-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_9551428-9816976

-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 Augustus_model.g36381.t1
Valid prediction for Augustus_model.g36399.t1
Valid prediction for GlimmerHMM_glimmerT_54832-T1
Valid prediction for snap_scaffold_25-snap.2081-T1
Valid prediction for snap_scaffold_25-snap.2059-T1
Valid prediction for snap_scaffold_25-snap.2083-T1
Valid prediction for snap_scaffold_25-snap.2069-T1
Valid prediction for Augustus_model.g36386.t1
Valid prediction for snap_scaffold_25-snap.2080-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g36387.t1
Valid prediction for snap_scaffold_25-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_54823-T1
Valid prediction for snap_scaffold_25-snap.2065-T1
Valid prediction for GlimmerHMM_glimmerT_54836-T1
Valid prediction for snap_scaffold_25-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_54828-T1
Valid prediction for GlimmerHMM_glimmerT_54837-T1
Valid prediction for Augustus_model.g36393.t1
Valid prediction for GlimmerHMM_glimmerT_54810-T1
Valid prediction for GlimmerHMM_glimmerT_54812-T1
Valid prediction for snap_scaffold_25-snap.2072-T1
Valid prediction for snap_scaffold_25-snap.2070-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54829-T1
Couldn't classify 153340, 153430
Couldn't classify 155828, 155866
Sorry, prediction pasa_asmbl_33838.p1 fails validation.
(CAG)	 AG	153340-153430	GT	TGG
(GTA)	 AG	153596-153695	GT	AGG
(GGC)	 AG	154877-154981	GT	GGG
(ATT)	 AG	155193-155328	GT	CAG
(ACA)	 AG	155409-155471	GT	TGG
(GCA)	 AG	155828-155866	TA	TGT
-recovered pasa_asmbl_33838.p1, internal, 153340, 153430
-recovered pasa_asmbl_33838.p1, internal, 153596, 153695
-recovered pasa_asmbl_33838.p1, internal, 154877, 154981
-recovered pasa_asmbl_33838.p1, internal, 155193, 155328
-recovered pasa_asmbl_33838.p1, internal, 155409, 155471
Valid prediction for GlimmerHMM_glimmerT_54822-T1
Valid prediction for GlimmerHMM_glimmerT_54816-T1
Valid prediction for GlimmerHMM_glimmerT_54814-T1
Valid prediction for pasa_asmbl_33839.p1
Valid prediction for GlimmerHMM_glimmerT_54824-T1
Valid prediction for Augustus_model.g36378.t1
Valid prediction for Augustus_model.g36395.t1
Valid prediction for Augustus_model.g36400.t1
Valid prediction for GlimmerHMM_glimmerT_54825-T1
Valid prediction for snap_scaffold_25-snap.2067-T1
Valid prediction for snap_scaffold_25-snap.2061-T1
Valid prediction for Augustus_model.g36392.t1
Valid prediction for Augustus_model.g36389.t1
Valid prediction for snap_scaffold_25-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_54820-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_25-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_54839-T1
Valid prediction for GlimmerHMM_glimmerT_54838-T1
Valid prediction for snap_scaffold_25-snap.2068-T1
Valid prediction for GlimmerHMM_glimmerT_54826-T1
Valid prediction for GlimmerHMM_glimmerT_54833-T1
Valid prediction for snap_scaffold_25-snap.2079-T1
Valid prediction for snap_scaffold_25-snap.2056-T1
Couldn't classify 192089, 192237
Sorry, prediction pasa_asmbl_34516.p2 fails validation.
(ATG)	 AC	189858-189870	GT	AGG
(GAA)	 AG	190899-191105	GT	AGG
(TCC)	 AG	192089-192237	GT	AGG
-recovered pasa_asmbl_34516.p2, initial, 189858, 189870
-recovered pasa_asmbl_34516.p2, internal, 190899, 191105
-recovered pasa_asmbl_34516.p2, internal, 192089, 192237
Valid prediction for Augustus_model.g36379.t1
Valid prediction for snap_scaffold_25-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_54827-T1
Valid prediction for Augustus_model.g36377.t1
Valid prediction for snap_scaffold_25-snap.2057-T1
Valid prediction for GlimmerHMM_glimmerT_54817-T1
Valid prediction for Augustus_model.g36380.t1
Valid prediction for Augustus_model.g36391.t1
Valid prediction for snap_scaffold_25-snap.2071-T1
Valid prediction for snap_scaffold_25-snap.2063-T1
Valid prediction for GlimmerHMM_glimmerT_54815-T1
Valid prediction for Augustus_model.g36390.t1
Valid prediction for Augustus_model.g36394.t1
Valid prediction for snap_scaffold_25-snap.2073-T1
Valid prediction for GlimmerHMM_glimmerT_54819-T1
Valid prediction for GlimmerHMM_glimmerT_54835-T1
Valid prediction for snap_scaffold_25-snap.2077-T1
Valid prediction for HiQ_model.g36385.t1
Valid prediction for Augustus_model.g36396.t1
Valid prediction for GlimmerHMM_glimmerT_54821-T1
Valid prediction for Augustus_model.g36383.t1
Valid prediction for snap_scaffold_25-snap.2064-T1
Couldn't classify 210821, 210960
Sorry, prediction pasa_asmbl_34515.p1 fails validation.
