-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_216008-445053

-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_51-T1
Valid prediction for snap_scaffold_1-snap.70-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.59_t
Valid prediction for GlimmerHMM_glimmerT_58-T1
Valid prediction for GlimmerHMM_glimmerT_28-T1
Valid prediction for GeneMark_model.42_t
Valid prediction for snap_scaffold_1-snap.48-T1
Valid prediction for snap_scaffold_1-snap.62-T1
Valid prediction for snap_scaffold_1-snap.61-T1
Valid prediction for Augustus_model.g24.t1
Valid prediction for snap_scaffold_1-snap.75-T1
Valid prediction for snap_scaffold_1-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_57-T1
Valid prediction for GeneMark_model.36_t
Valid prediction for GlimmerHMM_glimmerT_47-T1
Valid prediction for snap_scaffold_1-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_29-T1
Valid prediction for Augustus_model.g36.t1
Valid prediction for Augustus_model.g43.t1
Valid prediction for snap_scaffold_1-snap.47-T1
Valid prediction for GlimmerHMM_glimmerT_61-T1
Valid prediction for Augustus_model.g39.t1
Valid prediction for GeneMark_model.47_t
Valid prediction for snap_scaffold_1-snap.73-T1
Valid prediction for GeneMark_model.49_t
Valid prediction for GeneMark_model.54_t
Valid prediction for GeneMark_model.34_t
Valid prediction for GlimmerHMM_glimmerT_41-T1
Valid prediction for Augustus_model.g33.t1
Valid prediction for Augustus_model.g38.t1
Valid prediction for snap_scaffold_1-snap.60-T1
Valid prediction for Augustus_model.g25.t1
Valid prediction for snap_scaffold_1-snap.76-T1
Valid prediction for snap_scaffold_1-snap.79-T1
Valid prediction for snap_scaffold_1-snap.51-T1
Valid prediction for snap_scaffold_1-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_56-T1
Valid prediction for GeneMark_model.41_t
Valid prediction for GlimmerHMM_glimmerT_27-T1
Valid prediction for GeneMark_model.35_t
Valid prediction for snap_scaffold_1-snap.56-T1
Valid prediction for GeneMark_model.50_t
Valid prediction for GeneMark_model.40_t
Valid prediction for snap_scaffold_1-snap.84-T1
Valid prediction for snap_scaffold_1-snap.50-T1
Valid prediction for snap_scaffold_1-snap.69-T1
Valid prediction for GeneMark_model.55_t
Valid prediction for Augustus_model.g29.t1
Valid prediction for snap_scaffold_1-snap.89-T1
Valid prediction for snap_scaffold_1-snap.66-T1
Valid prediction for snap_scaffold_1-snap.64-T1
Valid prediction for Augustus_model.g23.t1
Valid prediction for Augustus_model.g32.t1
Valid prediction for snap_scaffold_1-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_32-T1
Valid prediction for GeneMark_model.33_t
Valid prediction for GlimmerHMM_glimmerT_33-T1
Valid prediction for snap_scaffold_1-snap.83-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.78-T1
Valid prediction for GlimmerHMM_glimmerT_45-T1
Valid prediction for GeneMark_model.31_t
Valid prediction for GlimmerHMM_glimmerT_38-T1
Valid prediction for GeneMark_model.57_t
Valid prediction for snap_scaffold_1-snap.49-T1
Valid prediction for Augustus_model.g35.t1
Valid prediction for GeneMark_model.30_t
Valid prediction for GeneMark_model.58_t
Valid prediction for GeneMark_model.52_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 GeneMark_model.37_t
Valid prediction for snap_scaffold_1-snap.88-T1
Valid prediction for GlimmerHMM_glimmerT_30-T1
Valid prediction for snap_scaffold_1-snap.86-T1
Valid prediction for snap_scaffold_1-snap.87-T1
Valid prediction for Augustus_model.g45.t1
Valid prediction for GeneMark_model.51_t
Valid prediction for Augustus_model.g46.t1
Valid prediction for Augustus_model.g44.t1
Valid prediction for GlimmerHMM_glimmerT_52-T1
Valid prediction for snap_scaffold_1-snap.54-T1
Valid prediction for GeneMark_model.48_t
Valid prediction for GeneMark_model.44_t
Valid prediction for GlimmerHMM_glimmerT_36-T1
Valid prediction for GlimmerHMM_glimmerT_40-T1
Valid prediction for GeneMark_model.60_t
Valid prediction for GlimmerHMM_glimmerT_39-T1
Valid prediction for Augustus_model.g28.t1
Valid prediction for snap_scaffold_1-snap.80-T1
Valid prediction for snap_scaffold_1-snap.68-T1
Valid prediction for Augustus_model.g30.t1
Valid prediction for GeneMark_model.43_t
Valid prediction for GlimmerHMM_glimmerT_49-T1
Valid prediction for GlimmerHMM_glimmerT_62-T1
Valid prediction for GlimmerHMM_glimmerT_43-T1
Valid prediction for snap_scaffold_1-snap.57-T1
Valid prediction for GlimmerHMM_glimmerT_53-T1
Valid prediction for snap_scaffold_1-snap.77-T1
Valid prediction for GeneMark_model.61_t
Couldn't classify 25943, 26005
Couldn't classify 26688, 27181
Sorry, prediction pasa_asmbl_21.p1 fails validation.
