-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_16281431-16435348

-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 CodingQuarry_transcript_13364-T1
Valid prediction for snap_scaffold_13-snap.3203-T1
Valid prediction for GlimmerHMM_glimmerT_33042-T1
Valid prediction for Augustus_model.g22056.t1
Valid prediction for Augustus_model.g22059.t1
Valid prediction for GlimmerHMM_glimmerT_33062-T1
Valid prediction for snap_scaffold_13-snap.3239-T1
Couldn't classify 3010, 3095
Sorry, prediction pasa_asmbl_11569.p1 fails validation.
(ATG)	 CC	2313-2871	GT	AGG
(GGT)	 AG	3010-3095	AC	CCA
-recovered pasa_asmbl_11569.p1, initial, 2313, 2871
Valid prediction for snap_scaffold_13-snap.3209-T1
Valid prediction for snap_scaffold_13-snap.3207-T1
Valid prediction for snap_scaffold_13-snap.3232-T1
Valid prediction for GlimmerHMM_glimmerT_33051-T1
Valid prediction for GlimmerHMM_glimmerT_33063-T1
Valid prediction for GlimmerHMM_glimmerT_33059-T1
Valid prediction for Augustus_model.g22065.t1
Valid prediction for HiQ_model.g22067.t1
Valid prediction for snap_scaffold_13-snap.3219-T1
Valid prediction for GlimmerHMM_glimmerT_33064-T1
Valid prediction for snap_scaffold_13-snap.3230-T1
Valid prediction for snap_scaffold_13-snap.3236-T1
Valid prediction for snap_scaffold_13-snap.3233-T1
Valid prediction for snap_scaffold_13-snap.3213-T1
Valid prediction for snap_scaffold_13-snap.3208-T1
Valid prediction for Augustus_model.g22064.t1
Valid prediction for GlimmerHMM_glimmerT_33054-T1
Valid prediction for CodingQuarry_transcript_13366-T1
Valid prediction for snap_scaffold_13-snap.3229-T1
Valid prediction for snap_scaffold_13-snap.3205-T1
Valid prediction for GlimmerHMM_glimmerT_33045-T1
Valid prediction for snap_scaffold_13-snap.3211-T1
Valid prediction for pasa_asmbl_11573.p1
Valid prediction for snap_scaffold_13-snap.3237-T1
Valid prediction for GlimmerHMM_glimmerT_33060-T1
Valid prediction for GlimmerHMM_glimmerT_33056-T1
Valid prediction for snap_scaffold_13-snap.3221-T1
Valid prediction for pasa_asmbl_11574.p1
Valid prediction for snap_scaffold_13-snap.3214-T1
Valid prediction for snap_scaffold_13-snap.3217-T1
Valid prediction for HiQ_model.g22066.t1
Valid prediction for snap_scaffold_13-snap.3224-T1
Valid prediction for GlimmerHMM_glimmerT_33048-T1
Valid prediction for snap_scaffold_13-snap.3223-T1
Valid prediction for snap_scaffold_13-snap.3220-T1
Valid prediction for snap_scaffold_13-snap.3226-T1
Valid prediction for HiQ_model.g22054.t1
Valid prediction for snap_scaffold_13-snap.3235-T1
Valid prediction for CodingQuarry_transcript_13365-T1
Valid prediction for GlimmerHMM_glimmerT_33066-T1
Valid prediction for snap_scaffold_13-snap.3216-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_33047-T1
Valid prediction for snap_scaffold_13-snap.3212-T1
Valid prediction for GlimmerHMM_glimmerT_33044-T1
Valid prediction for GlimmerHMM_glimmerT_33046-T1
Valid prediction for GlimmerHMM_glimmerT_33058-T1
Valid prediction for GlimmerHMM_glimmerT_33049-T1
Valid prediction for GlimmerHMM_glimmerT_33053-T1
Valid prediction for GlimmerHMM_glimmerT_33043-T1
Valid prediction for GlimmerHMM_glimmerT_33055-T1
Valid prediction for Augustus_model.g22060.t1
Valid prediction for snap_scaffold_13-snap.3210-T1
Valid prediction for snap_scaffold_13-snap.3238-T1
Valid prediction for snap_scaffold_13-snap.3206-T1
Valid prediction for snap_scaffold_13-snap.3231-T1
Valid prediction for snap_scaffold_13-snap.3228-T1
Couldn't classify 147346, 147521
Couldn't classify 148463, 148596
Sorry, prediction pasa_asmbl_10372.p1 fails validation.
(AGG)	 CC	147346-147521	GT	AAG
(CAC)	 AG	148083-148129	GT	ATG
(ATG)	 AG	148463-148596	CA	CAC
-recovered pasa_asmbl_10372.p1, internal, 148083, 148129
Couldn't classify 109571, 109804
Sorry, prediction pasa_asmbl_10291.p1 fails validation.
