-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_2015292-2139449

-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 CodingQuarry_transcript_35572-T1
Valid prediction for GlimmerHMM_glimmerT_50595-T1
Valid prediction for Augustus_model.g33800.t1
Valid prediction for snap_scaffold_23-snap.382-T1
Valid prediction for Augustus_model.g33797.t1
Valid prediction for snap_scaffold_23-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_50596-T1
Valid prediction for HiQ_model.g33795.t1
Valid prediction for snap_scaffold_23-snap.375-T1
Valid prediction for Augustus_model.g33792.t1
Valid prediction for GlimmerHMM_glimmerT_50603-T1
Valid prediction for snap_scaffold_23-snap.372-T1
Valid prediction for snap_scaffold_23-snap.367-T1
Valid prediction for CodingQuarry_transcript_35573-T1
Valid prediction for snap_scaffold_23-snap.369-T1
Valid prediction for HiQ_model.g33798.t1
Valid prediction for snap_scaffold_23-snap.384-T1
Valid prediction for Augustus_model.g33803.t1
Valid prediction for Augustus_model.g33801.t1
Valid prediction for GlimmerHMM_glimmerT_50598-T1
Valid prediction for snap_scaffold_23-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_50591-T1
Valid prediction for pasa_asmbl_31373.p1
Valid prediction for CodingQuarry_transcript_35571-T1
Valid prediction for snap_scaffold_23-snap.370-T1
Valid prediction for snap_scaffold_23-snap.374-T1
Valid prediction for Augustus_model.g33799.t1
Valid prediction for snap_scaffold_23-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_50600-T1
Valid prediction for GlimmerHMM_glimmerT_50599-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: -)Couldn't classify 104802, 104903
Sorry, prediction pasa_asmbl_30690.p1 fails validation.
(AAT)	 GC	104802-104903	GT	TGG
(GAG)	 AG	105111-105201	GT	AAG
(ATA)	 AG	105320-105356	GT	AGG
(CTT)	 AG	105455-105521	GT	AGG
(GAG)	 AG	105628-105824	GT	AGG
(TCA)	 AG	105945-106064	GT	AGG
(GTC)	 AG	106161-106245	GT	AGG
(TGG)	 AG	106338-106446	GT	AGG
(ACG)	 AG	106556-106962	GG	GAG
-recovered pasa_asmbl_30690.p1, terminal, 105111, 105201
add_exon() Sorry, pasa_asmbl_30690.p1 105945-106064-terminal-1 is invalid.
-recovered pasa_asmbl_30690.p1, terminal, 105945, 106064
-recovered pasa_asmbl_30690.p1, terminal, 106556, 106962
-recovered pasa_asmbl_30690.p1, internal, 105111, 105201
-recovered pasa_asmbl_30690.p1, internal, 105320, 105356
-recovered pasa_asmbl_30690.p1, internal, 105455, 105521
-recovered pasa_asmbl_30690.p1, internal, 105628, 105824
-recovered pasa_asmbl_30690.p1, internal, 105945, 106064
-recovered pasa_asmbl_30690.p1, internal, 106161, 106245
-recovered pasa_asmbl_30690.p1, internal, 106338, 106446
Valid prediction for snap_scaffold_23-snap.389-T1
Valid prediction for snap_scaffold_23-snap.388-T1
Valid prediction for snap_scaffold_23-snap.368-T1
Couldn't classify 109890, 109959
Couldn't classify 110848, 110855
Sorry, prediction pasa_asmbl_30688.p1 fails validation.
