-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_9336581-9597538

-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 248386, 248494
Couldn't classify 250085, 250117
Sorry, prediction pasa_asmbl_12272.p1 fails validation.
(CAG)	 TG	248386-248494	GT	AGG
(GTC)	 AG	248631-248755	GT	AGG
(GTA)	 AG	249041-249184	GT	ACG
(ACG)	 AG	249758-249799	GT	AGG
(CGT)	 AG	250085-250117	TG	CCT
-recovered pasa_asmbl_12272.p1, internal, 248631, 248755
-recovered pasa_asmbl_12272.p1, internal, 249041, 249184
-recovered pasa_asmbl_12272.p1, internal, 249758, 249799
Valid prediction for GeneMark_model.60356_t
Couldn't classify 114709, 114921
Couldn't classify 117016, 118494
Sorry, prediction pasa_asmbl_12263.p1 fails validation.
(AGG)	 CT	114709-114921	GT	CGG
(CAG)	 AG	117016-118494	AG	GCA
Valid prediction for GlimmerHMM_glimmerT_35185-T1
Valid prediction for GeneMark_model.60347_t
Valid prediction for snap_scaffold_14-snap.1963-T1
Valid prediction for Augustus_model.g23682.t1
Valid prediction for GeneMark_model.60359_t
Valid prediction for GlimmerHMM_glimmerT_35195-T1
Valid prediction for GeneMark_model.60364_t
Valid prediction for GeneMark_model.60326_t
Valid prediction for Augustus_model.g23683.t1
Valid prediction for GlimmerHMM_glimmerT_35202-T1
Valid prediction for snap_scaffold_14-snap.1969-T1
Valid prediction for GeneMark_model.60343_t
Valid prediction for Augustus_model.g23671.t1
Valid prediction for GeneMark_model.60370_t
Valid prediction for snap_scaffold_14-snap.1953-T1
Valid prediction for GeneMark_model.60372_t
Valid prediction for GlimmerHMM_glimmerT_35189-T1
Valid prediction for pasa_asmbl_12268.p1
Valid prediction for snap_scaffold_14-snap.1974-T1
Valid prediction for GeneMark_model.60345_t
Valid prediction for Augustus_model.g23670.t1
Valid prediction for GeneMark_model.60328_t
Valid prediction for GlimmerHMM_glimmerT_35186-T1
Valid prediction for CodingQuarry_transcript_15745-T1
Valid prediction for snap_scaffold_14-snap.1980-T1
Valid prediction for GeneMark_model.60357_t
Valid prediction for GlimmerHMM_glimmerT_35196-T1
Valid prediction for GeneMark_model.60344_t
Valid prediction for HiQ_model.g23676.t1
Valid prediction for snap_scaffold_14-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_35181-T1
Valid prediction for GeneMark_model.60349_t
Valid prediction for GeneMark_model.60324_t
Couldn't classify 118753, 119418
Sorry, prediction pasa_asmbl_12264.p1 fails validation.
(AAT)	 TG	118753-119418	AC	AAA
Valid prediction for Augustus_model.g23680.t1
Valid prediction for GlimmerHMM_glimmerT_35199-T1
Valid prediction for snap_scaffold_14-snap.1958-T1
Valid prediction for Augustus_model.g23672.t1
Valid prediction for GeneMark_model.60374_t
Valid prediction for GeneMark_model.60335_t
Valid prediction for GeneMark_model.60363_t
Valid prediction for snap_scaffold_14-snap.1973-T1
Valid prediction for snap_scaffold_14-snap.1982-T1
Valid prediction for snap_scaffold_14-snap.1978-T1
Valid prediction for GeneMark_model.60330_t
Valid prediction for CodingQuarry_transcript_15743-T1
Valid prediction for GeneMark_model.60342_t
Valid prediction for snap_scaffold_14-snap.1986-T1
Couldn't classify 102196, 102346
Couldn't classify 105211, 105306
Sorry, prediction pasa_asmbl_12683.p1 fails validation.
