-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_21986483-22220756

-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.4185-T1
Valid prediction for snap_scaffold_1-snap.4184-T1
Valid prediction for Augustus_model.g2044.t1
Valid prediction for snap_scaffold_1-snap.4166-T1
Couldn't classify 85341, 85365
Couldn't classify 86851, 87012
Sorry, prediction pasa_asmbl_2711.p1 fails validation.
(AAG)	 GC	85341-85365	GT	GGG
(ATT)	 AG	86081-86142	GT	TTG
(CTG)	 AG	86536-86634	GT	AGG
(GCC)	 AG	86851-87012	TA	AGT
-recovered pasa_asmbl_2711.p1, internal, 86081, 86142
-recovered pasa_asmbl_2711.p1, internal, 86536, 86634
Valid prediction for GlimmerHMM_glimmerT_2953-T1
Valid prediction for snap_scaffold_1-snap.4170-T1
Valid prediction for snap_scaffold_1-snap.4142-T1
Valid prediction for snap_scaffold_1-snap.4173-T1
Valid prediction for GlimmerHMM_glimmerT_2956-T1
Valid prediction for Augustus_model.g2045.t1
Valid prediction for GlimmerHMM_glimmerT_2957-T1
Valid prediction for GlimmerHMM_glimmerT_2940-T1
Valid prediction for GlimmerHMM_glimmerT_2955-T1
Valid prediction for snap_scaffold_1-snap.4153-T1
Valid prediction for GlimmerHMM_glimmerT_2939-T1
Valid prediction for GlimmerHMM_glimmerT_2961-T1
Valid prediction for GlimmerHMM_glimmerT_2964-T1
Valid prediction for CodingQuarry_transcript_3057-T1
Valid prediction for CodingQuarry_transcript_3056-T1
Valid prediction for snap_scaffold_1-snap.4154-T1
Valid prediction for snap_scaffold_1-snap.4162-T1
Valid prediction for snap_scaffold_1-snap.4179-T1
Valid prediction for GlimmerHMM_glimmerT_2941-T1
Valid prediction for GlimmerHMM_glimmerT_2949-T1
Valid prediction for snap_scaffold_1-snap.4180-T1
Valid prediction for snap_scaffold_1-snap.4190-T1
Valid prediction for snap_scaffold_1-snap.4193-T1
Valid prediction for snap_scaffold_1-snap.4145-T1
Valid prediction for snap_scaffold_1-snap.4149-T1
Valid prediction for snap_scaffold_1-snap.4151-T1
Valid prediction for snap_scaffold_1-snap.4160-T1
Valid prediction for snap_scaffold_1-snap.4144-T1
Valid prediction for snap_scaffold_1-snap.4183-T1
Valid prediction for snap_scaffold_1-snap.4158-T1
Valid prediction for snap_scaffold_1-snap.4165-T1
Valid prediction for snap_scaffold_1-snap.4195-T1
Valid prediction for snap_scaffold_1-snap.4188-T1
Valid prediction for snap_scaffold_1-snap.4147-T1
Valid prediction for GlimmerHMM_glimmerT_2962-T1
Valid prediction for GlimmerHMM_glimmerT_2948-T1
Valid prediction for pasa_asmbl_2684.p1
Valid prediction for snap_scaffold_1-snap.4157-T1
Valid prediction for snap_scaffold_1-snap.4167-T1
Valid prediction for snap_scaffold_1-snap.4178-T1
Valid prediction for GlimmerHMM_glimmerT_2946-T1
Valid prediction for GlimmerHMM_glimmerT_2959-T1
Valid prediction for snap_scaffold_1-snap.4186-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.4146-T1
Valid prediction for snap_scaffold_1-snap.4161-T1
Valid prediction for snap_scaffold_1-snap.4175-T1
Valid prediction for snap_scaffold_1-snap.4152-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.4194-T1
Valid prediction for snap_scaffold_1-snap.4191-T1
Valid prediction for GlimmerHMM_glimmerT_2963-T1
Valid prediction for snap_scaffold_1-snap.4187-T1
Valid prediction for snap_scaffold_1-snap.4148-T1
Valid prediction for GlimmerHMM_glimmerT_2944-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.4168-T1
Valid prediction for Augustus_model.g2046.t1
Valid prediction for GlimmerHMM_glimmerT_2950-T1
Valid prediction for GlimmerHMM_glimmerT_2942-T1
Valid prediction for snap_scaffold_1-snap.4159-T1
Valid prediction for snap_scaffold_1-snap.4177-T1
Valid prediction for snap_scaffold_1-snap.4192-T1
Valid prediction for GlimmerHMM_glimmerT_2943-T1
Valid prediction for snap_scaffold_1-snap.4181-T1
Valid prediction for GlimmerHMM_glimmerT_2945-T1
Valid prediction for GlimmerHMM_glimmerT_2947-T1
Valid prediction for snap_scaffold_1-snap.4150-T1
Valid prediction for snap_scaffold_1-snap.4176-T1
Valid prediction for snap_scaffold_1-snap.4164-T1
Valid prediction for snap_scaffold_1-snap.4163-T1
Valid prediction for GlimmerHMM_glimmerT_2952-T1
Valid prediction for snap_scaffold_1-snap.4143-T1
Valid prediction for GlimmerHMM_glimmerT_2958-T1
Valid prediction for snap_scaffold_1-snap.4171-T1
Valid prediction for snap_scaffold_1-snap.4189-T1
Valid prediction for snap_scaffold_1-snap.4156-T1
Valid prediction for snap_scaffold_1-snap.4155-T1
Valid prediction for snap_scaffold_1-snap.4174-T1
Valid prediction for snap_scaffold_1-snap.4172-T1
Couldn't classify 69591, 69634
Couldn't classify 76873, 77068
Sorry, prediction pasa_asmbl_1231.p1 fails validation.
