-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_14752776-14984245

-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_17-snap.3105-T1
Valid prediction for GlimmerHMM_glimmerT_41585-T1
Valid prediction for snap_scaffold_17-snap.3103-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_41588-T1
Valid prediction for snap_scaffold_17-snap.3086-T1
Valid prediction for snap_scaffold_17-snap.3084-T1
Couldn't classify 118919, 119089
Sorry, prediction pasa_asmbl_19431.p1 fails validation.
(GGG)	 CA	118919-119089	GT	AGG
(GAT)	 AG	119541-119741	GT	AGG
(GAC)	 AG	120699-120889	GT	TGG
(GTA)	 AG	121111-121210	GT	AGG
(GTG)	 AG	121611-121748	GT	GAG
-recovered pasa_asmbl_19431.p1, terminal, 121611, 121748
-recovered pasa_asmbl_19431.p1, internal, 119541, 119741
-recovered pasa_asmbl_19431.p1, internal, 120699, 120889
-recovered pasa_asmbl_19431.p1, internal, 121111, 121210
-recovered pasa_asmbl_19431.p1, internal, 121611, 121748
Valid prediction for GlimmerHMM_glimmerT_41580-T1
Valid prediction for GlimmerHMM_glimmerT_41576-T1
Valid prediction for GlimmerHMM_glimmerT_41555-T1
Couldn't classify 191107, 191595
Sorry, prediction pasa_asmbl_19434.p2 fails validation.
(CAC)	 CT	191107-191595	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_41565-T1
Valid prediction for GlimmerHMM_glimmerT_41559-T1
Valid prediction for GlimmerHMM_glimmerT_41572-T1
Valid prediction for snap_scaffold_17-snap.3115-T1
Valid prediction for snap_scaffold_17-snap.3104-T1
Valid prediction for snap_scaffold_17-snap.3109-T1
Couldn't classify 114557, 114782
Sorry, prediction pasa_asmbl_19502.p1 fails validation.
(ACC)	 TC	114557-114782	GT	GGG
(GTG)	 AG	114990-115168	GT	GTG
(GTG)	 AG	115874-116164	AA	AAA
-recovered pasa_asmbl_19502.p1, terminal, 115874, 116164
-recovered pasa_asmbl_19502.p1, internal, 114990, 115168
Valid prediction for GlimmerHMM_glimmerT_41558-T1
Valid prediction for GlimmerHMM_glimmerT_41571-T1
Valid prediction for GlimmerHMM_glimmerT_41567-T1
Valid prediction for snap_scaffold_17-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_41554-T1
Valid prediction for snap_scaffold_17-snap.3082-T1
Valid prediction for snap_scaffold_17-snap.3111-T1
Valid prediction for GlimmerHMM_glimmerT_41582-T1
Valid prediction for snap_scaffold_17-snap.3117-T1
Valid prediction for snap_scaffold_17-snap.3080-T1
Valid prediction for snap_scaffold_17-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_41574-T1
Valid prediction for GlimmerHMM_glimmerT_41573-T1
Valid prediction for GlimmerHMM_glimmerT_41584-T1
Valid prediction for CodingQuarry_transcript_22273-T1
Valid prediction for GlimmerHMM_glimmerT_41560-T1
Valid prediction for snap_scaffold_17-snap.3088-T1
Valid prediction for snap_scaffold_17-snap.3093-T1
Valid prediction for snap_scaffold_17-snap.3079-T1
Valid prediction for snap_scaffold_17-snap.3102-T1
Valid prediction for pasa_asmbl_19535.p1
Valid prediction for GlimmerHMM_glimmerT_41579-T1
Valid prediction for snap_scaffold_17-snap.3095-T1
Valid prediction for snap_scaffold_17-snap.3100-T1
Valid prediction for snap_scaffold_17-snap.3076-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_17-snap.3087-T1
Valid prediction for GlimmerHMM_glimmerT_41587-T1
Valid prediction for snap_scaffold_17-snap.3121-T1
Valid prediction for snap_scaffold_17-snap.3118-T1
Valid prediction for snap_scaffold_17-snap.3106-T1
Valid prediction for GlimmerHMM_glimmerT_41575-T1
Valid prediction for snap_scaffold_17-snap.3083-T1
Valid prediction for GlimmerHMM_glimmerT_41569-T1
Valid prediction for snap_scaffold_17-snap.3078-T1
Valid prediction for GlimmerHMM_glimmerT_41581-T1
Valid prediction for snap_scaffold_17-snap.3096-T1
Valid prediction for snap_scaffold_17-snap.3091-T1
Valid prediction for snap_scaffold_17-snap.3085-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41561-T1
Valid prediction for snap_scaffold_17-snap.3094-T1
Valid prediction for GlimmerHMM_glimmerT_41578-T1
Valid prediction for GlimmerHMM_glimmerT_41566-T1
Valid prediction for GlimmerHMM_glimmerT_41583-T1
Valid prediction for snap_scaffold_17-snap.3092-T1
Valid prediction for pasa_asmbl_18452.p1
Valid prediction for GlimmerHMM_glimmerT_41557-T1
Valid prediction for snap_scaffold_17-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_41577-T1
Valid prediction for snap_scaffold_17-snap.3081-T1
Valid prediction for snap_scaffold_17-snap.3116-T1
Valid prediction for GlimmerHMM_glimmerT_41570-T1
Valid prediction for GlimmerHMM_glimmerT_41562-T1
Valid prediction for snap_scaffold_17-snap.3098-T1
Valid prediction for snap_scaffold_17-snap.3097-T1
Valid prediction for GlimmerHMM_glimmerT_41586-T1
Valid prediction for snap_scaffold_17-snap.3101-T1
Valid prediction for snap_scaffold_17-snap.3107-T1
Valid prediction for snap_scaffold_17-snap.3077-T1
Valid prediction for GlimmerHMM_glimmerT_41564-T1
Valid prediction for snap_scaffold_17-snap.3075-T1
Valid prediction for snap_scaffold_17-snap.3112-T1