(CCT)	 GG	109890-109959	GT	TGG
(ACT)	 AG	110109-110287	GT	AGG
(GTC)	 AG	110383-110583	GT	AGG
(CTC)	 AG	110665-110737	GT	TGG
(GTT)	 AG	110848-110855	CA	CCC
-recovered pasa_asmbl_30688.p1, internal, 110109, 110287
-recovered pasa_asmbl_30688.p1, internal, 110383, 110583
-recovered pasa_asmbl_30688.p1, internal, 110665, 110737
Valid prediction for Augustus_model.g33794.t1
Valid prediction for Augustus_model.g33796.t1
Valid prediction for GlimmerHMM_glimmerT_50597-T1
Valid prediction for snap_scaffold_23-snap.387-T1
Valid prediction for snap_scaffold_23-snap.386-T1
Valid prediction for snap_scaffold_23-snap.378-T1
Valid prediction for Augustus_model.g33804.t1
Valid prediction for snap_scaffold_23-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_50605-T1
Valid prediction for CodingQuarry_transcript_35574-T1
Valid prediction for GlimmerHMM_glimmerT_50604-T1
Valid prediction for snap_scaffold_23-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_50592-T1
Valid prediction for GlimmerHMM_glimmerT_50602-T1
Valid prediction for GlimmerHMM_glimmerT_50593-T1
Valid prediction for snap_scaffold_23-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_50606-T1
Valid prediction for GlimmerHMM_glimmerT_50594-T1
Valid prediction for pasa_asmbl_30692.p1
Valid prediction for snap_scaffold_23-snap.381-T1
Valid prediction for snap_scaffold_23-snap.385-T1
Valid prediction for snap_scaffold_23-snap.380-T1
Valid prediction for snap_scaffold_23-snap.366-T1
Valid prediction for snap_scaffold_23-snap.377-T1
Valid prediction for Augustus_model.g33802.t1
Valid prediction for snap_scaffold_23-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_50601-T1
Valid prediction for pasa_asmbl_30686.p1
Valid prediction for snap_scaffold_23-snap.371-T1
Valid prediction for snap_scaffold_23-snap.392-T1
Valid prediction for snap_scaffold_23-snap.390-T1
Valid prediction for snap_scaffold_23-snap.364-T1
Valid prediction for snap_scaffold_23-snap.373-T1
Valid prediction for Augustus_model.g33793.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48904, rend_intergenic: 46747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77405, rend_intergenic: 74373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83603, rend_intergenic: 79767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122349, rend_intergenic: 120488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 124158
-exon list size: 246


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.4    
4.8    
5.2    
5.6    
6.0    
6.5    
6.9    
7.3    
7.7    
8.1    
8.5    
8.9    
9.3    
9.7    
10.1    
10.5    
10.9    
11.3    
11.7    
12.1    
12.5    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.3    
17.7    
18.1    
18.5    
19.0    
19.4    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.2    
22.6    
23.0    
23.4    
23.8    
24.2    
24.6    
25.0    
25.4    
25.8    
26.2    
26.6    
27.0    
27.4    
27.8    
28.2    
28.6    
29.0    
29.4    
29.8    
30.2    
30.6    
31.0    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.3    
34.7    
35.1    
35.5    
35.9    
36.3    
36.7    
37.1    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.9    
40.3    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.1    
43.5    
44.0    
44.4    
44.8    
45.2    
45.6    
46.0    
46.4    
46.8    
47.2    
47.6    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.4    
52.8    
53.2    
53.6    
54.0    
54.4    
54.8    
55.2    
55.6    
56.0    
56.5    
56.9    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.7    
60.1    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.9    
63.3    
63.7    
64.1    
64.5    
64.9    
65.3    
65.7    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
69.0    
69.4    
69.8    
70.2    
70.6    
71.0    
71.4    
71.8    
72.2    
72.6    
73.0    
73.4    
73.8    
74.2    
74.6    
75.0    
75.4    
75.8    
76.2    
76.6    
77.0    
77.4    
77.8    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.6    
81.0    
81.5    
81.9    
82.3    
82.7    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.5    
87.9    
88.3    
88.7    
89.1    
89.5    
89.9    
90.3    
90.7    
91.1    
91.5    
91.9    
92.3    
92.7    
93.1    
93.5    
94.0    
94.4    
94.8    
95.2    
95.6    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 48904, rend_intergenic: 46747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77405, rend_intergenic: 74373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83603, rend_intergenic: 79767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122349, rend_intergenic: 120488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support