmerT_12836-T1
Valid prediction for GeneMark_model.21693_t
Valid prediction for Augustus_model.g8523.t1
Valid prediction for GlimmerHMM_glimmerT_12827-T1
Couldn't classify 48306, 48614
Sorry, prediction pasa_asmbl_44336.p1 fails validation.
(CAC)	 CC	48306-48614	CC	CCC
Valid prediction for snap_scaffold_5-snap.1947-T1
Valid prediction for HiQ_model.g8509.t1
Valid prediction for pasa_asmbl_44346.p1
Valid prediction for GeneMark_model.21690_t
Valid prediction for GeneMark_model.21670_t
Valid prediction for snap_scaffold_5-snap.1960-T1
Valid prediction for GeneMark_model.21676_t
Valid prediction for CodingQuarry_transcript_52098-T1
Valid prediction for GeneMark_model.21680_t
Valid prediction for HiQ_model.g8519.t1
Valid prediction for GeneMark_model.21662_t
Valid prediction for HiQ_model.g8517.t1
Valid prediction for GlimmerHMM_glimmerT_12829-T1
Valid prediction for GlimmerHMM_glimmerT_12808-T1
Valid prediction for Augustus_model.g8518.t1
Valid prediction for CodingQuarry_transcript_52083-T1
Valid prediction for GeneMark_model.21674_t
Valid prediction for snap_scaffold_5-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_12811-T1
Valid prediction for snap_scaffold_5-snap.1948-T1
Valid prediction for pasa_asmbl_44335.p1
Valid prediction for snap_scaffold_5-snap.1958-T1
Valid prediction for GeneMark_model.21667_t
Valid prediction for Augustus_model.g8521.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 CodingQuarry_transcript_52084-T1
Valid prediction for GlimmerHMM_glimmerT_12809-T1
Valid prediction for GeneMark_model.21672_t
Valid prediction for GlimmerHMM_glimmerT_12824-T1
Valid prediction for CodingQuarry_transcript_52092-T1
Valid prediction for Augustus_model.g8524.t1
Valid prediction for CodingQuarry_transcript_52086-T1
Valid prediction for pasa_asmbl_45733.p1
Valid prediction for Augustus_model.g8529.t1
Valid prediction for CodingQuarry_transcript_52082-T1
Valid prediction for Augustus_model.g8507.t1
Valid prediction for GlimmerHMM_glimmerT_12814-T1
Valid prediction for HiQ_model.g8533.t1
Valid prediction for CodingQuarry_transcript_52088-T1
Valid prediction for Augustus_model.g8522.t1
Valid prediction for snap_scaffold_5-snap.1967-T1
Valid prediction for GlimmerHMM_glimmerT_12835-T1
Valid prediction for GeneMark_model.21678_t
Valid prediction for GeneMark_model.21684_t
Valid prediction for snap_scaffold_5-snap.1968-T1
Valid prediction for Augustus_model.g8515.t1
Valid prediction for HiQ_model.g8525.t1
Valid prediction for GlimmerHMM_glimmerT_12818-T1
Valid prediction for HiQ_model.g8514.t1
Valid prediction for pasa_asmbl_45737.p1
Valid prediction for snap_scaffold_5-snap.1961-T1
Valid prediction for GlimmerHMM_glimmerT_12810-T1
Valid prediction for GeneMark_model.21685_t
Valid prediction for GlimmerHMM_glimmerT_12833-T1
Valid prediction for snap_scaffold_5-snap.1949-T1
Valid prediction for GeneMark_model.21664_t
Valid prediction for snap_scaffold_5-snap.1973-T1
Valid prediction for pasa_asmbl_45749.p1
Valid prediction for GlimmerHMM_glimmerT_12825-T1
Valid prediction for GlimmerHMM_glimmerT_12812-T1
Valid prediction for GlimmerHMM_glimmerT_12807-T1
Valid prediction for snap_scaffold_5-snap.1965-T1
Valid prediction for HiQ_model.g8534.t1
Valid prediction for CodingQuarry_transcript_52090-T1
Valid prediction for snap_scaffold_5-snap.1940-T1
Couldn't classify 208074, 208093
Sorry, prediction pasa_asmbl_45729.p1 fails validation.
