-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_5679806-6013119

-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_12-snap.1152-T1
Valid prediction for snap_scaffold_12-snap.1127-T1
Valid prediction for snap_scaffold_12-snap.1143-T1
Valid prediction for snap_scaffold_12-snap.1150-T1
Valid prediction for GlimmerHMM_glimmerT_29401-T1
Valid prediction for GlimmerHMM_glimmerT_29402-T1
Valid prediction for snap_scaffold_12-snap.1130-T1
Valid prediction for snap_scaffold_12-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_29410-T1
Valid prediction for GlimmerHMM_glimmerT_29398-T1
Valid prediction for GlimmerHMM_glimmerT_29408-T1
Valid prediction for snap_scaffold_12-snap.1140-T1
Valid prediction for snap_scaffold_12-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_29413-T1
Valid prediction for snap_scaffold_12-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_29405-T1
Valid prediction for GlimmerHMM_glimmerT_29406-T1
Valid prediction for GlimmerHMM_glimmerT_29400-T1
Valid prediction for GlimmerHMM_glimmerT_29409-T1
Valid prediction for snap_scaffold_12-snap.1144-T1
Valid prediction for snap_scaffold_12-snap.1118-T1
Valid prediction for Augustus_model.g19404.t1
Valid prediction for GlimmerHMM_glimmerT_29397-T1
Valid prediction for snap_scaffold_12-snap.1129-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_12-snap.1151-T1
Valid prediction for Augustus_model.g19400.t1
Valid prediction for snap_scaffold_12-snap.1147-T1
Valid prediction for GlimmerHMM_glimmerT_29392-T1
Couldn't classify 308135, 308294
Sorry, prediction CodingQuarry_transcript_10236-T1 fails validation.
(ATG)	 AC	306790-306801	GT	CGG
(ATT)	 AG	306998-307136	GT	CAG
(GTG)	 AG	307474-307560	GC	AAG
(TCT)	 TC	308135-308294	GT	AGG
(GTC)	 AG	308382-308433	GT	AGG
(ATC)	 AG	308610-308759	CG	GAC
-recovered CodingQuarry_transcript_10236-T1, initial, 306790, 306801
add_exon() Sorry, CodingQuarry_transcript_10236-T1 307474-307560-terminal-1 is invalid.
-recovered CodingQuarry_transcript_10236-T1, terminal, 307474, 307560
-recovered CodingQuarry_transcript_10236-T1, terminal, 308610, 308759
-recovered CodingQuarry_transcript_10236-T1, internal, 306998, 307136
-recovered CodingQuarry_transcript_10236-T1, internal, 307474, 307560
-recovered CodingQuarry_transcript_10236-T1, internal, 308382, 308433
Valid prediction for snap_scaffold_12-snap.1119-T1
Valid prediction for snap_scaffold_12-snap.1141-T1
Valid prediction for snap_scaffold_12-snap.1124-T1
Valid prediction for Augustus_model.g19396.t1
Valid prediction for Augustus_model.g19397.t1
Valid prediction for Augustus_model.g19401.t1
Valid prediction for snap_scaffold_12-snap.1138-T1
Valid prediction for snap_scaffold_12-snap.1117-T1
Valid prediction for GlimmerHMM_glimmerT_29399-T1
Valid prediction for Augustus_model.g19398.t1
Valid prediction for snap_scaffold_12-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_29395-T1
Valid prediction for CodingQuarry_transcript_10238-T1
Valid prediction for snap_scaffold_12-snap.1132-T1
Valid prediction for Augustus_model.g19399.t1
Valid prediction for GlimmerHMM_glimmerT_29394-T1
Valid prediction for pasa_asmbl_8523.p1
Valid prediction for snap_scaffold_12-snap.1125-T1
Valid prediction for GlimmerHMM_glimmerT_29396-T1
Couldn't classify 292383, 292447
Sorry, prediction pasa_asmbl_8525.p1 fails validation.
(ACA)	 CC	292383-292447	GT	AGG
(TCC)	 AG	293398-295303	GT	GAG
-recovered pasa_asmbl_8525.p1, terminal, 293398, 295303
-recovered pasa_asmbl_8525.p1, internal, 293398, 295303
Valid prediction for snap_scaffold_12-snap.1121-T1
Valid prediction for snap_scaffold_12-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_29414-T1
Valid prediction for Augustus_model.g19402.t1
Valid prediction for snap_scaffold_12-snap.1149-T1
Couldn't classify 307474, 307577
Couldn't classify 307753, 307785
Sorry, prediction CodingQuarry_transcript_10237-T1 fails validation.
(ATG)	 AC	306790-306801	GT	CGG
(ATT)	 AG	306998-307136	GT	CAG
(GTG)	 AG	307474-307577	CT	CTC
(TTC)	 AC	307753-307785	CT	AAC
-recovered CodingQuarry_transcript_10237-T1, initial, 306790, 306801
-recovered CodingQuarry_transcript_10237-T1, internal, 306998, 307136
Valid prediction for snap_scaffold_12-snap.1145-T1
Valid prediction for GlimmerHMM_glimmerT_29403-T1
Valid prediction for snap_scaffold_12-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_29407-T1
Valid prediction for snap_scaffold_12-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_29411-T1
Valid prediction for Augustus_model.g19395.t1
Valid prediction for Augustus_model.g19403.t1
Valid prediction for snap_scaffold_12-snap.1146-T1
Valid prediction for snap_scaffold_12-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_29393-T1
Valid prediction for snap_scaffold_12-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_29412-T1
Valid prediction for snap_scaffold_12-snap.1135-T1
Valid prediction for snap_scaffold_12-snap.1137-T1
Valid prediction for snap_scaffold_12-snap.1122-T1
Valid prediction for snap_scaffold_12-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_29404-T1
Valid prediction for snap_scaffold_12-snap.1142-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12266, rend_intergenic: 10157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65583, rend_intergenic: 62215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94114, rend_intergenic: 92571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 333314
-exon list size: 233