(ATG)	 CT	208312-208425	GT	AGG
(ACA)	 AG	209250-209436	GT	TGG
(GCC)	 AG	210536-210664	GT	AGG
(GGA)	 AG	210821-210960	AG	TTA
-recovered pasa_asmbl_34515.p1, initial, 208312, 208425
-recovered pasa_asmbl_34515.p1, internal, 209250, 209436
-recovered pasa_asmbl_34515.p1, internal, 210536, 210664
Valid prediction for GlimmerHMM_glimmerT_54834-T1
Valid prediction for HiQ_model.g36384.t1
Valid prediction for GlimmerHMM_glimmerT_54830-T1
Valid prediction for Augustus_model.g36388.t1
Valid prediction for snap_scaffold_25-snap.2058-T1
Valid prediction for snap_scaffold_25-snap.2076-T1
Couldn't classify 250017, 250082
Sorry, prediction pasa_asmbl_34513.p1 fails validation.
(ACT)	 GT	250017-250082	GT	CTG
(GTT)	 AG	250644-250706	GT	AGG
(GTG)	 AG	251297-251366	GT	AGG
(GAC)	 AG	251464-251570	GT	AGG
(GCA)	 AG	251675-251842	GC	AGG
(GTT)	 AG	252307-252379	GT	AAG
(GCA)	 AG	255096-255170	GT	AGG
(ATC)	 AG	255997-256381	GT	GAG
(AAC)	 AG	256898-257075	GG	GAG
-recovered pasa_asmbl_34513.p1, terminal, 252307, 252379
add_exon() Sorry, pasa_asmbl_34513.p1 255997-256381-terminal-3 is invalid.
-recovered pasa_asmbl_34513.p1, terminal, 255997, 256381
-recovered pasa_asmbl_34513.p1, terminal, 256898, 257075
-recovered pasa_asmbl_34513.p1, internal, 250644, 250706
-recovered pasa_asmbl_34513.p1, internal, 251297, 251366
-recovered pasa_asmbl_34513.p1, internal, 251464, 251570
-recovered pasa_asmbl_34513.p1, internal, 251675, 251842
-recovered pasa_asmbl_34513.p1, internal, 252307, 252379
-recovered pasa_asmbl_34513.p1, internal, 255096, 255170
-recovered pasa_asmbl_34513.p1, internal, 255997, 256381
Valid prediction for Augustus_model.g36382.t1
Valid prediction for Augustus_model.g36397.t1
Valid prediction for Augustus_model.g36401.t1
Valid prediction for Augustus_model.g36398.t1
Valid prediction for snap_scaffold_25-snap.2078-T1
Valid prediction for snap_scaffold_25-snap.2074-T1
Couldn't classify 201008, 201150
Sorry, prediction pasa_asmbl_34560.p1 fails validation.
(ATG)	 GC	195624-195662	GT	AGG
(AAG)	 AG	196844-196948	GT	ATG
(ATG)	 AG	197072-197174	GT	AGG
(GTG)	 AG	198684-198844	GT	AGG
(GAG)	 AG	200639-200774	GT	AGG
(AGG)	 AG	201008-201150	GT	AGG
-recovered pasa_asmbl_34560.p1, initial, 195624, 195662
-recovered pasa_asmbl_34560.p1, initial, 197072, 197174
add_exon() Sorry, pasa_asmbl_34560.p1 197072-197174-terminal-3 is invalid.
-recovered pasa_asmbl_34560.p1, terminal, 197072, 197174
add_exon() Sorry, pasa_asmbl_34560.p1 200639-200774-terminal-3 is invalid.
-recovered pasa_asmbl_34560.p1, terminal, 200639, 200774
-recovered pasa_asmbl_34560.p1, internal, 196844, 196948
-recovered pasa_asmbl_34560.p1, internal, 197072, 197174
-recovered pasa_asmbl_34560.p1, internal, 198684, 198844
-recovered pasa_asmbl_34560.p1, internal, 200639, 200774
-recovered pasa_asmbl_34560.p1, internal, 201008, 201150
Valid prediction for GlimmerHMM_glimmerT_54831-T1
Valid prediction for GlimmerHMM_glimmerT_54818-T1
Valid prediction for GlimmerHMM_glimmerT_54811-T1
Valid prediction for GlimmerHMM_glimmerT_54813-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 265549
-exon list size: 268


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.6    
5.9    
6.3    
6.7    
7.0    
7.4    
7.8    
8.1    
8.5    
8.9    
9.3    
9.6    
10.0    
10.4    
10.7    
11.1    
11.5    
11.9    
12.2    
12.6    
13.0    
13.3    
13.7    
14.1    
14.4    
14.8    
15.2    
15.6    
15.9    
16.3    
16.7    
17.0    
17.4    
17.8    
18.1    
18.5    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.5    
21.9    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.4    
24.8    
25.2    
25.6    
25.9    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.9    
29.3    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.8    
38.1    
38.5    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.1    
44.4    
44.8    
45.2    
45.6    
45.9    
46.3    
46.7    
47.0    
47.4    
47.8    
48.1    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.9    
52.2    
52.6    
53.0    
53.3    
53.7    
54.1    
54.4    
54.8    
55.2    
55.6    
55.9    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.5    
61.9    
62.2    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.7    
71.1    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.1    
74.4    
74.8    
75.2    
75.6    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.1    
78.5    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.5    
81.9    
82.2    
82.6    
83.0    
83.3    
83.7    
84.1    
84.4    
84.8    
85.2    
85.6    
85.9    
86.3    
86.7    
87.0    
87.4    
87.8    
88.1    
88.5    
88.9    
89.3    
89.6    
90.0    
90.4    
90.7    
91.1    
91.5    
91.9    
92.2    
92.6    
93.0    
93.3    
93.7    
94.1    
94.4    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 34 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 254513 - 265549
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 254918 - 265549
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support