(ATG)	 AC	108290-108320	GT	CGG
(GGT)	 AG	109068-109120	GT	AGG
(GAA)	 AG	109268-109384	GT	AGG
(CTG)	 AG	109571-109804	TG	GGT
-recovered pasa_asmbl_10291.p1, initial, 108290, 108320
-recovered pasa_asmbl_10291.p1, internal, 109068, 109120
-recovered pasa_asmbl_10291.p1, internal, 109268, 109384
Valid prediction for Augustus_model.g22061.t1
Valid prediction for snap_scaffold_13-snap.3225-T1
Valid prediction for snap_scaffold_13-snap.3204-T1
Valid prediction for GlimmerHMM_glimmerT_33050-T1
Valid prediction for Augustus_model.g22057.t1
Valid prediction for snap_scaffold_13-snap.3218-T1
Valid prediction for Augustus_model.g22055.t1
Couldn't classify 68729, 68791
Sorry, prediction pasa_asmbl_10297.p1 fails validation.
(ATG)	 AC	66066-66197	GT	GGG
(GTG)	 AG	67837-68019	GT	AGG
(GAG)	 AG	68110-68184	GT	AGG
(GCC)	 AG	68412-68501	GT	GTG
(TGT)	 AG	68729-68791	TG	ACT
-recovered pasa_asmbl_10297.p1, initial, 66066, 66197
-recovered pasa_asmbl_10297.p1, internal, 67837, 68019
-recovered pasa_asmbl_10297.p1, internal, 68110, 68184
-recovered pasa_asmbl_10297.p1, internal, 68412, 68501
Valid prediction for GlimmerHMM_glimmerT_33052-T1
Valid prediction for snap_scaffold_13-snap.3227-T1
Valid prediction for Augustus_model.g22063.t1
Valid prediction for Augustus_model.g22062.t1
Valid prediction for snap_scaffold_13-snap.3234-T1
Valid prediction for snap_scaffold_13-snap.3240-T1
Valid prediction for GlimmerHMM_glimmerT_33057-T1
Valid prediction for GlimmerHMM_glimmerT_33061-T1
Valid prediction for HiQ_model.g22058.t1
Valid prediction for snap_scaffold_13-snap.3215-T1
Valid prediction for GlimmerHMM_glimmerT_33065-T1
Valid prediction for snap_scaffold_13-snap.3222-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15710, rend_intergenic: 12416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18894, rend_intergenic: 16935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36322, rend_intergenic: 29923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40653, rend_intergenic: 37747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45629, rend_intergenic: 42715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56684, rend_intergenic: 51409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60161, rend_intergenic: 57150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78860, rend_intergenic: 61894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81975, rend_intergenic: 79364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87853, rend_intergenic: 84306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100845, rend_intergenic: 88452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108704, rend_intergenic: 102211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115421, rend_intergenic: 114033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129203, rend_intergenic: 122806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136671, rend_intergenic: 129788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145132, rend_intergenic: 143725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152336, rend_intergenic: 149713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153918
-exon list size: 281


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.7    
6.0    
6.4    
6.7    
7.1    
7.4    
7.8    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
11.0    
11.3    
11.7    
12.0    
12.4    
12.7    
13.1    
13.4    
13.8    
14.1    
14.5    
14.8    
15.2    
15.5    
15.9    
16.3    
16.6    
17.0    
17.3    
17.7    
18.0    
18.4    
18.7    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.6    
21.9    
22.3    
22.6    
23.0    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.9    
27.2    
27.6    
27.9    
28.3    
28.6    
29.0    
29.3    
29.7    
30.0    
30.4    
30.7    
31.1    
31.4    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.6    
35.0    
35.3    
35.7    
36.0    
36.4    
36.7    
37.1    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.7    
42.0    
42.4    
42.8    
43.1    
43.5    
43.8    
44.2    
44.5    
44.9    
45.2    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.8    
55.1    
55.5    
55.8    
56.2    
56.5    
56.9    
57.2    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.9    
63.3    
63.6    
64.0    
64.3    
64.7    
65.0    
65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.6    
68.9    
69.3    
69.6    
70.0    
70.3    
70.7    
71.0    
71.4    
71.7    
72.1    
72.4    
72.8    
73.1    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.0    
77.4    
77.7    
78.1    
78.4    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.3    
81.6    
82.0    
82.3    
82.7    
83.0    
83.4    
83.7    
84.1    
84.5    
84.8    
85.2    
85.5    
85.9    
86.2    
86.6    
86.9    
87.3    
87.6    
88.0    
88.3    
88.7    
89.0    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.2    
92.6    
92.9    
93.3    
93.6    
94.0    
94.3    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 15710, rend_intergenic: 12416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18894, rend_intergenic: 16935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36322, rend_intergenic: 29923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40653, rend_intergenic: 37747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45629, rend_intergenic: 42715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56684, rend_intergenic: 51409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60161, rend_intergenic: 57150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78860, rend_intergenic: 61894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81975, rend_intergenic: 79364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87853, rend_intergenic: 84306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100845, rend_intergenic: 88452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108704, rend_intergenic: 102211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115421, rend_intergenic: 114033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129203, rend_intergenic: 122806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136671, rend_intergenic: 129788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145132, rend_intergenic: 143725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152336, rend_intergenic: 149713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support