-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_21343406-21488927

-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 Augustus_model.g2016.t1
Valid prediction for GlimmerHMM_glimmerT_2862-T1
Valid prediction for snap_scaffold_1-snap.4011-T1
Valid prediction for GlimmerHMM_glimmerT_2877-T1
Valid prediction for GlimmerHMM_glimmerT_2871-T1
Valid prediction for GlimmerHMM_glimmerT_2860-T1
Valid prediction for snap_scaffold_1-snap.4015-T1
Valid prediction for GlimmerHMM_glimmerT_2876-T1
Valid prediction for GlimmerHMM_glimmerT_2869-T1
Valid prediction for snap_scaffold_1-snap.4036-T1
Valid prediction for snap_scaffold_1-snap.4029-T1
Valid prediction for GlimmerHMM_glimmerT_2864-T1
Valid prediction for snap_scaffold_1-snap.4022-T1
Valid prediction for snap_scaffold_1-snap.4039-T1
Valid prediction for GlimmerHMM_glimmerT_2880-T1
Valid prediction for snap_scaffold_1-snap.4037-T1
Valid prediction for GlimmerHMM_glimmerT_2861-T1
Valid prediction for snap_scaffold_1-snap.4025-T1
Valid prediction for snap_scaffold_1-snap.4043-T1
Valid prediction for GlimmerHMM_glimmerT_2867-T1
Valid prediction for Augustus_model.g2014.t1
Valid prediction for snap_scaffold_1-snap.4023-T1
Valid prediction for snap_scaffold_1-snap.4027-T1
Valid prediction for Augustus_model.g2010.t1
Valid prediction for GlimmerHMM_glimmerT_2873-T1
Valid prediction for GlimmerHMM_glimmerT_2879-T1
Valid prediction for snap_scaffold_1-snap.4028-T1
Valid prediction for snap_scaffold_1-snap.4014-T1
Valid prediction for snap_scaffold_1-snap.4035-T1
Couldn't classify 18806, 18858
Couldn't classify 19744, 19821
Sorry, prediction pasa_asmbl_2812.p1 fails validation.
(CTC)	 AG	18806-18858	GT	GGG
(GAA)	 AG	19119-19338	GT	TGG
(GGG)	 AG	19744-19821	AC	CGA
-recovered pasa_asmbl_2812.p1, internal, 18806, 18858
-recovered pasa_asmbl_2812.p1, internal, 19119, 19338
Valid prediction for GlimmerHMM_glimmerT_2865-T1
Valid prediction for snap_scaffold_1-snap.4030-T1
Valid prediction for Augustus_model.g2011.t1
Couldn't classify 19888, 20196
Sorry, prediction pasa_asmbl_2678.p1 fails validation.
(GCC)	 TG	19888-20196	CA	AGC
Valid prediction for snap_scaffold_1-snap.4041-T1
Valid prediction for GlimmerHMM_glimmerT_2863-T1
Valid prediction for snap_scaffold_1-snap.4031-T1
Valid prediction for GlimmerHMM_glimmerT_2866-T1
Valid prediction for CodingQuarry_transcript_3048-T1
Valid prediction for snap_scaffold_1-snap.4020-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.4032-T1
Valid prediction for snap_scaffold_1-snap.4038-T1
Valid prediction for GlimmerHMM_glimmerT_2878-T1
Valid prediction for snap_scaffold_1-snap.4042-T1
Valid prediction for snap_scaffold_1-snap.4012-T1
Sorry, intron length (5) is less than minimum required (10)
Couldn't classify 63055, 63237
Sorry, prediction pasa_asmbl_1212.p1 fails validation.
(CCC)	 AG	63055-63237	GT	AGG
(AAC)	 AG	64813-64892	GT	AGG
(GTA)	 AG	65782-65982	GT	CAG
(TCT)	 AG	67166-67247	GT	ACG
(GCT)	 AG	69852-69974	GT	AGG
(CTG)	 AG	72259-72398	GT	AGG
(GGC)	 AG	72712-72874	GT	AGG
(GCG)	 AG	73673-73772	GT	AGG
(GCG)	 AG	73904-74059	GT	GGG
(GTG)	 AG	74166-74273	GT	TGG
(GAA)	 AG	75247-75374	AG	AGA
-recovered pasa_asmbl_1212.p1, terminal, 75247, 75374
-recovered pasa_asmbl_1212.p1, internal, 63055, 63237
-recovered pasa_asmbl_1212.p1, internal, 64813, 64892
-recovered pasa_asmbl_1212.p1, internal, 65782, 65982
-recovered pasa_asmbl_1212.p1, internal, 67166, 67247
-recovered pasa_asmbl_1212.p1, internal, 69852, 69974
-recovered pasa_asmbl_1212.p1, internal, 72259, 72398
-recovered pasa_asmbl_1212.p1, internal, 72712, 72874
-recovered pasa_asmbl_1212.p1, internal, 73673, 73772
-recovered pasa_asmbl_1212.p1, internal, 73904, 74059
-recovered pasa_asmbl_1212.p1, internal, 74166, 74273
Valid prediction for snap_scaffold_1-snap.4013-T1
Valid prediction for snap_scaffold_1-snap.4019-T1
Valid prediction for GlimmerHMM_glimmerT_2868-T1
Valid prediction for Augustus_model.g2012.t1
Valid prediction for snap_scaffold_1-snap.4026-T1
Valid prediction for GlimmerHMM_glimmerT_2874-T1
Valid prediction for snap_scaffold_1-snap.4018-T1
Valid prediction for HiQ_model.g2013.t1
Valid prediction for snap_scaffold_1-snap.4024-T1
Valid prediction for snap_scaffold_1-snap.4034-T1
Valid prediction for Augustus_model.g2015.t1
Valid prediction for Augustus_model.g2017.t1
Valid prediction for snap_scaffold_1-snap.4040-T1
Valid prediction for snap_scaffold_1-snap.4021-T1
Valid prediction for snap_scaffold_1-snap.4010-T1
Valid prediction for GlimmerHMM_glimmerT_2859-T1
Valid prediction for GlimmerHMM_glimmerT_2870-T1
Valid prediction for snap_scaffold_1-snap.4033-T1
Valid prediction for GlimmerHMM_glimmerT_2875-T1
Valid prediction for snap_scaffold_1-snap.4017-T1
Valid prediction for GlimmerHMM_glimmerT_2881-T1
Valid prediction for GlimmerHMM_glimmerT_2872-T1
Valid prediction for snap_scaffold_1-snap.4016-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14992, rend_intergenic: 7646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17680, rend_intergenic: 15780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23423, rend_intergenic: 18369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39447, rend_intergenic: 36417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45415, rend_intergenic: 43155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57768, rend_intergenic: 47729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60843, rend_intergenic: 57793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69150, rend_intergenic: 65734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85439, rend_intergenic: 70219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86483, rend_intergenic: 85545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101783, rend_intergenic: 95109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109082, rend_intergenic: 106190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125050, rend_intergenic: 109250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133656, rend_intergenic: 126430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144481, rend_intergenic: 133674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145522
-exon list size: 241