(TCA)	 CC	102196-102346	GT	GAG
(TCA)	 AG	103305-103357	GT	TGG
(ATA)	 AG	105211-105306	AG	AGA
-recovered pasa_asmbl_12683.p1, internal, 103305, 103357
Valid prediction for snap_scaffold_14-snap.1962-T1
Valid prediction for snap_scaffold_14-snap.1984-T1
Valid prediction for GeneMark_model.60368_t
Valid prediction for GlimmerHMM_glimmerT_35193-T1
Valid prediction for GeneMark_model.60380_t
Valid prediction for GlimmerHMM_glimmerT_35183-T1
Valid prediction for snap_scaffold_14-snap.1967-T1
Valid prediction for GlimmerHMM_glimmerT_35192-T1
Valid prediction for snap_scaffold_14-snap.1955-T1
Valid prediction for snap_scaffold_14-snap.1979-T1
Valid prediction for GeneMark_model.60339_t
Valid prediction for Augustus_model.g23673.t1
Valid prediction for Augustus_model.g23666.t1
Valid prediction for snap_scaffold_14-snap.1971-T1
Valid prediction for GeneMark_model.60362_t
Valid prediction for Augustus_model.g23679.t1
Valid prediction for GeneMark_model.60338_t
Valid prediction for snap_scaffold_14-snap.1961-T1
Valid prediction for snap_scaffold_14-snap.1965-T1
Valid prediction for Augustus_model.g23674.t1
Valid prediction for GeneMark_model.60384_t
Valid prediction for GlimmerHMM_glimmerT_35188-T1
Valid prediction for GeneMark_model.60376_t
Valid prediction for GeneMark_model.60366_t
Couldn't classify 252452, 253231
Couldn't classify 254587, 254748
Sorry, prediction pasa_asmbl_12273.p1 fails validation.
(CTC)	 CA	252452-253231	GT	GGG
(AAT)	 AG	254587-254748	CT	ACC
Valid prediction for GeneMark_model.60377_t
Valid prediction for snap_scaffold_14-snap.1970-T1
Valid prediction for Augustus_model.g23669.t1
Valid prediction for GeneMark_model.60360_t
Valid prediction for GeneMark_model.60382_t
Valid prediction for GeneMark_model.60337_t
Valid prediction for GeneMark_model.60333_t
Valid prediction for snap_scaffold_14-snap.1976-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 GeneMark_model.60353_t
Valid prediction for GeneMark_model.60351_t
Valid prediction for GlimmerHMM_glimmerT_35194-T1
Valid prediction for GlimmerHMM_glimmerT_35191-T1
Valid prediction for snap_scaffold_14-snap.1989-T1
Valid prediction for GeneMark_model.60352_t
Valid prediction for GeneMark_model.60375_t
Valid prediction for GlimmerHMM_glimmerT_35190-T1
Valid prediction for snap_scaffold_14-snap.1960-T1
Valid prediction for HiQ_model.g23677.t1
Valid prediction for GeneMark_model.60378_t
Valid prediction for GeneMark_model.60336_t
Valid prediction for CodingQuarry_transcript_15744-T1
Valid prediction for GeneMark_model.60350_t
Valid prediction for GeneMark_model.60381_t
Valid prediction for GeneMark_model.60340_t
Valid prediction for snap_scaffold_14-snap.1992-T1
Valid prediction for snap_scaffold_14-snap.1981-T1
Valid prediction for GeneMark_model.60379_t
Valid prediction for snap_scaffold_14-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_35201-T1
Valid prediction for snap_scaffold_14-snap.1987-T1
Valid prediction for GeneMark_model.60383_t
Valid prediction for GeneMark_model.60348_t
Valid prediction for GlimmerHMM_glimmerT_35200-T1
Valid prediction for GlimmerHMM_glimmerT_35197-T1
Valid prediction for GeneMark_model.60361_t
Valid prediction for snap_scaffold_14-snap.1956-T1
Valid prediction for GeneMark_model.60355_t
Valid prediction for Augustus_model.g23667.t1
Valid prediction for GeneMark_model.60346_t
Valid prediction for snap_scaffold_14-snap.1959-T1
Valid prediction for CodingQuarry_transcript_15746-T1
Valid prediction for GlimmerHMM_glimmerT_35203-T1
Couldn't classify 86542, 86618
Sorry, prediction pasa_asmbl_13364.p1 fails validation.
