-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_16104588-16319877

-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_38420-T1
Valid prediction for GeneMark_model.65871_t
Valid prediction for GeneMark_model.65869_t
Valid prediction for snap_scaffold_15-snap.3212-T1
Valid prediction for snap_scaffold_15-snap.3203-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38422-T1
Valid prediction for GeneMark_model.65882_t
Valid prediction for GeneMark_model.65875_t
Valid prediction for GeneMark_model.65874_t
Valid prediction for snap_scaffold_15-snap.3201-T1
Valid prediction for GlimmerHMM_glimmerT_38440-T1
Valid prediction for GlimmerHMM_glimmerT_38418-T1
Valid prediction for GlimmerHMM_glimmerT_38408-T1
Valid prediction for snap_scaffold_15-snap.3198-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.3190-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38426-T1
Valid prediction for snap_scaffold_15-snap.3197-T1
Valid prediction for GlimmerHMM_glimmerT_38413-T1
Valid prediction for CodingQuarry_transcript_18247-T1
Valid prediction for snap_scaffold_15-snap.3188-T1
Valid prediction for GlimmerHMM_glimmerT_38424-T1
Valid prediction for GlimmerHMM_glimmerT_38419-T1
Valid prediction for GeneMark_model.65872_t
Valid prediction for GlimmerHMM_glimmerT_38412-T1
Valid prediction for GeneMark_model.65870_t
Valid prediction for snap_scaffold_15-snap.3217-T1
Valid prediction for GlimmerHMM_glimmerT_38435-T1
Valid prediction for snap_scaffold_15-snap.3219-T1
Valid prediction for snap_scaffold_15-snap.3191-T1
Couldn't classify 172333, 172506
Sorry, prediction pasa_asmbl_14802.p1 fails validation.
(TTA)	 AT	172333-172506	GT	CCG
(CCC)	 AG	172605-172772	GT	AGG
(GCT)	 AG	175581-175710	GT	TGG
(ATT)	 AG	175880-176002	GT	GGG
(GCA)	 AG	176096-176280	GT	AAG
(GGT)	 AG	176472-176837	AT	GAA
-recovered pasa_asmbl_14802.p1, terminal, 176472, 176837
-recovered pasa_asmbl_14802.p1, internal, 172605, 172772
-recovered pasa_asmbl_14802.p1, internal, 175581, 175710
-recovered pasa_asmbl_14802.p1, internal, 175880, 176002
-recovered pasa_asmbl_14802.p1, internal, 176096, 176280
Valid prediction for snap_scaffold_15-snap.3196-T1
Valid prediction for GlimmerHMM_glimmerT_38430-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 53961, 54142
Sorry, prediction pasa_asmbl_15833.p1 fails validation.
(GAG)	 AT	53961-54142	GT	AGG
(GCC)	 AG	55205-55357	GT	AAG
(AGC)	 AG	55480-55705	GT	AGG
(GTG)	 AG	55888-56205	GT	AGG
(ATT)	 AG	57592-57726	GT	GGG
(ACG)	 AG	58018-58110	GG	AGG
add_exon() Sorry, pasa_asmbl_15833.p1 55205-55357-terminal-1 is invalid.
-recovered pasa_asmbl_15833.p1, terminal, 55205, 55357
-recovered pasa_asmbl_15833.p1, terminal, 58018, 58110
-recovered pasa_asmbl_15833.p1, internal, 55205, 55357
-recovered pasa_asmbl_15833.p1, internal, 55480, 55705
-recovered pasa_asmbl_15833.p1, internal, 55888, 56205
-recovered pasa_asmbl_15833.p1, internal, 57592, 57726
Valid prediction for snap_scaffold_15-snap.3202-T1
Valid prediction for snap_scaffold_15-snap.3194-T1
Valid prediction for snap_scaffold_15-snap.3205-T1
Valid prediction for snap_scaffold_15-snap.3208-T1
Valid prediction for pasa_asmbl_15840.p1
Couldn't classify 53672, 53767
Sorry, prediction pasa_asmbl_15836.p1 fails validation.
(ATG)	 GG	53227-53508	GT	AGG
(ATT)	 AG	53672-53767	AA	CGA
-recovered pasa_asmbl_15836.p1, initial, 53227, 53508
Valid prediction for GeneMark_model.65889_t
Valid prediction for GlimmerHMM_glimmerT_38428-T1
Valid prediction for GeneMark_model.65880_t
Valid prediction for GlimmerHMM_glimmerT_38434-T1
Valid prediction for snap_scaffold_15-snap.3216-T1
Valid prediction for snap_scaffold_15-snap.3222-T1
Valid prediction for snap_scaffold_15-snap.3209-T1
Valid prediction for snap_scaffold_15-snap.3215-T1
Valid prediction for GlimmerHMM_glimmerT_38409-T1
Valid prediction for GeneMark_model.65883_t
Valid prediction for GlimmerHMM_glimmerT_38411-T1
Valid prediction for GeneMark_model.65873_t
Valid prediction for GlimmerHMM_glimmerT_38437-T1
Valid prediction for GeneMark_model.65885_t
