-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_18352084-18563543

-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 snap_scaffold_4-snap.3783-T1
Valid prediction for GlimmerHMM_glimmerT_11123-T1
Valid prediction for Augustus_model.g7302.t1
Valid prediction for Augustus_model.g7314.t1
Valid prediction for snap_scaffold_4-snap.3807-T1
Valid prediction for snap_scaffold_4-snap.3793-T1
Valid prediction for GlimmerHMM_glimmerT_11127-T1
Valid prediction for GlimmerHMM_glimmerT_11121-T1
Valid prediction for snap_scaffold_4-snap.3791-T1
Valid prediction for snap_scaffold_4-snap.3771-T1
Valid prediction for GlimmerHMM_glimmerT_11128-T1
Valid prediction for snap_scaffold_4-snap.3801-T1
Valid prediction for GlimmerHMM_glimmerT_11135-T1
Valid prediction for snap_scaffold_4-snap.3768-T1
Valid prediction for GlimmerHMM_glimmerT_11131-T1
Valid prediction for snap_scaffold_4-snap.3797-T1
Valid prediction for snap_scaffold_4-snap.3786-T1
Valid prediction for Augustus_model.g7305.t1
Valid prediction for snap_scaffold_4-snap.3770-T1
Valid prediction for snap_scaffold_4-snap.3782-T1
Valid prediction for Augustus_model.g7306.t1
Valid prediction for snap_scaffold_4-snap.3784-T1
Valid prediction for snap_scaffold_4-snap.3774-T1
Valid prediction for snap_scaffold_4-snap.3776-T1
Valid prediction for snap_scaffold_4-snap.3775-T1
Valid prediction for GlimmerHMM_glimmerT_11122-T1
Valid prediction for snap_scaffold_4-snap.3794-T1
Valid prediction for snap_scaffold_4-snap.3772-T1
Valid prediction for Augustus_model.g7313.t1
Valid prediction for GlimmerHMM_glimmerT_11134-T1
Valid prediction for snap_scaffold_4-snap.3780-T1
Valid prediction for snap_scaffold_4-snap.3789-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_4-snap.3803-T1
Valid prediction for GlimmerHMM_glimmerT_11130-T1
Valid prediction for CodingQuarry_transcript_49373-T1
Valid prediction for pasa_asmbl_43378.p1
Valid prediction for snap_scaffold_4-snap.3790-T1
Valid prediction for snap_scaffold_4-snap.3779-T1
Valid prediction for HiQ_model.g7311.t1
Valid prediction for GlimmerHMM_glimmerT_11125-T1
Valid prediction for Augustus_model.g7307.t1
Valid prediction for snap_scaffold_4-snap.3785-T1
Valid prediction for snap_scaffold_4-snap.3781-T1
Valid prediction for GlimmerHMM_glimmerT_11120-T1
Valid prediction for HiQ_model.g7309.t1
Valid prediction for snap_scaffold_4-snap.3798-T1
Valid prediction for GlimmerHMM_glimmerT_11137-T1
Valid prediction for snap_scaffold_4-snap.3777-T1
Valid prediction for GlimmerHMM_glimmerT_11119-T1
Valid prediction for GlimmerHMM_glimmerT_11133-T1
Valid prediction for CodingQuarry_transcript_49374-T1
Valid prediction for snap_scaffold_4-snap.3805-T1
Couldn't classify 101665, 102819
Sorry, prediction pasa_asmbl_43370.p1 fails validation.
(CTC)	 GG	101665-102819	AA	CCA
Valid prediction for snap_scaffold_4-snap.3773-T1
Valid prediction for CodingQuarry_transcript_49372-T1
Valid prediction for snap_scaffold_4-snap.3787-T1
Valid prediction for snap_scaffold_4-snap.3778-T1
Valid prediction for snap_scaffold_4-snap.3769-T1
Valid prediction for GlimmerHMM_glimmerT_11126-T1
Valid prediction for pasa_asmbl_43376.p3
Couldn't classify 103042, 103107
Couldn't classify 103696, 103765
Sorry, prediction pasa_asmbl_43369.p1 fails validation.
(TTT)	 CG	103042-103107	GT	GGG
(GAG)	 AG	103270-103538	GT	AGG
(ATT)	 AG	103696-103765	AA	CGA
-recovered pasa_asmbl_43369.p1, internal, 103270, 103538
Valid prediction for snap_scaffold_4-snap.3806-T1
Couldn't classify 106298, 106431
Couldn't classify 111241, 111481
Sorry, prediction pasa_asmbl_43368.p1 fails validation.
