-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_16457302-16595969

-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_2-snap.3181-T1
Valid prediction for snap_scaffold_2-snap.3160-T1
Valid prediction for snap_scaffold_2-snap.3183-T1
Valid prediction for snap_scaffold_2-snap.3168-T1
Valid prediction for Augustus_model.g3553.t1
Valid prediction for GlimmerHMM_glimmerT_5233-T1
Valid prediction for snap_scaffold_2-snap.3185-T1
Valid prediction for GlimmerHMM_glimmerT_5244-T1
Valid prediction for snap_scaffold_2-snap.3162-T1
Valid prediction for GlimmerHMM_glimmerT_5240-T1
Valid prediction for snap_scaffold_2-snap.3161-T1
Valid prediction for GlimmerHMM_glimmerT_5236-T1
Valid prediction for snap_scaffold_2-snap.3188-T1
Valid prediction for GlimmerHMM_glimmerT_5235-T1
Valid prediction for snap_scaffold_2-snap.3172-T1
Valid prediction for Augustus_model.g3547.t1
Valid prediction for snap_scaffold_2-snap.3158-T1
Valid prediction for snap_scaffold_2-snap.3174-T1
Valid prediction for snap_scaffold_2-snap.3155-T1
Valid prediction for Augustus_model.g3542.t1
Valid prediction for Augustus_model.g3550.t1
Valid prediction for GlimmerHMM_glimmerT_5245-T1
Valid prediction for GlimmerHMM_glimmerT_5232-T1
Valid prediction for snap_scaffold_2-snap.3187-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3156-T1
Valid prediction for Augustus_model.g3544.t1
Valid prediction for snap_scaffold_2-snap.3165-T1
Valid prediction for GlimmerHMM_glimmerT_5249-T1
Valid prediction for snap_scaffold_2-snap.3152-T1
Valid prediction for GlimmerHMM_glimmerT_5247-T1
Valid prediction for GlimmerHMM_glimmerT_5237-T1
Valid prediction for snap_scaffold_2-snap.3175-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_2-snap.3154-T1
Valid prediction for snap_scaffold_2-snap.3164-T1
Valid prediction for GlimmerHMM_glimmerT_5234-T1
Valid prediction for snap_scaffold_2-snap.3176-T1
Valid prediction for GlimmerHMM_glimmerT_5243-T1
Valid prediction for GlimmerHMM_glimmerT_5231-T1
Valid prediction for snap_scaffold_2-snap.3178-T1
Valid prediction for Augustus_model.g3546.t1
Valid prediction for GlimmerHMM_glimmerT_5228-T1
Couldn't classify 64975, 65100
Sorry, prediction pasa_asmbl_23701.p1 fails validation.
(GAG)	 CA	64975-65100	GT	TGG
(TAC)	 AG	65918-65992	GT	TGG
(CTG)	 AG	67534-67632	GT	CTG
(ATG)	 AG	68171-68344	GT	CGG
(GGC)	 AG	69054-69137	GT	AGG
(CTT)	 AG	69632-69709	GA	GAG
-recovered pasa_asmbl_23701.p1, initial, 68171, 68344
-recovered pasa_asmbl_23701.p1, terminal, 69632, 69709
-recovered pasa_asmbl_23701.p1, internal, 65918, 65992
-recovered pasa_asmbl_23701.p1, internal, 67534, 67632
-recovered pasa_asmbl_23701.p1, internal, 68171, 68344
-recovered pasa_asmbl_23701.p1, internal, 69054, 69137
Valid prediction for Augustus_model.g3555.t1
Valid prediction for Augustus_model.g3551.t1
Valid prediction for GlimmerHMM_glimmerT_5229-T1
Valid prediction for Augustus_model.g3554.t1
Couldn't classify 119414, 119467
Sorry, prediction pasa_asmbl_23695.p1 fails validation.
