-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_16213153-16416864

-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 GlimmerHMM_glimmerT_37629-T1
Valid prediction for snap_scaffold_15-snap.3187-T1
Valid prediction for GlimmerHMM_glimmerT_37628-T1
Valid prediction for GlimmerHMM_glimmerT_37610-T1
Couldn't classify 63768, 63941
Sorry, prediction pasa_asmbl_15850.p1 fails validation.
(TTA)	 AT	63768-63941	GT	CCG
(CCC)	 AG	64040-64207	GT	AGG
(GCT)	 AG	67016-67145	GT	TGG
(ATT)	 AG	67315-67437	GT	GGG
(GCA)	 AG	67531-67715	GT	AAG
(GGT)	 AG	67907-68272	AT	GAA
-recovered pasa_asmbl_15850.p1, terminal, 67907, 68272
-recovered pasa_asmbl_15850.p1, internal, 64040, 64207
-recovered pasa_asmbl_15850.p1, internal, 67016, 67145
-recovered pasa_asmbl_15850.p1, internal, 67315, 67437
-recovered pasa_asmbl_15850.p1, internal, 67531, 67715
Couldn't classify 137640, 137735
Couldn't classify 141069, 141209
Sorry, prediction pasa_asmbl_15852.p1 fails validation.
(CTC)	 AA	137640-137735	GT	CGG
(GTA)	 AG	138167-138292	GT	AGG
(GAA)	 AG	141069-141209	TA	GGT
-recovered pasa_asmbl_15852.p1, internal, 138167, 138292
Valid prediction for GlimmerHMM_glimmerT_37635-T1
Valid prediction for snap_scaffold_15-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_37632-T1
Valid prediction for GlimmerHMM_glimmerT_37630-T1
Valid prediction for snap_scaffold_15-snap.3210-T1
Valid prediction for snap_scaffold_15-snap.3200-T1
Valid prediction for snap_scaffold_15-snap.3211-T1
Valid prediction for CodingQuarry_transcript_18283-T1
Couldn't classify 145289, 145393
Sorry, prediction pasa_asmbl_15853.p1 fails validation.
(CTC)	 TT	145289-145393	GC	ATG
(GAT)	 AG	145489-145602	GT	AGG
(AAT)	 AG	145693-145799	GT	GTG
(GTA)	 AG	145929-146036	GT	AGG
(GTC)	 AG	147623-147657	GT	TTG
(CTA)	 AG	150530-150708	GT	AGG
(GTG)	 AG	150798-150902	GT	AGG
(GAG)	 AG	151000-151141	GT	AGG
(AGG)	 AG	151225-151345	GT	AGG
(ATT)	 AG	151455-151554	GT	AGG
(CAT)	 AG	151671-151757	GT	AGG
(ATT)	 AG	151880-151939	TA	AAT
-recovered pasa_asmbl_15853.p1, terminal, 151880, 151939
-recovered pasa_asmbl_15853.p1, internal, 145489, 145602
-recovered pasa_asmbl_15853.p1, internal, 145693, 145799
-recovered pasa_asmbl_15853.p1, internal, 145929, 146036
-recovered pasa_asmbl_15853.p1, internal, 147623, 147657
-recovered pasa_asmbl_15853.p1, internal, 150530, 150708
-recovered pasa_asmbl_15853.p1, internal, 150798, 150902
-recovered pasa_asmbl_15853.p1, internal, 151000, 151141
-recovered pasa_asmbl_15853.p1, internal, 151225, 151345
-recovered pasa_asmbl_15853.p1, internal, 151455, 151554
-recovered pasa_asmbl_15853.p1, internal, 151671, 151757
Valid prediction for snap_scaffold_15-snap.3207-T1
Valid prediction for snap_scaffold_15-snap.3201-T1
Valid prediction for GlimmerHMM_glimmerT_37626-T1
Valid prediction for GlimmerHMM_glimmerT_37608-T1
Valid prediction for GlimmerHMM_glimmerT_37619-T1
Valid prediction for GlimmerHMM_glimmerT_37614-T1
Valid prediction for snap_scaffold_15-snap.3209-T1
Valid prediction for CodingQuarry_transcript_18285-T1
Valid prediction for GlimmerHMM_glimmerT_37624-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_15-snap.3213-T1
Valid prediction for snap_scaffold_15-snap.3217-T1
Valid prediction for snap_scaffold_15-snap.3192-T1
Valid prediction for GlimmerHMM_glimmerT_37627-T1
Couldn't classify 150948, 151129
Sorry, prediction pasa_asmbl_14820.p1 fails validation.
