-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_19441828-19580349

-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_3-snap.3849-T1
Valid prediction for GlimmerHMM_glimmerT_8504-T1
Valid prediction for GlimmerHMM_glimmerT_8506-T1
Valid prediction for snap_scaffold_3-snap.3864-T1
Valid prediction for GlimmerHMM_glimmerT_8518-T1
Valid prediction for Augustus_model.g5583.t1
Valid prediction for snap_scaffold_3-snap.3854-T1
Valid prediction for GlimmerHMM_glimmerT_8510-T1
Valid prediction for GlimmerHMM_glimmerT_8522-T1
Valid prediction for snap_scaffold_3-snap.3862-T1
Valid prediction for snap_scaffold_3-snap.3859-T1
Valid prediction for GlimmerHMM_glimmerT_8514-T1
Valid prediction for GlimmerHMM_glimmerT_8509-T1
Valid prediction for snap_scaffold_3-snap.3863-T1
Valid prediction for snap_scaffold_3-snap.3857-T1
Valid prediction for GlimmerHMM_glimmerT_8520-T1
Valid prediction for snap_scaffold_3-snap.3845-T1
Valid prediction for snap_scaffold_3-snap.3865-T1
Valid prediction for snap_scaffold_3-snap.3836-T1
Valid prediction for GlimmerHMM_glimmerT_8525-T1
Valid prediction for snap_scaffold_3-snap.3846-T1
Couldn't classify 20329, 20458
Sorry, prediction pasa_asmbl_40844.p1 fails validation.
(GGG)	 GA	20329-20458	GT	AGG
(ATA)	 AG	22343-22510	GT	AGG
(GGA)	 AG	23142-23298	GT	AGG
(GTA)	 AG	24794-24918	GT	GGG
(GAA)	 AG	26878-27008	GT	AGG
(GCT)	 AG	27945-28070	CC	AGC
-recovered pasa_asmbl_40844.p1, terminal, 27945, 28070
-recovered pasa_asmbl_40844.p1, internal, 22343, 22510
-recovered pasa_asmbl_40844.p1, internal, 23142, 23298
-recovered pasa_asmbl_40844.p1, internal, 24794, 24918
-recovered pasa_asmbl_40844.p1, internal, 26878, 27008
Valid prediction for GlimmerHMM_glimmerT_8503-T1
Valid prediction for snap_scaffold_3-snap.3839-T1
Valid prediction for GlimmerHMM_glimmerT_8515-T1
Valid prediction for GlimmerHMM_glimmerT_8524-T1
Valid prediction for snap_scaffold_3-snap.3842-T1
Valid prediction for snap_scaffold_3-snap.3838-T1
Valid prediction for GlimmerHMM_glimmerT_8505-T1
Valid prediction for Augustus_model.g5580.t1
Valid prediction for GlimmerHMM_glimmerT_8523-T1
Valid prediction for Augustus_model.g5582.t1
Valid prediction for GlimmerHMM_glimmerT_8508-T1
Valid prediction for GlimmerHMM_glimmerT_8517-T1
Valid prediction for GlimmerHMM_glimmerT_8516-T1
Valid prediction for snap_scaffold_3-snap.3841-T1
Valid prediction for snap_scaffold_3-snap.3851-T1
Valid prediction for Augustus_model.g5581.t1
Valid prediction for GlimmerHMM_glimmerT_8507-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 Augustus_model.g5584.t1
Valid prediction for snap_scaffold_3-snap.3835-T1
Valid prediction for snap_scaffold_3-snap.3847-T1
Valid prediction for GlimmerHMM_glimmerT_8521-T1
Valid prediction for snap_scaffold_3-snap.3858-T1
Valid prediction for snap_scaffold_3-snap.3837-T1
Valid prediction for snap_scaffold_3-snap.3861-T1
Valid prediction for snap_scaffold_3-snap.3840-T1
Valid prediction for Augustus_model.g5585.t1
Valid prediction for snap_scaffold_3-snap.3860-T1
Valid prediction for snap_scaffold_3-snap.3834-T1
Valid prediction for snap_scaffold_3-snap.3843-T1
Couldn't classify 89358, 90107
Sorry, prediction pasa_asmbl_39656.p1 fails validation.
(CAC)	 AA	89358-90107	GT	CCG
Couldn't classify 95002, 95055
Sorry, prediction pasa_asmbl_39655.p1 fails validation.