(GAA)	 GT	25943-26005	GT	TGG
(CAA)	 AG	26200-26428	GT	AAG
(TTG)	 AG	26688-27181	TA	AGT
-recovered pasa_asmbl_21.p1, internal, 26200, 26428
Valid prediction for GlimmerHMM_glimmerT_59-T1
Couldn't classify 27494, 28461
Couldn't classify 30365, 30527
Sorry, prediction pasa_asmbl_20.p1 fails validation.
(GAA)	 TC	27494-28461	GT	CTG
(GCT)	 AG	28604-28765	GT	AGG
(GCT)	 AG	29270-29440	GT	AGG
(GCT)	 AG	30365-30527	GG	TGG
-recovered pasa_asmbl_20.p1, internal, 28604, 28765
-recovered pasa_asmbl_20.p1, internal, 29270, 29440
Valid prediction for Augustus_model.g34.t1
Valid prediction for GeneMark_model.53_t
Valid prediction for GlimmerHMM_glimmerT_44-T1
Valid prediction for GlimmerHMM_glimmerT_55-T1
Valid prediction for GeneMark_model.56_t
Couldn't classify 194002, 194184
Sorry, prediction pasa_asmbl_16.p1 fails validation.
(GGC)	 CA	194002-194184	GT	GGG
(GTG)	 AG	194297-194528	GT	AGG
(TGG)	 AG	196773-197455	CC	GAC
-recovered pasa_asmbl_16.p1, terminal, 196773, 197455
-recovered pasa_asmbl_16.p1, internal, 194297, 194528
Valid prediction for Augustus_model.g41.t1
Valid prediction for Augustus_model.g26.t1
Valid prediction for GlimmerHMM_glimmerT_37-T1
Valid prediction for GeneMark_model.45_t
Valid prediction for snap_scaffold_1-snap.58-T1
Valid prediction for Augustus_model.g31.t1
Valid prediction for GlimmerHMM_glimmerT_46-T1
Valid prediction for GeneMark_model.32_t
Valid prediction for snap_scaffold_1-snap.67-T1
Valid prediction for GlimmerHMM_glimmerT_50-T1
Valid prediction for GlimmerHMM_glimmerT_31-T1
Valid prediction for snap_scaffold_1-snap.53-T1
Valid prediction for snap_scaffold_1-snap.82-T1
Valid prediction for Augustus_model.g42.t1
Valid prediction for snap_scaffold_1-snap.81-T1
Valid prediction for Augustus_model.g40.t1
Valid prediction for snap_scaffold_1-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_48-T1
Valid prediction for GlimmerHMM_glimmerT_35-T1
Valid prediction for GlimmerHMM_glimmerT_42-T1
Valid prediction for Augustus_model.g27.t1
Valid prediction for GeneMark_model.38_t
Couldn't classify 20287, 20790
Sorry, prediction pasa_asmbl_22.p1 fails validation.
(ATA)	 CA	20287-20790	AT	AGA
Valid prediction for GeneMark_model.39_t
Valid prediction for snap_scaffold_1-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_60-T1
Valid prediction for snap_scaffold_1-snap.71-T1
Valid prediction for snap_scaffold_1-snap.59-T1
Valid prediction for snap_scaffold_1-snap.90-T1
Valid prediction for snap_scaffold_1-snap.85-T1
Valid prediction for GeneMark_model.46_t
Valid prediction for GlimmerHMM_glimmerT_54-T1
Valid prediction for Augustus_model.g37.t1
Couldn't classify 31151, 31196
Couldn't classify 31524, 31774
Sorry, prediction pasa_asmbl_18.p1 fails validation.
(GTG)	 GT	31151-31196	GT	ATG
(ATG)	 AG	31524-31774	GN	GAG
Valid prediction for GlimmerHMM_glimmerT_34-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25934, rend_intergenic: 23768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117915, rend_intergenic: 116623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140198, rend_intergenic: 138928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224226, rend_intergenic: 222344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229046
-exon list size: 519


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
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    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 25934, rend_intergenic: 23768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117915, rend_intergenic: 116623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140198, rend_intergenic: 138928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224226, rend_intergenic: 222344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support