(CAG)	 TT	208074-208093	GT	AGG
(GTT)	 AG	208211-208343	GT	AGG
(ATG)	 AG	208481-208585	GT	AGG
(AAA)	 AG	208719-208769	GT	GGG
(GAA)	 AG	209008-209058	GT	AGG
(CAG)	 AG	209761-209802	AA	GAA
-recovered pasa_asmbl_45729.p1, initial, 208481, 208585
-recovered pasa_asmbl_45729.p1, terminal, 209761, 209802
-recovered pasa_asmbl_45729.p1, internal, 208211, 208343
-recovered pasa_asmbl_45729.p1, internal, 208481, 208585
-recovered pasa_asmbl_45729.p1, internal, 208719, 208769
-recovered pasa_asmbl_45729.p1, internal, 209008, 209058
Valid prediction for pasa_asmbl_45713.p1
Valid prediction for GeneMark_model.21691_t
Valid prediction for GlimmerHMM_glimmerT_12806-T1
Valid prediction for snap_scaffold_5-snap.1942-T1
Valid prediction for CodingQuarry_transcript_52095-T1
Valid prediction for snap_scaffold_5-snap.1959-T1
Valid prediction for pasa_asmbl_45711.p1
Couldn't classify 273144, 273280
Sorry, prediction pasa_asmbl_45723.p1 fails validation.
(TGG)	 TG	273144-273280	GT	AAG
(ACA)	 AG	273484-273571	GT	AGG
(TTA)	 AG	273661-273738	GT	CAG
(GTG)	 AG	273927-274131	GT	AGG
(ATA)	 AG	274244-274320	GT	AGG
(GCA)	 AG	274445-274546	GT	AGG
(AAT)	 AG	274667-274794	GT	GGG
(GTC)	 AG	274932-274977	GT	AGG
(GCT)	 AG	275135-275286	GT	ACG
(TGT)	 AG	275394-275556	CC	GAC
-recovered pasa_asmbl_45723.p1, terminal, 275394, 275556
-recovered pasa_asmbl_45723.p1, internal, 273484, 273571
-recovered pasa_asmbl_45723.p1, internal, 273661, 273738
-recovered pasa_asmbl_45723.p1, internal, 273927, 274131
-recovered pasa_asmbl_45723.p1, internal, 274244, 274320
-recovered pasa_asmbl_45723.p1, internal, 274445, 274546
-recovered pasa_asmbl_45723.p1, internal, 274667, 274794
-recovered pasa_asmbl_45723.p1, internal, 274932, 274977
-recovered pasa_asmbl_45723.p1, internal, 275135, 275286
Valid prediction for GeneMark_model.21668_t
Valid prediction for GlimmerHMM_glimmerT_12820-T1
Valid prediction for HiQ_model.g8510.t1
Valid prediction for CodingQuarry_transcript_52093-T1
Valid prediction for GeneMark_model.21669_t
Valid prediction for snap_scaffold_5-snap.1966-T1
Valid prediction for GlimmerHMM_glimmerT_12830-T1
Valid prediction for Augustus_model.g8511.t1
Valid prediction for snap_scaffold_5-snap.1939-T1
Valid prediction for Augustus_model.g8516.t1
Valid prediction for snap_scaffold_5-snap.1962-T1
Valid prediction for GeneMark_model.21683_t
Valid prediction for pasa_asmbl_45735.p2
Valid prediction for pasa_asmbl_45717.p1
Valid prediction for snap_scaffold_5-snap.1972-T1
Valid prediction for snap_scaffold_5-snap.1950-T1
Valid prediction for CodingQuarry_transcript_52087-T1
Valid prediction for snap_scaffold_5-snap.1944-T1
Couldn't classify 127704, 127840
Couldn't classify 129989, 130074
Sorry, prediction pasa_asmbl_46315.p1 fails validation.