(ATG)	 AC	92814-92836	GT	AGG
(ATG)	 AG	93025-93142	GT	AGG
(ATC)	 AG	93556-93882	GT	TGG
(GTT)	 AG	94295-94378	GT	AGG
(AGT)	 AG	94597-94743	GT	TGG
(GCG)	 AG	95002-95055	CT	GGC
-recovered pasa_asmbl_39655.p1, initial, 92814, 92836
-recovered pasa_asmbl_39655.p1, initial, 93025, 93142
-recovered pasa_asmbl_39655.p1, internal, 93025, 93142
-recovered pasa_asmbl_39655.p1, internal, 93556, 93882
-recovered pasa_asmbl_39655.p1, internal, 94295, 94378
-recovered pasa_asmbl_39655.p1, internal, 94597, 94743
Valid prediction for snap_scaffold_3-snap.3856-T1
Valid prediction for snap_scaffold_3-snap.3853-T1
Valid prediction for GlimmerHMM_glimmerT_8513-T1
Valid prediction for snap_scaffold_3-snap.3850-T1
Valid prediction for snap_scaffold_3-snap.3855-T1
Valid prediction for GlimmerHMM_glimmerT_8519-T1
Valid prediction for GlimmerHMM_glimmerT_8512-T1
Valid prediction for snap_scaffold_3-snap.3852-T1
Valid prediction for GlimmerHMM_glimmerT_8511-T1
Valid prediction for snap_scaffold_3-snap.3848-T1
Valid prediction for snap_scaffold_3-snap.3844-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17039, rend_intergenic: 11014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23389, rend_intergenic: 18135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41607, rend_intergenic: 35653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65693, rend_intergenic: 60837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79461, rend_intergenic: 76846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86878, rend_intergenic: 80349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89992, rend_intergenic: 88090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104569, rend_intergenic: 101797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108747, rend_intergenic: 106167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129095, rend_intergenic: 117244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138522
-exon list size: 221


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.7    
3.1    
3.6    
4.0    
4.5    
4.9    
5.4    
5.8    
6.3    
6.7    
7.2    
7.6    
8.1    
8.5    
9.0    
9.4    
9.9    
10.3    
10.8    
11.2    
11.7    
12.1    
12.6    
13.0    
13.5    
13.9    
14.3    
14.8    
15.2    
15.7    
16.1    
16.6    
17.0    
17.5    
17.9    
18.4    
18.8    
19.3    
19.7    
20.2    
20.6    
21.1    
21.5    
22.0    
22.4    
22.9    
23.3    
23.8    
24.2    
24.7    
25.1    
25.6    
26.0    
26.5    
26.9    
27.4    
27.8    
28.3    
28.7    
29.1    
29.6    
30.0    
30.5    
30.9    
31.4    
31.8    
32.3    
32.7    
33.2    
33.6    
34.1    
34.5    
35.0    
35.4    
35.9    
36.3    
36.8    
37.2    
37.7    
38.1    
38.6    
39.0    
39.5    
39.9    
40.4    
40.8    
41.3    
41.7    
42.2    
42.6    
43.0    
43.5    
43.9    
44.4    
44.8    
45.3    
45.7    
46.2    
46.6    
47.1    
47.5    
48.0    
48.4    
48.9    
49.3    
49.8    
50.2    
50.7    
51.1    
51.6    
52.0    
52.5    
52.9    
53.4    
53.8    
54.3    
54.7    
55.2    
55.6    
56.1    
56.5    
57.0    
57.4    
57.8    
58.3    
58.7    
59.2    
59.6    
60.1    
60.5    
61.0    
61.4    
61.9    
62.3    
62.8    
63.2    
63.7    
64.1    
64.6    
65.0    
65.5    
65.9    
66.4    
66.8    
67.3    
67.7    
68.2    
68.6    
69.1    
69.5    
70.0    
70.4    
70.9    
71.3    
71.7    
72.2    
72.6    
73.1    
73.5    
74.0    
74.4    
74.9    
75.3    
75.8    
76.2    
76.7    
77.1    
77.6    
78.0    
78.5    
78.9    
79.4    
79.8    
80.3    
80.7    
81.2    
81.6    
82.1    
82.5    
83.0    
83.4    
83.9    
84.3    
84.8    
85.2    
85.7    
86.1    
86.5    
87.0    
87.4    
87.9    
88.3    
88.8    
89.2    
89.7    
90.1    
90.6    
91.0    
91.5    
91.9    
92.4    
92.8    
93.3    
93.7    
94.2    
94.6    
95.1    
95.5    
96.0    
96.4    
96.9    
97.3    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 17039, rend_intergenic: 11014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23389, rend_intergenic: 18135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41607, rend_intergenic: 35653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65693, rend_intergenic: 60837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79461, rend_intergenic: 76846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86878, rend_intergenic: 80349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89992, rend_intergenic: 88090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104569, rend_intergenic: 101797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108747, rend_intergenic: 106167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129095, rend_intergenic: 117244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support