building trellis

0.4    
0.9    
1.3    
1.7    
2.1    
2.6    
3.0    
3.4    
3.8    
4.3    
4.7    
5.1    
5.5    
6.0    
6.4    
6.8    
7.2    
7.7    
8.1    
8.5    
8.9    
9.4    
9.8    
10.2    
10.6    
11.1    
11.5    
11.9    
12.3    
12.8    
13.2    
13.6    
14.0    
14.5    
14.9    
15.3    
15.7    
16.2    
16.6    
17.0    
17.4    
17.9    
18.3    
18.7    
19.1    
19.6    
20.0    
20.4    
20.9    
21.3    
21.7    
22.1    
22.6    
23.0    
23.4    
23.8    
24.3    
24.7    
25.1    
25.5    
26.0    
26.4    
26.8    
27.2    
27.7    
28.1    
28.5    
28.9    
29.4    
29.8    
30.2    
30.6    
31.1    
31.5    
31.9    
32.3    
32.8    
33.2    
33.6    
34.0    
34.5    
34.9    
35.3    
35.7    
36.2    
36.6    
37.0    
37.4    
37.9    
38.3    
38.7    
39.1    
39.6    
40.0    
40.4    
40.9    
41.3    
41.7    
42.1    
42.6    
43.0    
43.4    
43.8    
44.3    
44.7    
45.1    
45.5    
46.0    
46.4    
46.8    
47.2    
47.7    
48.1    
48.5    
48.9    
49.4    
49.8    
50.2    
50.6    
51.1    
51.5    
51.9    
52.3    
52.8    
53.2    
53.6    
54.0    
54.5    
54.9    
55.3    
55.7    
56.2    
56.6    
57.0    
57.4    
57.9    
58.3    
58.7    
59.1    
59.6    
60.0    
60.4    
60.9    
61.3    
61.7    
62.1    
62.6    
63.0    
63.4    
63.8    
64.3    
64.7    
65.1    
65.5    
66.0    
66.4    
66.8    
67.2    
67.7    
68.1    
68.5    
68.9    
69.4    
69.8    
70.2    
70.6    
71.1    
71.5    
71.9    
72.3    
72.8    
73.2    
73.6    
74.0    
74.5    
74.9    
75.3    
75.7    
76.2    
76.6    
77.0    
77.4    
77.9    
78.3    
78.7    
79.1    
79.6    
80.0    
80.4    
80.9    
81.3    
81.7    
82.1    
82.6    
83.0    
83.4    
83.8    
84.3    
84.7    
85.1    
85.5    
86.0    
86.4    
86.8    
87.2    
87.7    
88.1    
88.5    
88.9    
89.4    
89.8    
90.2    
90.6    
91.1    
91.5    
91.9    
92.3    
92.8    
93.2    
93.6    
94.0    
94.5    
94.9    
95.3    
95.7    
96.2    
96.6    
97.0    
97.4    
97.9    
98.3    
98.7    
99.1    
99.6    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 12266, rend_intergenic: 10157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65583, rend_intergenic: 62215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94114, rend_intergenic: 92571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support