-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_15889545-16008420

-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.3015_t
Valid prediction for snap_scaffold_1-snap.2792-T1
Valid prediction for GeneMark_model.3013_t
Valid prediction for GeneMark_model.3017_t
Valid prediction for Augustus_model.g1574.t1
Valid prediction for GeneMark_model.3018_t
Valid prediction for GeneMark_model.3031_t
Valid prediction for GlimmerHMM_glimmerT_2139-T1
Valid prediction for GlimmerHMM_glimmerT_2146-T1
Valid prediction for GeneMark_model.3026_t
Valid prediction for GlimmerHMM_glimmerT_2153-T1
Valid prediction for GeneMark_model.3028_t
Valid prediction for GeneMark_model.3002_t
Valid prediction for snap_scaffold_1-snap.2801-T1
Valid prediction for snap_scaffold_1-snap.2804-T1
Valid prediction for GeneMark_model.3007_t
Valid prediction for snap_scaffold_1-snap.2788-T1
Valid prediction for snap_scaffold_1-snap.2798-T1
Valid prediction for Augustus_model.g1578.t1
Valid prediction for GeneMark_model.3020_t
Valid prediction for GeneMark_model.3005_t
Valid prediction for snap_scaffold_1-snap.2790-T1
Valid prediction for Augustus_model.g1572.t1
Valid prediction for Augustus_model.g1575.t1
Valid prediction for GlimmerHMM_glimmerT_2142-T1
Valid prediction for GlimmerHMM_glimmerT_2144-T1
Valid prediction for snap_scaffold_1-snap.2808-T1
Valid prediction for snap_scaffold_1-snap.2789-T1
Valid prediction for GlimmerHMM_glimmerT_2152-T1
Valid prediction for snap_scaffold_1-snap.2806-T1
Couldn't classify 97972, 98185
Sorry, prediction pasa_asmbl_2439.p1 fails validation.
(CAG)	 AG	97972-98185	GT	AGG
(TTC)	 AG	98357-98403	GT	ACG
(CCC)	 AG	98522-98720	GT	AGG
(CAG)	 AG	98837-98988	AC	GAA
-recovered pasa_asmbl_2439.p1, terminal, 98837, 98988
-recovered pasa_asmbl_2439.p1, internal, 97972, 98185
-recovered pasa_asmbl_2439.p1, internal, 98357, 98403
-recovered pasa_asmbl_2439.p1, internal, 98522, 98720
Valid prediction for Augustus_model.g1576.t1
Valid prediction for GlimmerHMM_glimmerT_2150-T1
Valid prediction for GlimmerHMM_glimmerT_2155-T1
Valid prediction for snap_scaffold_1-snap.2803-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.3027_t
Valid prediction for GeneMark_model.3022_t
Valid prediction for GeneMark_model.3003_t
Valid prediction for GeneMark_model.3023_t
Valid prediction for GeneMark_model.3033_t
Valid prediction for snap_scaffold_1-snap.2802-T1
Valid prediction for Augustus_model.g1569.t1
Valid prediction for GeneMark_model.3009_t
Valid prediction for GeneMark_model.3004_t
Valid prediction for snap_scaffold_1-snap.2793-T1
Valid prediction for GeneMark_model.3010_t
Valid prediction for GeneMark_model.3008_t
Valid prediction for snap_scaffold_1-snap.2799-T1
Valid prediction for Augustus_model.g1571.t1
Valid prediction for pasa_asmbl_973.p1
Valid prediction for snap_scaffold_1-snap.2794-T1
Valid prediction for GlimmerHMM_glimmerT_2141-T1
Valid prediction for snap_scaffold_1-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_2140-T1
Valid prediction for snap_scaffold_1-snap.2807-T1
Valid prediction for Augustus_model.g1579.t1
Valid prediction for GlimmerHMM_glimmerT_2143-T1
Valid prediction for snap_scaffold_1-snap.2795-T1
Valid prediction for GeneMark_model.3025_t
Valid prediction for GeneMark_model.3021_t
Valid prediction for GlimmerHMM_glimmerT_2151-T1
Valid prediction for snap_scaffold_1-snap.2810-T1
Valid prediction for Augustus_model.g1573.t1
Valid prediction for GeneMark_model.3012_t
Valid prediction for Augustus_model.g1577.t1
Valid prediction for GlimmerHMM_glimmerT_2149-T1
Couldn't classify 63611, 63790
Couldn't classify 67548, 67656
Sorry, prediction pasa_asmbl_972.p1 fails validation.