(GAG)	 AT	150948-151129	GT	AGG
(GCC)	 AG	152192-152344	GT	AAG
(AGC)	 AG	152467-152692	GT	AGG
(GTG)	 AG	152875-153192	GT	AGG
(ATT)	 AG	154579-154713	GT	GGG
(ACG)	 AG	155005-155097	GG	AGG
add_exon() Sorry, pasa_asmbl_14820.p1 152192-152344-terminal-1 is invalid.
-recovered pasa_asmbl_14820.p1, terminal, 152192, 152344
-recovered pasa_asmbl_14820.p1, terminal, 155005, 155097
-recovered pasa_asmbl_14820.p1, internal, 152192, 152344
-recovered pasa_asmbl_14820.p1, internal, 152467, 152692
-recovered pasa_asmbl_14820.p1, internal, 152875, 153192
-recovered pasa_asmbl_14820.p1, internal, 154579, 154713
Valid prediction for pasa_asmbl_14829.p1
Valid prediction for GlimmerHMM_glimmerT_37634-T1
Valid prediction for GlimmerHMM_glimmerT_37636-T1
Valid prediction for GlimmerHMM_glimmerT_37618-T1
Valid prediction for snap_scaffold_15-snap.3198-T1
Valid prediction for pasa_asmbl_14827.p1
Valid prediction for snap_scaffold_15-snap.3204-T1
Valid prediction for snap_scaffold_15-snap.3216-T1
Valid prediction for GlimmerHMM_glimmerT_37617-T1
Valid prediction for snap_scaffold_15-snap.3214-T1
Valid prediction for GlimmerHMM_glimmerT_37612-T1
Valid prediction for snap_scaffold_15-snap.3189-T1
Valid prediction for snap_scaffold_15-snap.3221-T1
Valid prediction for snap_scaffold_15-snap.3203-T1
Valid prediction for GlimmerHMM_glimmerT_37623-T1
Valid prediction for GlimmerHMM_glimmerT_37631-T1
Valid prediction for snap_scaffold_15-snap.3190-T1
Valid prediction for snap_scaffold_15-snap.3220-T1
Valid prediction for snap_scaffold_15-snap.3197-T1
Valid prediction for snap_scaffold_15-snap.3205-T1
Valid prediction for snap_scaffold_15-snap.3212-T1
Couldn't classify 10164, 10478
Sorry, prediction pasa_asmbl_14858.p1 fails validation.
(TAT)	 TG	10164-10478	AA	ACA
Valid prediction for snap_scaffold_15-snap.3194-T1
Valid prediction for GlimmerHMM_glimmerT_37637-T1
Couldn't classify 149778, 149902
Sorry, prediction pasa_asmbl_14825.p1 fails validation.
(ATG)	 GA	147303-147451	GT	AGG
(ATA)	 AG	147557-147716	GT	AGG
(TCT)	 AG	147808-147913	GT	GGG
(GTA)	 AG	148012-148141	GT	ATG
(CCA)	 AG	148250-148365	GT	CAG
(CCA)	 AG	149778-149902	GT	GTG
-recovered pasa_asmbl_14825.p1, initial, 147303, 147451
-recovered pasa_asmbl_14825.p1, internal, 147557, 147716
-recovered pasa_asmbl_14825.p1, internal, 147808, 147913
-recovered pasa_asmbl_14825.p1, internal, 148012, 148141
-recovered pasa_asmbl_14825.p1, internal, 148250, 148365
-recovered pasa_asmbl_14825.p1, internal, 149778, 149902
Couldn't classify 70359, 71144
Sorry, prediction pasa_asmbl_14830.p1 fails validation.