(NNN)	 NN	69591-69634	GT	ATG
(TCT)	 AG	69899-70015	GT	AGG
(GTA)	 AG	70433-70636	GT	GAG
(GGT)	 AG	71250-71451	GT	GGG
(AAC)	 AG	71971-72045	GT	AGG
(TTG)	 AG	72366-72536	GT	AGG
(GTG)	 AG	74437-74532	GT	AGG
(GTG)	 AG	74660-74777	GT	GGG
(AGT)	 AG	75120-75333	GT	AGG
(GGC)	 AG	75797-75928	GT	AGG
(GAT)	 AG	76453-76557	GT	AAG
(GGA)	 AG	76873-77068	GT	CGG
-recovered pasa_asmbl_1231.p1, internal, 69899, 70015
-recovered pasa_asmbl_1231.p1, internal, 70433, 70636
-recovered pasa_asmbl_1231.p1, internal, 71250, 71451
-recovered pasa_asmbl_1231.p1, internal, 71971, 72045
-recovered pasa_asmbl_1231.p1, internal, 72366, 72536
-recovered pasa_asmbl_1231.p1, internal, 74437, 74532
-recovered pasa_asmbl_1231.p1, internal, 74660, 74777
-recovered pasa_asmbl_1231.p1, internal, 75120, 75333
-recovered pasa_asmbl_1231.p1, internal, 75797, 75928
-recovered pasa_asmbl_1231.p1, internal, 76453, 76557
-recovered pasa_asmbl_1231.p1, internal, 76873, 77068
Valid prediction for snap_scaffold_1-snap.4169-T1
Valid prediction for GlimmerHMM_glimmerT_2954-T1
Valid prediction for snap_scaffold_1-snap.4182-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2960-T1
Valid prediction for GlimmerHMM_glimmerT_2951-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10298, rend_intergenic: 7374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14404, rend_intergenic: 12285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17946, rend_intergenic: 14978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18344, rend_intergenic: 18154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28027, rend_intergenic: 26625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37887, rend_intergenic: 29516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55169, rend_intergenic: 38345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55966, rend_intergenic: 55318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64897, rend_intergenic: 59619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65598, rend_intergenic: 64900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71402, rend_intergenic: 66851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88392, rend_intergenic: 80771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104417, rend_intergenic: 89881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114032, rend_intergenic: 106028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128223, rend_intergenic: 114137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143385, rend_intergenic: 136325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164928, rend_intergenic: 156309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191065, rend_intergenic: 174780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196059, rend_intergenic: 193031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198848, rend_intergenic: 196962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202562, rend_intergenic: 200865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209837, rend_intergenic: 204262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213760, rend_intergenic: 209887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222693, rend_intergenic: 214228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233118, rend_intergenic: 227302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 97824, rend_intergenic: 97821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234274
-exon list size: 387


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
6.9    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10298, rend_intergenic: 7374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14404, rend_intergenic: 12285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17946, rend_intergenic: 14978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18344, rend_intergenic: 18154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28027, rend_intergenic: 26625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37887, rend_intergenic: 29516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55169, rend_intergenic: 38345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55966, rend_intergenic: 55318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64897, rend_intergenic: 59619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65598, rend_intergenic: 64900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71402, rend_intergenic: 66851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88392, rend_intergenic: 80771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104417, rend_intergenic: 89881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114032, rend_intergenic: 106028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128223, rend_intergenic: 114137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143385, rend_intergenic: 136325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164928, rend_intergenic: 156309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191065, rend_intergenic: 174780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196059, rend_intergenic: 193031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198848, rend_intergenic: 196962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202562, rend_intergenic: 200865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209837, rend_intergenic: 204262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213760, rend_intergenic: 209887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222693, rend_intergenic: 214228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233118, rend_intergenic: 227302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 97824, rend_intergenic: 97821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support