-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_8578932-8708217

-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.105814_t
Valid prediction for GeneMark_model.105819_t
Valid prediction for snap_scaffold_28-snap.1976-T1
Valid prediction for snap_scaffold_28-snap.1972-T1
Valid prediction for GeneMark_model.105817_t
Valid prediction for GeneMark_model.105825_t
Valid prediction for GeneMark_model.105837_t
Valid prediction for snap_scaffold_28-snap.1982-T1
Valid prediction for GlimmerHMM_glimmerT_60740-T1
Valid prediction for GeneMark_model.105820_t
Valid prediction for snap_scaffold_28-snap.1985-T1
Valid prediction for GeneMark_model.105827_t
Valid prediction for snap_scaffold_28-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_60741-T1
Valid prediction for GeneMark_model.105816_t
Valid prediction for snap_scaffold_28-snap.1980-T1
Valid prediction for GeneMark_model.105807_t
Valid prediction for snap_scaffold_28-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_60744-T1
Valid prediction for GlimmerHMM_glimmerT_60739-T1
Valid prediction for Augustus_model.g40437.t1
Valid prediction for snap_scaffold_28-snap.1960-T1
Valid prediction for snap_scaffold_28-snap.1958-T1
Valid prediction for snap_scaffold_28-snap.1979-T1
Valid prediction for GeneMark_model.105813_t
Valid prediction for snap_scaffold_28-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_60738-T1
Valid prediction for GlimmerHMM_glimmerT_60745-T1
Valid prediction for snap_scaffold_28-snap.1974-T1
Valid prediction for snap_scaffold_28-snap.1949-T1
Valid prediction for snap_scaffold_28-snap.1962-T1
Valid prediction for snap_scaffold_28-snap.1965-T1
Valid prediction for GeneMark_model.105805_t
Valid prediction for GlimmerHMM_glimmerT_60742-T1
Valid prediction for GeneMark_model.105832_t
Valid prediction for snap_scaffold_28-snap.1981-T1
Valid prediction for GeneMark_model.105830_t
Valid prediction for GeneMark_model.105811_t
Valid prediction for snap_scaffold_28-snap.1961-T1
Valid prediction for GeneMark_model.105822_t
Valid prediction for GeneMark_model.105835_t

