-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_21126999-21349372

-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.3971-T1
Valid prediction for snap_scaffold_1-snap.3978-T1
Couldn't classify 121158, 121244
Couldn't classify 126387, 126415
Sorry, prediction pasa_asmbl_2676.p1 fails validation.
(TCC)	 GC	121158-121244	GT	AGG
(GTG)	 AG	122848-122944	GT	AGG
(AGG)	 AG	123728-123975	GT	AGG
(ACC)	 AG	124533-124602	GT	AGG
(CTG)	 AG	125364-125518	GT	CAG
(AGA)	 AG	126018-126183	GT	AGG
(AGA)	 AG	126387-126415	TC	CCT
-recovered pasa_asmbl_2676.p1, internal, 122848, 122944
-recovered pasa_asmbl_2676.p1, internal, 123728, 123975
-recovered pasa_asmbl_2676.p1, internal, 124533, 124602
-recovered pasa_asmbl_2676.p1, internal, 125364, 125518
-recovered pasa_asmbl_2676.p1, internal, 126018, 126183
Valid prediction for snap_scaffold_1-snap.4005-T1
Valid prediction for snap_scaffold_1-snap.3976-T1
Valid prediction for Augustus_model.g2009.t1
Valid prediction for Augustus_model.g2007.t1
Valid prediction for snap_scaffold_1-snap.3992-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3990-T1
Valid prediction for snap_scaffold_1-snap.3986-T1
Valid prediction for snap_scaffold_1-snap.4003-T1
Valid prediction for snap_scaffold_1-snap.3988-T1
Valid prediction for GlimmerHMM_glimmerT_2842-T1
Valid prediction for snap_scaffold_1-snap.3983-T1
Valid prediction for CodingQuarry_transcript_3047-T1
Valid prediction for Augustus_model.g2005.t1
Valid prediction for snap_scaffold_1-snap.3997-T1
Valid prediction for GlimmerHMM_glimmerT_2838-T1
Valid prediction for snap_scaffold_1-snap.3973-T1
Valid prediction for pasa_asmbl_2674.p1
Valid prediction for GlimmerHMM_glimmerT_2847-T1
Valid prediction for snap_scaffold_1-snap.3987-T1
Valid prediction for GlimmerHMM_glimmerT_2858-T1
Valid prediction for snap_scaffold_1-snap.4008-T1
Valid prediction for snap_scaffold_1-snap.3993-T1
Valid prediction for GlimmerHMM_glimmerT_2843-T1
Valid prediction for snap_scaffold_1-snap.3975-T1
Valid prediction for GlimmerHMM_glimmerT_2850-T1
Valid prediction for snap_scaffold_1-snap.3981-T1
Valid prediction for snap_scaffold_1-snap.3985-T1
Valid prediction for HiQ_model.g2002.t1
Valid prediction for GlimmerHMM_glimmerT_2846-T1
Valid prediction for GlimmerHMM_glimmerT_2841-T1
Valid prediction for GlimmerHMM_glimmerT_2857-T1
Valid prediction for Augustus_model.g2003.t1
Valid prediction for snap_scaffold_1-snap.3970-T1
Valid prediction for GlimmerHMM_glimmerT_2839-T1
Valid prediction for snap_scaffold_1-snap.4000-T1
Valid prediction for snap_scaffold_1-snap.4004-T1
Valid prediction for GlimmerHMM_glimmerT_2837-T1
Valid prediction for GlimmerHMM_glimmerT_2853-T1
Valid prediction for GlimmerHMM_glimmerT_2840-T1
Valid prediction for snap_scaffold_1-snap.4007-T1
Valid prediction for GlimmerHMM_glimmerT_2848-T1
Valid prediction for Augustus_model.g2004.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_1-snap.3980-T1
Valid prediction for Augustus_model.g2006.t1
Valid prediction for snap_scaffold_1-snap.3982-T1
Valid prediction for snap_scaffold_1-snap.3995-T1
Valid prediction for snap_scaffold_1-snap.3969-T1
Valid prediction for snap_scaffold_1-snap.3979-T1
Valid prediction for GlimmerHMM_glimmerT_2852-T1
Valid prediction for snap_scaffold_1-snap.3999-T1
Valid prediction for GlimmerHMM_glimmerT_2844-T1
Valid prediction for GlimmerHMM_glimmerT_2856-T1
Valid prediction for Augustus_model.g2000.t1
Valid prediction for Augustus_model.g2001.t1
Valid prediction for GlimmerHMM_glimmerT_2855-T1
Valid prediction for snap_scaffold_1-snap.4006-T1
Valid prediction for snap_scaffold_1-snap.3977-T1
Valid prediction for GlimmerHMM_glimmerT_2836-T1
Valid prediction for GlimmerHMM_glimmerT_2851-T1
Valid prediction for snap_scaffold_1-snap.3998-T1
Valid prediction for snap_scaffold_1-snap.3984-T1
Valid prediction for snap_scaffold_1-snap.4009-T1
Valid prediction for snap_scaffold_1-snap.3968-T1
Valid prediction for snap_scaffold_1-snap.4002-T1
Valid prediction for snap_scaffold_1-snap.3996-T1
Valid prediction for snap_scaffold_1-snap.4001-T1
Valid prediction for snap_scaffold_1-snap.3994-T1
Valid prediction for snap_scaffold_1-snap.3972-T1
Valid prediction for snap_scaffold_1-snap.3989-T1
Valid prediction for snap_scaffold_1-snap.3991-T1
Valid prediction for GlimmerHMM_glimmerT_2849-T1
Valid prediction for GlimmerHMM_glimmerT_2845-T1
Valid prediction for Augustus_model.g2008.t1
Valid prediction for snap_scaffold_1-snap.3974-T1