building trellis

0.4    
0.8    
1.2    
1.6    
2.1    
2.5    
2.9    
3.3    
3.7    
4.1    
4.5    
4.9    
5.3    
5.8    
6.2    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
9.1    
9.5    
9.9    
10.3    
10.7    
11.1    
11.5    
11.9    
12.3    
12.8    
13.2    
13.6    
14.0    
14.4    
14.8    
15.2    
15.6    
16.0    
16.5    
16.9    
17.3    
17.7    
18.1    
18.5    
18.9    
19.3    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.2    
22.6    
23.0    
23.5    
23.9    
24.3    
24.7    
25.1    
25.5    
25.9    
26.3    
26.7    
27.2    
27.6    
28.0    
28.4    
28.8    
29.2    
29.6    
30.0    
30.5    
30.9    
31.3    
31.7    
32.1    
32.5    
32.9    
33.3    
33.7    
34.2    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.9    
38.3    
38.7    
39.1    
39.5    
39.9    
40.3    
40.7    
41.2    
41.6    
42.0    
42.4    
42.8    
43.2    
43.6    
44.0    
44.4    
44.9    
45.3    
45.7    
46.1    
46.5    
46.9    
47.3    
47.7    
48.1    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.9    
52.3    
52.7    
53.1    
53.5    
53.9    
54.3    
54.7    
55.1    
55.6    
56.0    
56.4    
56.8    
57.2    
57.6    
58.0    
58.4    
58.8    
59.3    
59.7    
60.1    
60.5    
60.9    
61.3    
61.7    
62.1    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.8    
66.3    
66.7    
67.1    
67.5    
67.9    
68.3    
68.7    
69.1    
69.5    
70.0    
70.4    
70.8    
71.2    
71.6    
72.0    
72.4    
72.8    
73.3    
73.7    
74.1    
74.5    
74.9    
75.3    
75.7    
76.1    
76.5    
77.0    
77.4    
77.8    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.7    
81.1    
81.5    
81.9    
82.3    
82.7    
83.1    
83.5    
84.0    
84.4    
84.8    
85.2    
85.6    
86.0    
86.4    
86.8    
87.2    
87.7    
88.1    
88.5    
88.9    
89.3    
89.7    
90.1    
90.5    
90.9    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.8    
94.2    
94.7    
95.1    
95.5    
95.9    
96.3    
96.7    
97.1    
97.5    
97.9    
98.4    
98.8    
99.2    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 14992, rend_intergenic: 7646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17680, rend_intergenic: 15780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23423, rend_intergenic: 18369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39447, rend_intergenic: 36417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45415, rend_intergenic: 43155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57768, rend_intergenic: 47729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60843, rend_intergenic: 57793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69150, rend_intergenic: 65734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85439, rend_intergenic: 70219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86483, rend_intergenic: 85545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101783, rend_intergenic: 95109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109082, rend_intergenic: 106190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125050, rend_intergenic: 109250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133656, rend_intergenic: 126430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144481, rend_intergenic: 133674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support