(GGA)	 CA	127704-127840	GT	AGG
(ACG)	 AG	129551-129705	GT	AGG
(GAT)	 AG	129989-130074	TG	AGT
-recovered pasa_asmbl_46315.p1, internal, 129551, 129705
Valid prediction for GeneMark_model.21661_t
Valid prediction for GeneMark_model.21681_t
Valid prediction for snap_scaffold_5-snap.1964-T1
Valid prediction for GeneMark_model.21689_t
Valid prediction for GlimmerHMM_glimmerT_12822-T1
Valid prediction for Augustus_model.g8520.t1
Valid prediction for GlimmerHMM_glimmerT_12826-T1
Valid prediction for snap_scaffold_5-snap.1974-T1
Valid prediction for pasa_asmbl_45743.p1
Valid prediction for GeneMark_model.21686_t
Valid prediction for GeneMark_model.21679_t
Valid prediction for snap_scaffold_5-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_12828-T1
Valid prediction for GeneMark_model.21682_t
Valid prediction for snap_scaffold_5-snap.1945-T1
Valid prediction for GeneMark_model.21663_t
Valid prediction for GlimmerHMM_glimmerT_12832-T1
Valid prediction for snap_scaffold_5-snap.1951-T1
Valid prediction for CodingQuarry_transcript_52096-T1
Valid prediction for Augustus_model.g8528.t1
Valid prediction for CodingQuarry_transcript_52091-T1
Valid prediction for GlimmerHMM_glimmerT_12813-T1
Valid prediction for HiQ_model.g8527.t1
Valid prediction for GeneMark_model.21687_t
Valid prediction for snap_scaffold_5-snap.1943-T1
Valid prediction for Augustus_model.g8530.t1
Couldn't classify 184416, 184540
Couldn't classify 185636, 185782
Sorry, prediction CodingQuarry_transcript_52094-T1 fails validation.
(ATG)	 AG	177825-177870	GT	AGG
(CTG)	 AG	179407-179529	GT	AGG
(GGA)	 AG	179635-179774	GT	AGG
(ATG)	 AG	179891-179990	GT	GGG
(TCG)	 AG	180111-180152	GT	CTG
(CAT)	 AG	180321-180363	GT	AGG
(AGC)	 AG	180481-180667	GT	AGG
(TAT)	 AG	180832-180945	GT	AGG
(GAT)	 AG	181218-181380	GT	GAG
(TTC)	 AG	181526-181798	GT	AGG
(CTG)	 AG	181900-182307	GT	AGG
(AAC)	 AG	182451-182552	GT	TGG
(GCC)	 AG	183455-183583	GT	TGG
(GCC)	 AG	184416-184540	AT	TGA
(ACC)	 TC	185636-185782	CT	GAC
-recovered CodingQuarry_transcript_52094-T1, initial, 177825, 177870
-recovered CodingQuarry_transcript_52094-T1, initial, 179891, 179990
-recovered CodingQuarry_transcript_52094-T1, internal, 177825, 177870
-recovered CodingQuarry_transcript_52094-T1, internal, 179407, 179529
-recovered CodingQuarry_transcript_52094-T1, internal, 179635, 179774
-recovered CodingQuarry_transcript_52094-T1, internal, 179891, 179990
-recovered CodingQuarry_transcript_52094-T1, internal, 180111, 180152
-recovered CodingQuarry_transcript_52094-T1, internal, 180321, 180363
-recovered CodingQuarry_transcript_52094-T1, internal, 180481, 180667
-recovered CodingQuarry_transcript_52094-T1, internal, 180832, 180945
-recovered CodingQuarry_transcript_52094-T1, internal, 181218, 181380
-recovered CodingQuarry_transcript_52094-T1, internal, 181526, 181798
-recovered CodingQuarry_transcript_52094-T1, internal, 181900, 182307
-recovered CodingQuarry_transcript_52094-T1, internal, 182451, 182552
-recovered CodingQuarry_transcript_52094-T1, internal, 183455, 183583
Valid prediction for snap_scaffold_5-snap.1963-T1
Valid prediction for Augustus_model.g8526.t1
Valid prediction for HiQ_model.g8508.t1
Valid prediction for GlimmerHMM_glimmerT_12823-T1
Valid prediction for Augustus_model.g8531.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 133158, rend_intergenic: 129539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 340941
-exon list size: 535


building trellis

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91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 133158, rend_intergenic: 129539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10539
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 - 10491
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support