Valid prediction for GlimmerHMM_glimmerT_2854-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14233, rend_intergenic: 8522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15977, rend_intergenic: 14450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20741, rend_intergenic: 17053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48540, rend_intergenic: 22145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58920, rend_intergenic: 51822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61162, rend_intergenic: 59209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71434, rend_intergenic: 69284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72575, rend_intergenic: 71850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84515, rend_intergenic: 78271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96100, rend_intergenic: 93633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111540, rend_intergenic: 110969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127167, rend_intergenic: 111561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133444, rend_intergenic: 129152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140399, rend_intergenic: 139969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142879, rend_intergenic: 140783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156516, rend_intergenic: 151293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172016, rend_intergenic: 156826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177824, rend_intergenic: 172096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194624, rend_intergenic: 192374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202771, rend_intergenic: 194919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222374
-exon list size: 288


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.4    
3.8    
4.1    
4.5    
4.8    
5.2    
5.5    
5.9    
6.2    
6.6    
6.9    
7.2    
7.6    
7.9    
8.3    
8.6    
9.0    
9.3    
9.7    
10.0    
10.3    
10.7    
11.0    
11.4    
11.7    
12.1    
12.4    
12.8    
13.1    
13.4    
13.8    
14.1    
14.5    
14.8    
15.2    
15.5    
15.9    
16.2    
16.6    
16.9    
17.2    
17.6    
17.9    
18.3    
18.6    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.4    
21.7    
22.1    
22.4    
22.8    
23.1    
23.4    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.6    
26.9    
27.2    
27.6    
27.9    
28.3    
28.6    
29.0    
29.3    
29.7    
30.0    
30.3    
30.7    
31.0    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.9    
36.2    
36.6    
36.9    
37.2    
37.6    
37.9    
38.3    
38.6    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.4    
41.7    
42.1    
42.4    
42.8    
43.1    
43.4    
43.8    
44.1    
44.5    
44.8    
45.2    
45.5    
45.9    
46.2    
46.6    
46.9    
47.2    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.8    
53.1    
53.4    
53.8    
54.1    
54.5    
54.8    
55.2    
55.5    
55.9    
56.2    
56.6    
56.9    
57.2    
57.6    
57.9    
58.3    
58.6    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.4    
61.7    
62.1    
62.4    
62.8    
63.1    
63.4    
63.8    
64.1    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
69.0    
69.3    
69.7    
70.0    
70.3    
70.7    
71.0    
71.4    
71.7    
72.1    
72.4    
72.8    
73.1    
73.4    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.6    
76.9    
77.2    
77.6    
77.9    
78.3    
78.6    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.4    
81.7    
82.1    
82.4    
82.8    
83.1    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.5    
85.9    
86.2    
86.6    
86.9    
87.2    
87.6    
87.9    
88.3    
88.6    
89.0    
89.3    
89.7    
90.0    
90.3    
90.7    
91.0    
91.4    
91.7    
92.1    
92.4    
92.8    
93.1    
93.4    
93.8    
94.1    
94.5    
94.8    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 14233, rend_intergenic: 8522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15977, rend_intergenic: 14450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20741, rend_intergenic: 17053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48540, rend_intergenic: 22145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58920, rend_intergenic: 51822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61162, rend_intergenic: 59209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71434, rend_intergenic: 69284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72575, rend_intergenic: 71850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84515, rend_intergenic: 78271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96100, rend_intergenic: 93633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111540, rend_intergenic: 110969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127167, rend_intergenic: 111561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133444, rend_intergenic: 129152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140399, rend_intergenic: 139969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142879, rend_intergenic: 140783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156516, rend_intergenic: 151293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172016, rend_intergenic: 156826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177824, rend_intergenic: 172096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194624, rend_intergenic: 192374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202771, rend_intergenic: 194919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support