Valid prediction for snap_scaffold_17-snap.3114-T1
Valid prediction for GlimmerHMM_glimmerT_41568-T1
Valid prediction for snap_scaffold_17-snap.3120-T1
Valid prediction for snap_scaffold_17-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_41563-T1
Valid prediction for snap_scaffold_17-snap.3089-T1
Valid prediction for snap_scaffold_17-snap.3110-T1
Valid prediction for snap_scaffold_17-snap.3099-T1
Valid prediction for snap_scaffold_17-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_41556-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5700, rend_intergenic: 1617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36105, rend_intergenic: 8427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40192, rend_intergenic: 36550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51673, rend_intergenic: 45471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55591, rend_intergenic: 52845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67235, rend_intergenic: 56508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72274, rend_intergenic: 67752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74236, rend_intergenic: 72483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77144, rend_intergenic: 74820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83781, rend_intergenic: 79132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100862, rend_intergenic: 98988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102880, rend_intergenic: 101176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103973, rend_intergenic: 103225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116939, rend_intergenic: 104336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122603, rend_intergenic: 120720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144726, rend_intergenic: 130300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165808, rend_intergenic: 149847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170722, rend_intergenic: 166163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173097, rend_intergenic: 170830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178179, rend_intergenic: 174040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199941, rend_intergenic: 190482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210895, rend_intergenic: 208697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223376, rend_intergenic: 216821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227303, rend_intergenic: 225096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231470
-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 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 5700, rend_intergenic: 1617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36105, rend_intergenic: 8427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40192, rend_intergenic: 36550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51673, rend_intergenic: 45471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55591, rend_intergenic: 52845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67235, rend_intergenic: 56508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72274, rend_intergenic: 67752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74236, rend_intergenic: 72483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77144, rend_intergenic: 74820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83781, rend_intergenic: 79132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100862, rend_intergenic: 98988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102880, rend_intergenic: 101176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103973, rend_intergenic: 103225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116939, rend_intergenic: 104336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122603, rend_intergenic: 120720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144726, rend_intergenic: 130300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165808, rend_intergenic: 149847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170722, rend_intergenic: 166163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173097, rend_intergenic: 170830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178179, rend_intergenic: 174040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199941, rend_intergenic: 190482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210895, rend_intergenic: 208697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223376, rend_intergenic: 216821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227303, rend_intergenic: 225096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 23896
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17132
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16382
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 5701 - 16382
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support