(GTG)	 AG	86542-86618	GT	TGG
(GTT)	 AG	86991-87111	GT	GGG
(GAG)	 AG	87333-87446	GC	AGG
(GGC)	 AG	89188-89341	GT	AGG
(AGT)	 AG	91615-91751	GT	AAG
(GTG)	 AG	91886-91957	CC	GAC
-recovered pasa_asmbl_13364.p1, terminal, 91886, 91957
-recovered pasa_asmbl_13364.p1, internal, 86542, 86618
-recovered pasa_asmbl_13364.p1, internal, 86991, 87111
-recovered pasa_asmbl_13364.p1, internal, 87333, 87446
-recovered pasa_asmbl_13364.p1, internal, 89188, 89341
-recovered pasa_asmbl_13364.p1, internal, 91615, 91751
Valid prediction for GeneMark_model.60369_t
Valid prediction for GeneMark_model.60341_t
Valid prediction for GeneMark_model.60371_t
Valid prediction for GeneMark_model.60358_t
Valid prediction for GlimmerHMM_glimmerT_35182-T1
Valid prediction for GlimmerHMM_glimmerT_35198-T1
Valid prediction for GeneMark_model.60327_t
Valid prediction for GeneMark_model.60385_t
Valid prediction for GeneMark_model.60329_t
Valid prediction for GeneMark_model.60325_t
Valid prediction for snap_scaffold_14-snap.1964-T1
Valid prediction for snap_scaffold_14-snap.1957-T1
Valid prediction for GeneMark_model.60367_t
Valid prediction for snap_scaffold_14-snap.1966-T1
Valid prediction for Augustus_model.g23678.t1
Valid prediction for Augustus_model.g23681.t1
Valid prediction for snap_scaffold_14-snap.1991-T1
Valid prediction for pasa_asmbl_13363.p1
Valid prediction for HiQ_model.g23675.t1
Valid prediction for snap_scaffold_14-snap.1990-T1
Valid prediction for snap_scaffold_14-snap.1954-T1
Valid prediction for GeneMark_model.60331_t
Valid prediction for GeneMark_model.60373_t
Valid prediction for GeneMark_model.60332_t
Valid prediction for GeneMark_model.60323_t
Valid prediction for snap_scaffold_14-snap.1972-T1
Valid prediction for GeneMark_model.60334_t
Valid prediction for snap_scaffold_14-snap.1968-T1
Valid prediction for snap_scaffold_14-snap.1985-T1
Valid prediction for GeneMark_model.60365_t
Valid prediction for Augustus_model.g23668.t1
Valid prediction for GlimmerHMM_glimmerT_35184-T1
Valid prediction for snap_scaffold_14-snap.1977-T1
Valid prediction for snap_scaffold_14-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_35187-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8859, rend_intergenic: 6731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12489, rend_intergenic: 10784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17687, rend_intergenic: 13335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37234, rend_intergenic: 29724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115889, rend_intergenic: 115574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119226, rend_intergenic: 116864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174964, rend_intergenic: 169731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196625, rend_intergenic: 192147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197942, rend_intergenic: 197142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205713, rend_intergenic: 198100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207510, rend_intergenic: 206552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212428, rend_intergenic: 207904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217681, rend_intergenic: 212513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258640, rend_intergenic: 218317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 260958
-exon list size: 687


building trellis

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93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 8859, rend_intergenic: 6731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12489, rend_intergenic: 10784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17687, rend_intergenic: 13335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37234, rend_intergenic: 29724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115889, rend_intergenic: 115574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119226, rend_intergenic: 116864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174964, rend_intergenic: 169731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196625, rend_intergenic: 192147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197942, rend_intergenic: 197142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205713, rend_intergenic: 198100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207510, rend_intergenic: 206552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212428, rend_intergenic: 207904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217681, rend_intergenic: 212513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258640, rend_intergenic: 218317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14353
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-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 - 13504
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-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 - 13375
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-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 - 12386
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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