Valid prediction for GlimmerHMM_glimmerT_38423-T1
Valid prediction for GlimmerHMM_glimmerT_38427-T1
Valid prediction for GlimmerHMM_glimmerT_38438-T1
Valid prediction for GlimmerHMM_glimmerT_38421-T1
Valid prediction for snap_scaffold_15-snap.3189-T1
Valid prediction for GlimmerHMM_glimmerT_38439-T1
Valid prediction for GeneMark_model.65890_t
Valid prediction for GlimmerHMM_glimmerT_38436-T1
Valid prediction for GlimmerHMM_glimmerT_38410-T1
Valid prediction for snap_scaffold_15-snap.3214-T1
Valid prediction for GeneMark_model.65886_t
Valid prediction for GlimmerHMM_glimmerT_38433-T1
Valid prediction for snap_scaffold_15-snap.3195-T1
Valid prediction for GlimmerHMM_glimmerT_38414-T1
Valid prediction for GlimmerHMM_glimmerT_38415-T1
Valid prediction for CodingQuarry_transcript_18246-T1
Valid prediction for snap_scaffold_15-snap.3223-T1
Valid prediction for snap_scaffold_15-snap.3207-T1
Valid prediction for snap_scaffold_15-snap.3193-T1
Valid prediction for GlimmerHMM_glimmerT_38441-T1
Couldn't classify 52791, 52915
Sorry, prediction pasa_asmbl_15838.p1 fails validation.
(ATG)	 GA	50316-50464	GT	AGG
(ATA)	 AG	50570-50729	GT	AGG
(TCT)	 AG	50821-50926	GT	GGG
(GTA)	 AG	51025-51154	GT	ATG
(CCA)	 AG	51263-51378	GT	CAG
(CCA)	 AG	52791-52915	GT	GTG
-recovered pasa_asmbl_15838.p1, initial, 50316, 50464
-recovered pasa_asmbl_15838.p1, internal, 50570, 50729
-recovered pasa_asmbl_15838.p1, internal, 50821, 50926
-recovered pasa_asmbl_15838.p1, internal, 51025, 51154
-recovered pasa_asmbl_15838.p1, internal, 51263, 51378
-recovered pasa_asmbl_15838.p1, internal, 52791, 52915
Valid prediction for snap_scaffold_15-snap.3206-T1
Valid prediction for GlimmerHMM_glimmerT_38417-T1
Valid prediction for GlimmerHMM_glimmerT_38429-T1
Valid prediction for GeneMark_model.65884_t
Valid prediction for GeneMark_model.65881_t
Valid prediction for snap_scaffold_15-snap.3210-T1
Valid prediction for snap_scaffold_15-snap.3213-T1
Valid prediction for snap_scaffold_15-snap.3200-T1
Valid prediction for snap_scaffold_15-snap.3211-T1
Valid prediction for GlimmerHMM_glimmerT_38432-T1
Valid prediction for snap_scaffold_15-snap.3204-T1
Valid prediction for snap_scaffold_15-snap.3221-T1
Valid prediction for GlimmerHMM_glimmerT_38416-T1
Valid prediction for GlimmerHMM_glimmerT_38431-T1
Valid prediction for GeneMark_model.65876_t
Valid prediction for CodingQuarry_transcript_18248-T1
Valid prediction for snap_scaffold_15-snap.3192-T1
Valid prediction for GlimmerHMM_glimmerT_38425-T1
Valid prediction for snap_scaffold_15-snap.3220-T1

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

-building trellis in range 1 - 215290
-exon list size: 300


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.3    
9.6    
9.9    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.9    
18.2    
18.5    
18.9    
19.2    
19.5    
19.9    
20.2    
20.5    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.2    
26.5    
26.8    
27.2    
27.5    
27.8    
28.1    
28.5    
28.8    
29.1    
29.5    
29.8    
30.1    
30.5    
30.8    
31.1    
31.5    
31.8    
32.1    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.8    
35.1    
35.4    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.1    
38.4    
38.7    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.4    
44.7    
45.0    
45.4    
45.7    
46.0    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
54.0    
54.3    
54.6    
55.0    
55.3    
55.6    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.3    
61.6    
61.9    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.6    
64.9    
65.2    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.9    
68.2    
68.5    
68.9    
69.2    
69.5    
69.9    
70.2    
70.5    
70.9    
71.2    
71.5    
71.9    
72.2    
72.5    
72.8    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.5    
79.8    
80.1    
80.5    
80.8    
81.1    
81.5    
81.8    
82.1    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.1    
90.4    
90.7    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support