-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_7919698-8182790

-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_4147-T1
Valid prediction for GlimmerHMM_glimmerT_4157-T1
Valid prediction for pasa_asmbl_24609.p1
Valid prediction for snap_scaffold_2-snap.1662-T1
Valid prediction for HiQ_model.g2788.t1
Valid prediction for GlimmerHMM_glimmerT_4162-T1
Valid prediction for snap_scaffold_2-snap.1655-T1
Valid prediction for pasa_asmbl_24614.p1
Valid prediction for snap_scaffold_2-snap.1654-T1
Valid prediction for Augustus_model.g2798.t1
Valid prediction for snap_scaffold_2-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_4149-T1
Valid prediction for GlimmerHMM_glimmerT_4160-T1
Valid prediction for CodingQuarry_transcript_28620-T1
Valid prediction for CodingQuarry_transcript_28619-T1
Valid prediction for GlimmerHMM_glimmerT_4144-T1
Valid prediction for Augustus_model.g2789.t1
Valid prediction for Augustus_model.g2794.t1
Valid prediction for pasa_asmbl_24601.p1
Valid prediction for GlimmerHMM_glimmerT_4151-T1
Valid prediction for snap_scaffold_2-snap.1664-T1
Couldn't classify 210847, 210864
Couldn't classify 212456, 212553
Sorry, prediction pasa_asmbl_24613.p1 fails validation.
(CCC)	 GT	210847-210864	GT	TAG
(AAC)	 AG	211612-211723	GT	CGG
(AGG)	 AG	211957-212073	GT	AGG
(ACC)	 AG	212456-212553	GG	CGG
-recovered pasa_asmbl_24613.p1, internal, 211612, 211723
-recovered pasa_asmbl_24613.p1, internal, 211957, 212073
Valid prediction for GlimmerHMM_glimmerT_4145-T1
Valid prediction for snap_scaffold_2-snap.1661-T1
Valid prediction for pasa_asmbl_24606.p1
Valid prediction for GlimmerHMM_glimmerT_4153-T1
Valid prediction for HiQ_model.g2796.t1
Valid prediction for snap_scaffold_2-snap.1652-T1
Valid prediction for Augustus_model.g2799.t1
Valid prediction for GlimmerHMM_glimmerT_4154-T1
Valid prediction for GlimmerHMM_glimmerT_4158-T1
Valid prediction for GlimmerHMM_glimmerT_4135-T1
Valid prediction for snap_scaffold_2-snap.1643-T1
Valid prediction for snap_scaffold_2-snap.1656-T1
Valid prediction for pasa_asmbl_24599.p1
Valid prediction for snap_scaffold_2-snap.1663-T1
Valid prediction for snap_scaffold_2-snap.1640-T1
Valid prediction for Augustus_model.g2801.t1
Valid prediction for snap_scaffold_2-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_4139-T1
Valid prediction for snap_scaffold_2-snap.1645-T1
Valid prediction for snap_scaffold_2-snap.1649-T1
Valid prediction for CodingQuarry_transcript_28622-T1
Valid prediction for GlimmerHMM_glimmerT_4155-T1
Valid prediction for Augustus_model.g2800.t1
Valid prediction for CodingQuarry_transcript_28618-T1
Valid prediction for snap_scaffold_2-snap.1642-T1
Valid prediction for HiQ_model.g2790.t1
Valid prediction for GlimmerHMM_glimmerT_4138-T1
Valid prediction for snap_scaffold_2-snap.1651-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_2-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_4140-T1
Valid prediction for GlimmerHMM_glimmerT_4150-T1
Valid prediction for pasa_asmbl_23295.p1
Valid prediction for snap_scaffold_2-snap.1650-T1
Couldn't classify 111212, 111250
Couldn't classify 113035, 113937
Sorry, prediction pasa_asmbl_23313.p1 fails validation.