-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_28-snap.1970-T1
Couldn't classify 18200, 18396
Couldn't classify 22508, 22546
Sorry, prediction pasa_asmbl_37809.p1 fails validation.
(GCT)	 AT	18200-18396	GT	AGG
(TAG)	 AG	19099-19208	GT	AGG
(GCC)	 AG	19684-19866	GT	GGG
(CTC)	 AG	20512-20669	GT	AGG
(GAG)	 AG	21751-21828	GT	AGG
(AGG)	 AG	22508-22546	GC	GGG
-recovered pasa_asmbl_37809.p1, internal, 19099, 19208
-recovered pasa_asmbl_37809.p1, internal, 19684, 19866
-recovered pasa_asmbl_37809.p1, internal, 20512, 20669
-recovered pasa_asmbl_37809.p1, internal, 21751, 21828
-recovered pasa_asmbl_37809.p1, internal, 22508, 22546
Valid prediction for GeneMark_model.105838_t
Valid prediction for GeneMark_model.105809_t
Valid prediction for snap_scaffold_28-snap.1969-T1
Valid prediction for GeneMark_model.105823_t
Valid prediction for GeneMark_model.105829_t
Valid prediction for GlimmerHMM_glimmerT_60746-T1
Valid prediction for GeneMark_model.105812_t
Valid prediction for Augustus_model.g40442.t1
Valid prediction for snap_scaffold_28-snap.1967-T1
Valid prediction for GeneMark_model.105826_t
Valid prediction for GeneMark_model.105836_t
Valid prediction for snap_scaffold_28-snap.1983-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_60747-T1
Valid prediction for snap_scaffold_28-snap.1955-T1
Valid prediction for GeneMark_model.105815_t
Valid prediction for snap_scaffold_28-snap.1954-T1
Valid prediction for snap_scaffold_28-snap.1966-T1
Valid prediction for GeneMark_model.105821_t
Valid prediction for Augustus_model.g40440.t1
Valid prediction for GlimmerHMM_glimmerT_60736-T1
Valid prediction for snap_scaffold_28-snap.1977-T1
Valid prediction for snap_scaffold_28-snap.1957-T1
Valid prediction for GeneMark_model.105831_t
Valid prediction for snap_scaffold_28-snap.1951-T1
Valid prediction for Augustus_model.g40438.t1
Valid prediction for GeneMark_model.105834_t
Valid prediction for GeneMark_model.105818_t
Valid prediction for GlimmerHMM_glimmerT_60737-T1
Valid prediction for snap_scaffold_28-snap.1963-T1
Valid prediction for Augustus_model.g40441.t1
Valid prediction for GeneMark_model.105806_t
Valid prediction for GeneMark_model.105828_t
Valid prediction for snap_scaffold_28-snap.1950-T1
Valid prediction for GlimmerHMM_glimmerT_60749-T1
Valid prediction for GeneMark_model.105833_t
Couldn't classify 32163, 32250
Sorry, prediction pasa_asmbl_37804.p1 fails validation.
(CAC)	 AG	32163-32250	GT	CGG
(GCT)	 AG	32359-32470	GT	AAG
(AGA)	 AG	32718-32915	GT	AAG
(GTG)	 AG	33370-33490	GG	GAG
-recovered pasa_asmbl_37804.p1, terminal, 33370, 33490
-recovered pasa_asmbl_37804.p1, internal, 32163, 32250
-recovered pasa_asmbl_37804.p1, internal, 32359, 32470
-recovered pasa_asmbl_37804.p1, internal, 32718, 32915
Valid prediction for GeneMark_model.105808_t
Valid prediction for GlimmerHMM_glimmerT_60748-T1
Valid prediction for GeneMark_model.105810_t
Couldn't classify 22619, 22738
Couldn't classify 24465, 24515
Sorry, prediction pasa_asmbl_37807.p1 fails validation.
(TTC)	 AG	22619-22738	GT	CGG
(AAG)	 AG	23547-23712	GT	AGG
(GCC)	 AG	24181-24374	GT	AGG
(ATC)	 AG	24465-24515	GG	AGG
-recovered pasa_asmbl_37807.p1, internal, 22619, 22738
-recovered pasa_asmbl_37807.p1, internal, 23547, 23712
-recovered pasa_asmbl_37807.p1, internal, 24181, 24374
Valid prediction for GlimmerHMM_glimmerT_60743-T1
Valid prediction for snap_scaffold_28-snap.1952-T1
Valid prediction for snap_scaffold_28-snap.1984-T1
Valid prediction for Augustus_model.g40439.t1
Valid prediction for snap_scaffold_28-snap.1964-T1
Valid prediction for snap_scaffold_28-snap.1973-T1
Valid prediction for snap_scaffold_28-snap.1978-T1
Valid prediction for GeneMark_model.105824_t
Couldn't classify 24974, 25009
Couldn't classify 31664, 31824
Sorry, prediction pasa_asmbl_37805.p1 fails validation.
(ATC)	 AC	24974-25009	GT	AGG
(CCG)	 AG	25124-25209	GT	AGG
(GTT)	 AG	25369-25449	GT	GGG
(GTC)	 AG	25584-25638	GT	AGG
(CGA)	 AG	25741-25860	GT	AGG
(GAG)	 AG	26272-26389	GT	CGG
(GAG)	 AG	26553-26659	GT	AGG
(GGA)	 AG	27048-27201	GT	GGG
(GAA)	 AG	27320-27411	GT	AGG
(GCG)	 AG	28521-28733	GT	AGG
(CTG)	 AG	28891-29038	GT	AGG
(AGC)	 AG	29237-29391	GT	AGG
(GCG)	 AG	29902-30060	GT	AGG
(GCT)	 AG	30337-30516	GT	CGG
(GGA)	 AG	30799-30981	GT	GGG
(TTC)	 AG	31235-31325	GT	GGG
(TTG)	 AG	31664-31824	AC	GTA
-recovered pasa_asmbl_37805.p1, internal, 25124, 25209
-recovered pasa_asmbl_37805.p1, internal, 25369, 25449
-recovered pasa_asmbl_37805.p1, internal, 25584, 25638
-recovered pasa_asmbl_37805.p1, internal, 25741, 25860
-recovered pasa_asmbl_37805.p1, internal, 26272, 26389
-recovered pasa_asmbl_37805.p1, internal, 26553, 26659
-recovered pasa_asmbl_37805.p1, internal, 27048, 27201
-recovered pasa_asmbl_37805.p1, internal, 27320, 27411
-recovered pasa_asmbl_37805.p1, internal, 28521, 28733
-recovered pasa_asmbl_37805.p1, internal, 28891, 29038
-recovered pasa_asmbl_37805.p1, internal, 29237, 29391
-recovered pasa_asmbl_37805.p1, internal, 29902, 30060
-recovered pasa_asmbl_37805.p1, internal, 30337, 30516
-recovered pasa_asmbl_37805.p1, internal, 30799, 30981
-recovered pasa_asmbl_37805.p1, internal, 31235, 31325
Valid prediction for snap_scaffold_28-snap.1959-T1
Valid prediction for snap_scaffold_28-snap.1953-T1
Valid prediction for CodingQuarry_transcript_43648-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20495, rend_intergenic: 3156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32831, rend_intergenic: 30055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48263, rend_intergenic: 44349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54551, rend_intergenic: 52940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58337, rend_intergenic: 55564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67427, rend_intergenic: 63382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75673, rend_intergenic: 71320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87145, rend_intergenic: 85902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98147, rend_intergenic: 95460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110654, rend_intergenic: 98298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119987, rend_intergenic: 110706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126471, rend_intergenic: 120131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 129286
-exon list size: 533


building trellis

0.2    
0.4    
0.6    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 20495, rend_intergenic: 3156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32831, rend_intergenic: 30055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48263, rend_intergenic: 44349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54551, rend_intergenic: 52940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58337, rend_intergenic: 55564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67427, rend_intergenic: 63382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75673, rend_intergenic: 71320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87145, rend_intergenic: 85902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98147, rend_intergenic: 95460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110654, rend_intergenic: 98298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119987, rend_intergenic: 110706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126471, rend_intergenic: 120131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support