(GGA)	 GG	63611-63790	GT	AGG
(GCA)	 AG	64857-64964	GT	CGG
(CTC)	 AG	65657-65764	GT	GGG
(AAA)	 AG	65983-66055	GT	GAG
(AAT)	 AG	66816-66873	GT	TGG
(GAT)	 AG	67548-67656	GT	GGG
-recovered pasa_asmbl_972.p1, internal, 64857, 64964
-recovered pasa_asmbl_972.p1, internal, 65657, 65764
-recovered pasa_asmbl_972.p1, internal, 65983, 66055
-recovered pasa_asmbl_972.p1, internal, 66816, 66873
-recovered pasa_asmbl_972.p1, internal, 67548, 67656
Valid prediction for GeneMark_model.3024_t
Valid prediction for GeneMark_model.3006_t
Valid prediction for GeneMark_model.3014_t
Valid prediction for CodingQuarry_transcript_2940-T1
Valid prediction for snap_scaffold_1-snap.2791-T1
Valid prediction for GeneMark_model.3016_t
Valid prediction for GlimmerHMM_glimmerT_2157-T1
Valid prediction for GlimmerHMM_glimmerT_2156-T1
Valid prediction for GlimmerHMM_glimmerT_2148-T1
Valid prediction for GeneMark_model.3001_t
Valid prediction for GlimmerHMM_glimmerT_2145-T1
Valid prediction for GlimmerHMM_glimmerT_2158-T1
Valid prediction for GeneMark_model.3030_t
Valid prediction for GeneMark_model.3029_t
Valid prediction for GeneMark_model.3019_t
Valid prediction for snap_scaffold_1-snap.2809-T1
Couldn't classify 71146, 71223
Sorry, prediction pasa_asmbl_970.p1 fails validation.
(ATT)	 AG	71146-71223	GT	AGG
(GGA)	 AG	71356-71469	GT	AGG
(ATG)	 AG	72027-72161	GC	GAG
add_exon() Sorry, pasa_asmbl_970.p1 72027-72161-initial-1 is invalid.
-recovered pasa_asmbl_970.p1, initial, 72027, 72161
-recovered pasa_asmbl_970.p1, terminal, 72027, 72161
-recovered pasa_asmbl_970.p1, internal, 71146, 71223
-recovered pasa_asmbl_970.p1, internal, 71356, 71469
-recovered pasa_asmbl_970.p1, internal, 72027, 72161
Valid prediction for GlimmerHMM_glimmerT_2147-T1
Valid prediction for snap_scaffold_1-snap.2800-T1
Valid prediction for GeneMark_model.3032_t
Valid prediction for GlimmerHMM_glimmerT_2154-T1
Valid prediction for snap_scaffold_1-snap.2805-T1
Valid prediction for snap_scaffold_1-snap.2787-T1
Valid prediction for snap_scaffold_1-snap.2796-T1
Valid prediction for GeneMark_model.3011_t
Valid prediction for Augustus_model.g1570.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17961, rend_intergenic: 7279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30332, rend_intergenic: 21491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64452, rend_intergenic: 55887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71861, rend_intergenic: 69940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87509, rend_intergenic: 85382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 118876
-exon list size: 373


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
6.9    
7.2    
7.5    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.7    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.3    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.5    
92.8    
93.1    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 17961, rend_intergenic: 7279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30332, rend_intergenic: 21491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64452, rend_intergenic: 55887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71861, rend_intergenic: 69940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87509, rend_intergenic: 85382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support