(TCC)	 GA	111212-111250	GT	TGG
(GAG)	 AG	113035-113937	GT	ATG
-recovered pasa_asmbl_23313.p1, internal, 113035, 113937
Valid prediction for Augustus_model.g2793.t1
Valid prediction for snap_scaffold_2-snap.1639-T1
Valid prediction for snap_scaffold_2-snap.1653-T1
Valid prediction for GlimmerHMM_glimmerT_4159-T1
Valid prediction for CodingQuarry_transcript_28621-T1
Valid prediction for GlimmerHMM_glimmerT_4156-T1
Valid prediction for pasa_asmbl_23304.p1
Valid prediction for snap_scaffold_2-snap.1637-T1
Valid prediction for GlimmerHMM_glimmerT_4137-T1
Valid prediction for CodingQuarry_transcript_28623-T1
Couldn't classify 188608, 188650
Couldn't classify 188996, 189144
Sorry, prediction pasa_asmbl_23300.p1 fails validation.
(TAC)	 AT	188608-188650	GT	CGG
(AGA)	 AG	188778-188900	GT	TGG
(CAG)	 AG	188996-189144	GC	GAG
-recovered pasa_asmbl_23300.p1, internal, 188778, 188900
-recovered pasa_asmbl_23300.p1, internal, 188996, 189144
Valid prediction for GlimmerHMM_glimmerT_4148-T1
Valid prediction for GlimmerHMM_glimmerT_4134-T1
Valid prediction for snap_scaffold_2-snap.1659-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1644-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 114352, 114534
Sorry, prediction pasa_asmbl_23311.p2 fails validation.
(CAG)	 AC	114352-114534	GT	AGG
(GGC)	 AG	115236-115427	GT	AGG
(GTG)	 AG	115520-115694	GT	AGG
(AAA)	 AG	116158-116324	AT	GAA
-recovered pasa_asmbl_23311.p2, terminal, 116158, 116324
-recovered pasa_asmbl_23311.p2, internal, 115236, 115427
-recovered pasa_asmbl_23311.p2, internal, 115520, 115694
Valid prediction for snap_scaffold_2-snap.1647-T1
Valid prediction for GlimmerHMM_glimmerT_4152-T1
Valid prediction for snap_scaffold_2-snap.1641-T1
Valid prediction for HiQ_model.g2797.t1
Valid prediction for HiQ_model.g2795.t1
Valid prediction for Augustus_model.g2792.t1
Valid prediction for Augustus_model.g2803.t1
Valid prediction for Augustus_model.g2802.t1
Valid prediction for GlimmerHMM_glimmerT_4143-T1
Valid prediction for snap_scaffold_2-snap.1657-T1
Valid prediction for Augustus_model.g2791.t1
Valid prediction for CodingQuarry_transcript_28617-T1
Valid prediction for snap_scaffold_2-snap.1665-T1
Valid prediction for snap_scaffold_2-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_4142-T1
Valid prediction for HiQ_model.g2787.t1
Valid prediction for GlimmerHMM_glimmerT_4146-T1
Valid prediction for GlimmerHMM_glimmerT_4161-T1
Valid prediction for snap_scaffold_2-snap.1638-T1
Valid prediction for GlimmerHMM_glimmerT_4163-T1
Couldn't classify 25513, 25705
Sorry, prediction pasa_asmbl_23319.p1 fails validation.
(CCT)	 CA	25513-25705	GT	AGG
(ACG)	 AG	26776-26957	GT	AGG
(CTT)	 AG	27144-27221	GT	AGG
(GCC)	 AG	28142-28279	GT	CTG
(GGA)	 AG	28389-28475	CG	GAC
-recovered pasa_asmbl_23319.p1, terminal, 28389, 28475
-recovered pasa_asmbl_23319.p1, internal, 26776, 26957
-recovered pasa_asmbl_23319.p1, internal, 27144, 27221
-recovered pasa_asmbl_23319.p1, internal, 28142, 28279
Valid prediction for snap_scaffold_2-snap.1648-T1
Valid prediction for GlimmerHMM_glimmerT_4141-T1
Valid prediction for snap_scaffold_2-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_4136-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 66889, rend_intergenic: 63868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150086, rend_intergenic: 147751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170676, rend_intergenic: 169994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263093
-exon list size: 340


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 66889, rend_intergenic: 63868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150086, rend_intergenic: 147751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170676, rend_intergenic: 169994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support