(GAC)	 GC	119414-119467	GT	TTG
(TTG)	 AG	121223-121417	GT	TTG
(TTT)	 AG	121999-122073	GT	ACG
(CTG)	 AG	122200-122298	GT	CGG
(TTT)	 AG	122783-122959	GT	AGG
(GGT)	 AG	123745-123828	GT	AGG
(CTT)	 AG	124083-124130	AT	AGA
-recovered pasa_asmbl_23695.p1, terminal, 124083, 124130
-recovered pasa_asmbl_23695.p1, internal, 121223, 121417
-recovered pasa_asmbl_23695.p1, internal, 121999, 122073
-recovered pasa_asmbl_23695.p1, internal, 122200, 122298
-recovered pasa_asmbl_23695.p1, internal, 122783, 122959
-recovered pasa_asmbl_23695.p1, internal, 123745, 123828
Valid prediction for GlimmerHMM_glimmerT_5238-T1
Valid prediction for snap_scaffold_2-snap.3169-T1
Valid prediction for snap_scaffold_2-snap.3153-T1
Valid prediction for snap_scaffold_2-snap.3166-T1
Valid prediction for Augustus_model.g3543.t1
Valid prediction for GlimmerHMM_glimmerT_5241-T1
Valid prediction for snap_scaffold_2-snap.3182-T1
Valid prediction for snap_scaffold_2-snap.3157-T1
Valid prediction for snap_scaffold_2-snap.3170-T1
Valid prediction for snap_scaffold_2-snap.3177-T1
Valid prediction for Augustus_model.g3548.t1
Valid prediction for GlimmerHMM_glimmerT_5239-T1
Valid prediction for GlimmerHMM_glimmerT_5246-T1
Valid prediction for Augustus_model.g3552.t1
Valid prediction for Augustus_model.g3545.t1
Valid prediction for Augustus_model.g3549.t1
Valid prediction for GlimmerHMM_glimmerT_5230-T1
Valid prediction for GlimmerHMM_glimmerT_5242-T1
Valid prediction for snap_scaffold_2-snap.3180-T1
Valid prediction for GlimmerHMM_glimmerT_5248-T1
Valid prediction for snap_scaffold_2-snap.3159-T1
Valid prediction for snap_scaffold_2-snap.3179-T1
Valid prediction for snap_scaffold_2-snap.3171-T1
Valid prediction for snap_scaffold_2-snap.3173-T1
Valid prediction for snap_scaffold_2-snap.3163-T1
Valid prediction for snap_scaffold_2-snap.3167-T1
Valid prediction for snap_scaffold_2-snap.3186-T1
Valid prediction for snap_scaffold_2-snap.3184-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20937, rend_intergenic: 17899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27709, rend_intergenic: 23759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42883, rend_intergenic: 41320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47845, rend_intergenic: 45415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57115, rend_intergenic: 48028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61350, rend_intergenic: 57978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66615, rend_intergenic: 61930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75646, rend_intergenic: 70341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82018, rend_intergenic: 78140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110107, rend_intergenic: 109028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122440, rend_intergenic: 119278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123813, rend_intergenic: 122829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126647, rend_intergenic: 124416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138316, rend_intergenic: 128024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138668
-exon list size: 286


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.2    
6.6    
6.9    
7.3    
7.6    
8.0    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.4    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.5    
21.9    
22.2    
22.6    
22.9    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
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    
42.7    
43.1    
43.4    
43.8    
44.1    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.5    
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    
53.5    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
55.9    
56.2    
56.6    
56.9    
57.3    
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    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.1    
77.4    
77.8    
78.1    
78.5    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.6    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.0    
92.4    
92.7    
93.1    
93.4    
93.8    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 20937, rend_intergenic: 17899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27709, rend_intergenic: 23759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42883, rend_intergenic: 41320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47845, rend_intergenic: 45415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57115, rend_intergenic: 48028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61350, rend_intergenic: 57978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66615, rend_intergenic: 61930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75646, rend_intergenic: 70341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82018, rend_intergenic: 78140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110107, rend_intergenic: 109028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122440, rend_intergenic: 119278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123813, rend_intergenic: 122829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126647, rend_intergenic: 124416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138316, rend_intergenic: 128024  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