(GAG)	 AC	106298-106431	GT	AAG
(GTT)	 AG	107147-107315	GT	TGG
(CTA)	 AG	107708-107876	GT	AGG
(GAA)	 AG	108051-108144	GT	AGG
(GTT)	 AG	108971-109087	GT	AGG
(CAC)	 AG	109321-109451	GT	TGG
(GTG)	 AG	109856-110038	GT	GGG
(GCT)	 AG	110611-110723	GT	AGG
(GTG)	 AG	110820-110947	GT	GGG
(GCC)	 AG	111241-111481	GG	CGG
-recovered pasa_asmbl_43368.p1, internal, 107147, 107315
-recovered pasa_asmbl_43368.p1, internal, 107708, 107876
-recovered pasa_asmbl_43368.p1, internal, 108051, 108144
-recovered pasa_asmbl_43368.p1, internal, 108971, 109087
-recovered pasa_asmbl_43368.p1, internal, 109321, 109451
-recovered pasa_asmbl_43368.p1, internal, 109856, 110038
-recovered pasa_asmbl_43368.p1, internal, 110611, 110723
-recovered pasa_asmbl_43368.p1, internal, 110820, 110947
Valid prediction for Augustus_model.g7299.t1
Valid prediction for snap_scaffold_4-snap.3799-T1
Valid prediction for snap_scaffold_4-snap.3792-T1
Valid prediction for HiQ_model.g7310.t1
Valid prediction for GlimmerHMM_glimmerT_11129-T1
Valid prediction for GlimmerHMM_glimmerT_11118-T1
Valid prediction for Augustus_model.g7303.t1
Couldn't classify 65819, 66049
Couldn't classify 67326, 67366
Sorry, prediction pasa_asmbl_43373.p1 fails validation.
(AAT)	 GG	65819-66049	GT	TGG
(GTA)	 AG	66478-66670	GT	AGG
(TGT)	 AG	67326-67366	GA	AGG
-recovered pasa_asmbl_43373.p1, internal, 66478, 66670
Valid prediction for CodingQuarry_transcript_49371-T1
Valid prediction for Augustus_model.g7312.t1
Valid prediction for GlimmerHMM_glimmerT_11124-T1
Valid prediction for Augustus_model.g7308.t1
Valid prediction for CodingQuarry_transcript_49376-T1
Valid prediction for Augustus_model.g7301.t1
Valid prediction for GlimmerHMM_glimmerT_11132-T1
Valid prediction for Augustus_model.g7304.t1
Valid prediction for HiQ_model.g7315.t1
Valid prediction for snap_scaffold_4-snap.3804-T1
Valid prediction for GlimmerHMM_glimmerT_11136-T1
Valid prediction for snap_scaffold_4-snap.3800-T1
Valid prediction for CodingQuarry_transcript_49370-T1
Valid prediction for snap_scaffold_4-snap.3788-T1
Valid prediction for snap_scaffold_4-snap.3795-T1
Valid prediction for CodingQuarry_transcript_49375-T1
Valid prediction for Augustus_model.g7300.t1
Couldn't classify 73363, 73506
Couldn't classify 75740, 75868
Sorry, prediction pasa_asmbl_43372.p1 fails validation.
(GAG)	 AT	73363-73506	GT	AGG
(GCA)	 AG	74623-74712	GT	TGG
(TAT)	 AG	75137-75286	GT	AGG
(AAC)	 AG	75740-75868	GT	ATG
-recovered pasa_asmbl_43372.p1, internal, 74623, 74712
-recovered pasa_asmbl_43372.p1, internal, 75137, 75286
-recovered pasa_asmbl_43372.p1, internal, 75740, 75868
Valid prediction for snap_scaffold_4-snap.3796-T1
Valid prediction for snap_scaffold_4-snap.3802-T1
Valid prediction for pasa_asmbl_43381.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18231, rend_intergenic: 5535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30391, rend_intergenic: 18286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44235, rend_intergenic: 33849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82255, rend_intergenic: 49399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90932, rend_intergenic: 82944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97533, rend_intergenic: 94037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110066, rend_intergenic: 101362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123375, rend_intergenic: 116111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126331, rend_intergenic: 123607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126679, rend_intergenic: 126368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132975, rend_intergenic: 132109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145573, rend_intergenic: 133265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150700, rend_intergenic: 145783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151872, rend_intergenic: 151046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161148, rend_intergenic: 152403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162168, rend_intergenic: 161400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169683, rend_intergenic: 167166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191169, rend_intergenic: 182331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206749, rend_intergenic: 196060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211460
-exon list size: 353


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.4    
19.7    
20.0    
20.3    
20.6    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
40.0    
40.3    
40.6    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.4    
59.7    
60.0    
60.3    
60.6    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.4    
79.7    
80.0    
80.3    
80.6    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 18231, rend_intergenic: 5535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30391, rend_intergenic: 18286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44235, rend_intergenic: 33849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82255, rend_intergenic: 49399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90932, rend_intergenic: 82944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97533, rend_intergenic: 94037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110066, rend_intergenic: 101362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123375, rend_intergenic: 116111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126331, rend_intergenic: 123607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126679, rend_intergenic: 126368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132975, rend_intergenic: 132109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145573, rend_intergenic: 133265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150700, rend_intergenic: 145783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151872, rend_intergenic: 151046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161148, rend_intergenic: 152403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162168, rend_intergenic: 161400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169683, rend_intergenic: 167166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191169, rend_intergenic: 182331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206749, rend_intergenic: 196060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support