-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_20820146-21006579

-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_1-snap.3906-T1
Valid prediction for GlimmerHMM_glimmerT_2797-T1
Valid prediction for CodingQuarry_transcript_3044-T1
Valid prediction for snap_scaffold_1-snap.3896-T1
Valid prediction for snap_scaffold_1-snap.3927-T1
Valid prediction for Augustus_model.g1989.t1
Valid prediction for snap_scaffold_1-snap.3907-T1
Valid prediction for GlimmerHMM_glimmerT_2800-T1
Valid prediction for GlimmerHMM_glimmerT_2807-T1
Valid prediction for Augustus_model.g1977.t1
Valid prediction for snap_scaffold_1-snap.3919-T1
Couldn't classify 78290, 78673
Sorry, prediction pasa_asmbl_2661.p2 fails validation.
(GGT)	 CA	78290-78673	GG	AGG
Valid prediction for GlimmerHMM_glimmerT_2806-T1
Valid prediction for Augustus_model.g1980.t1
Valid prediction for GlimmerHMM_glimmerT_2802-T1
Valid prediction for GlimmerHMM_glimmerT_2803-T1
Valid prediction for snap_scaffold_1-snap.3886-T1
Couldn't classify 170590, 170760
Sorry, prediction pasa_asmbl_2668.p2 fails validation.
(ATG)	 GC	168674-168832	GT	AGG
(GTG)	 AG	170590-170760	CC	CGC
-recovered pasa_asmbl_2668.p2, initial, 168674, 168832
Valid prediction for snap_scaffold_1-snap.3899-T1
Valid prediction for GlimmerHMM_glimmerT_2793-T1
Valid prediction for GlimmerHMM_glimmerT_2814-T1
Valid prediction for snap_scaffold_1-snap.3885-T1
Valid prediction for snap_scaffold_1-snap.3913-T1
Valid prediction for Augustus_model.g1984.t1
Valid prediction for CodingQuarry_transcript_3043-T1
Valid prediction for snap_scaffold_1-snap.3887-T1
Valid prediction for Augustus_model.g1981.t1
Valid prediction for GlimmerHMM_glimmerT_2789-T1
Valid prediction for GlimmerHMM_glimmerT_2808-T1
Valid prediction for snap_scaffold_1-snap.3922-T1
Valid prediction for CodingQuarry_transcript_3046-T1
Valid prediction for Augustus_model.g1985.t1
Valid prediction for snap_scaffold_1-snap.3916-T1
Valid prediction for GlimmerHMM_glimmerT_2810-T1
Couldn't classify 153774, 154130
Sorry, prediction pasa_asmbl_1207.p1 fails validation.
(CTC)	 TC	153774-154130	TT	TTT
Valid prediction for snap_scaffold_1-snap.3890-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2812-T1
Valid prediction for snap_scaffold_1-snap.3929-T1
Valid prediction for pasa_asmbl_2664.p1
Valid prediction for GlimmerHMM_glimmerT_2811-T1
Valid prediction for snap_scaffold_1-snap.3900-T1
Valid prediction for snap_scaffold_1-snap.3904-T1
Valid prediction for Augustus_model.g1990.t1
Valid prediction for GlimmerHMM_glimmerT_2798-T1
Valid prediction for snap_scaffold_1-snap.3912-T1
Valid prediction for snap_scaffold_1-snap.3932-T1
Valid prediction for Augustus_model.g1986.t1
Valid prediction for snap_scaffold_1-snap.3910-T1
Valid prediction for HiQ_model.g1987.t1
Valid prediction for snap_scaffold_1-snap.3893-T1
Valid prediction for GlimmerHMM_glimmerT_2792-T1
Valid prediction for GlimmerHMM_glimmerT_2796-T1
Valid prediction for GlimmerHMM_glimmerT_2805-T1
Valid prediction for Augustus_model.g1979.t1
Valid prediction for snap_scaffold_1-snap.3925-T1
Valid prediction for snap_scaffold_1-snap.3891-T1
Valid prediction for Augustus_model.g1991.t1
Valid prediction for GlimmerHMM_glimmerT_2787-T1
Valid prediction for snap_scaffold_1-snap.3917-T1
Valid prediction for snap_scaffold_1-snap.3920-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 GlimmerHMM_glimmerT_2813-T1
Valid prediction for GlimmerHMM_glimmerT_2804-T1
Valid prediction for snap_scaffold_1-snap.3924-T1
Valid prediction for snap_scaffold_1-snap.3909-T1
Valid prediction for snap_scaffold_1-snap.3901-T1
Valid prediction for snap_scaffold_1-snap.3889-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3903-T1
Valid prediction for snap_scaffold_1-snap.3892-T1
Valid prediction for GlimmerHMM_glimmerT_2801-T1
Valid prediction for snap_scaffold_1-snap.3902-T1
Valid prediction for snap_scaffold_1-snap.3918-T1
Valid prediction for Augustus_model.g1983.t1
Valid prediction for snap_scaffold_1-snap.3905-T1
Valid prediction for snap_scaffold_1-snap.3908-T1
Valid prediction for Augustus_model.g1978.t1
Valid prediction for GlimmerHMM_glimmerT_2809-T1