(CTA)	 AT	70359-71144	GA	GTG
Valid prediction for snap_scaffold_15-snap.3195-T1
Valid prediction for GlimmerHMM_glimmerT_37609-T1
Valid prediction for snap_scaffold_15-snap.3193-T1
Valid prediction for snap_scaffold_15-snap.3218-T1
Valid prediction for snap_scaffold_15-snap.3199-T1
Valid prediction for snap_scaffold_15-snap.3208-T1
Valid prediction for GlimmerHMM_glimmerT_37621-T1
Valid prediction for GlimmerHMM_glimmerT_37638-T1
Valid prediction for snap_scaffold_15-snap.3206-T1
Couldn't classify 11979, 11996
Sorry, prediction pasa_asmbl_14835.p1 fails validation.
(CTC)	 GA	11979-11996	GT	CTG
(TCT)	 AG	12072-13064	GT	AAG
-recovered pasa_asmbl_14835.p1, terminal, 12072, 13064
-recovered pasa_asmbl_14835.p1, internal, 12072, 13064
Valid prediction for CodingQuarry_transcript_18282-T1
Valid prediction for GlimmerHMM_glimmerT_37613-T1
Valid prediction for snap_scaffold_15-snap.3219-T1
Valid prediction for GlimmerHMM_glimmerT_37611-T1
Couldn't classify 11810, 11996
Sorry, prediction GlimmerHMM_glimmerT_37639-T1 fails validation.
(TGT)	 AG	11810-11996	GT	CTG
(TCT)	 AG	12072-12761	GT	AGG
(GTT)	 AG	22269-22414	GT	AAG
(ACA)	 AG	22529-22676	GT	TGG
(CCT)	 AG	22835-22987	GT	TGG
(CAC)	 AG	23074-23202	GC	GAG
-recovered GlimmerHMM_glimmerT_37639-T1, terminal, 23074, 23202
-recovered GlimmerHMM_glimmerT_37639-T1, internal, 11810, 11996
-recovered GlimmerHMM_glimmerT_37639-T1, internal, 12072, 12761
-recovered GlimmerHMM_glimmerT_37639-T1, internal, 22269, 22414
-recovered GlimmerHMM_glimmerT_37639-T1, internal, 22529, 22676
-recovered GlimmerHMM_glimmerT_37639-T1, internal, 22835, 22987
-recovered GlimmerHMM_glimmerT_37639-T1, internal, 23074, 23202
Valid prediction for GlimmerHMM_glimmerT_37620-T1
Valid prediction for snap_scaffold_15-snap.3191-T1
Valid prediction for snap_scaffold_15-snap.3215-T1
Valid prediction for CodingQuarry_transcript_18284-T1
Valid prediction for snap_scaffold_15-snap.3188-T1
Valid prediction for GlimmerHMM_glimmerT_37633-T1
Valid prediction for GlimmerHMM_glimmerT_37615-T1
Valid prediction for GlimmerHMM_glimmerT_37622-T1
Valid prediction for GlimmerHMM_glimmerT_37616-T1
Couldn't classify 150659, 150754
Sorry, prediction pasa_asmbl_14823.p1 fails validation.
(ATG)	 GG	150214-150495	GT	AGG
(ATT)	 AG	150659-150754	AA	CGA
-recovered pasa_asmbl_14823.p1, initial, 150214, 150495
Valid prediction for snap_scaffold_15-snap.3196-T1
Valid prediction for GlimmerHMM_glimmerT_37625-T1

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

-building trellis in range 1 - 203712
-exon list size: 275


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.2    
2.5    
2.9    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.4    
5.8    
6.1    
6.5    
6.9    
7.2    
7.6    
7.9    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.5    
10.8    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.2    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.7    
22.0    
22.4    
22.7    
23.1    
23.5    
23.8    
24.2    
24.5    
24.9    
25.3    
25.6    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.8    
32.1    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.7    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.3    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
75.8    
76.2    
76.5    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.2    
89.5    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.1    
92.4    
92.8    
93.1    
93.5    
93.9    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 39 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 191904 - 203712
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-found 4 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support