Valid prediction for GlimmerHMM_glimmerT_2788-T1
Valid prediction for Augustus_model.g1993.t1
Valid prediction for GlimmerHMM_glimmerT_2795-T1
Valid prediction for GlimmerHMM_glimmerT_2799-T1
Valid prediction for snap_scaffold_1-snap.3894-T1
Valid prediction for snap_scaffold_1-snap.3888-T1
Valid prediction for Augustus_model.g1992.t1
Valid prediction for snap_scaffold_1-snap.3923-T1
Valid prediction for snap_scaffold_1-snap.3931-T1
Valid prediction for snap_scaffold_1-snap.3911-T1
Valid prediction for snap_scaffold_1-snap.3921-T1
Valid prediction for GlimmerHMM_glimmerT_2790-T1
Valid prediction for snap_scaffold_1-snap.3914-T1
Valid prediction for snap_scaffold_1-snap.3897-T1
Valid prediction for snap_scaffold_1-snap.3915-T1
Valid prediction for GlimmerHMM_glimmerT_2794-T1
Valid prediction for GlimmerHMM_glimmerT_2791-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3930-T1
Valid prediction for snap_scaffold_1-snap.3926-T1
Valid prediction for snap_scaffold_1-snap.3895-T1
Valid prediction for Augustus_model.g1982.t1
Valid prediction for snap_scaffold_1-snap.3898-T1
Valid prediction for Augustus_model.g1988.t1
Valid prediction for snap_scaffold_1-snap.3928-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14979, rend_intergenic: 10803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40654, rend_intergenic: 18732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42468, rend_intergenic: 40914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63174, rend_intergenic: 47276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71130, rend_intergenic: 63438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79207, rend_intergenic: 77592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93156, rend_intergenic: 88940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99033, rend_intergenic: 93181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101674, rend_intergenic: 99051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106848, rend_intergenic: 101706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121976, rend_intergenic: 111075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124699, rend_intergenic: 122759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128711, rend_intergenic: 126573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132538, rend_intergenic: 129294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151303, rend_intergenic: 147064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160272, rend_intergenic: 155962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169214, rend_intergenic: 167566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186434
-exon list size: 315


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 14979, rend_intergenic: 10803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40654, rend_intergenic: 18732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42468, rend_intergenic: 40914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63174, rend_intergenic: 47276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71130, rend_intergenic: 63438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79207, rend_intergenic: 77592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93156, rend_intergenic: 88940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99033, rend_intergenic: 93181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101674, rend_intergenic: 99051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106848, rend_intergenic: 101706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121976, rend_intergenic: 111075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124699, rend_intergenic: 122759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128711, rend_intergenic: 126573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132538, rend_intergenic: 129294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151303, rend_intergenic: 147064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160272, rend_intergenic: 155962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169214, rend_intergenic: 167566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support