-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_913252-1125590

-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 GeneMark_model.66040_t
Valid prediction for snap_scaffold_16-snap.175-T1
Valid prediction for GeneMark_model.66039_t
Valid prediction for GeneMark_model.66050_t
Valid prediction for GlimmerHMM_glimmerT_38590-T1
Valid prediction for snap_scaffold_16-snap.174-T1
Valid prediction for GeneMark_model.66037_t
Valid prediction for GeneMark_model.66045_t
Valid prediction for GeneMark_model.66043_t
add_exon() Sorry, GeneMark_model.66043_t 130523-130862-initial-1 is invalid.
Valid prediction for snap_scaffold_16-snap.171-T1
Valid prediction for GeneMark_model.66035_t
Valid prediction for Augustus_model.g25899.t1
Valid prediction for GlimmerHMM_glimmerT_38604-T1
Valid prediction for GlimmerHMM_glimmerT_38599-T1
Valid prediction for Augustus_model.g25901.t1
Valid prediction for GlimmerHMM_glimmerT_38597-T1
Valid prediction for Augustus_model.g25904.t1
Valid prediction for snap_scaffold_16-snap.166-T1
Valid prediction for GlimmerHMM_glimmerT_38585-T1
Valid prediction for GlimmerHMM_glimmerT_38592-T1
Valid prediction for Augustus_model.g25900.t1
Valid prediction for GlimmerHMM_glimmerT_38601-T1
Valid prediction for Augustus_model.g25897.t1
Valid prediction for GlimmerHMM_glimmerT_38595-T1
Valid prediction for GeneMark_model.66042_t
Valid prediction for GeneMark_model.66046_t
Valid prediction for HiQ_model.g25902.t1
Valid prediction for snap_scaffold_16-snap.177-T1
Valid prediction for snap_scaffold_16-snap.165-T1
Valid prediction for GlimmerHMM_glimmerT_38594-T1
Valid prediction for Augustus_model.g25909.t1
Valid prediction for GlimmerHMM_glimmerT_38605-T1
Valid prediction for GlimmerHMM_glimmerT_38588-T1
Valid prediction for GeneMark_model.66036_t
Valid prediction for snap_scaffold_16-snap.176-T1
Valid prediction for Augustus_model.g25895.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 GlimmerHMM_glimmerT_38591-T1
Valid prediction for GeneMark_model.66032_t
Valid prediction for Augustus_model.g25896.t1
Valid prediction for snap_scaffold_16-snap.164-T1
Valid prediction for Augustus_model.g25898.t1
Valid prediction for GeneMark_model.66038_t
Valid prediction for Augustus_model.g25908.t1
Valid prediction for Augustus_model.g25903.t1
Valid prediction for snap_scaffold_16-snap.180-T1
Valid prediction for GlimmerHMM_glimmerT_38589-T1
Couldn't classify 18219, 18349
Sorry, prediction pasa_asmbl_16098.p1 fails validation.
(ATG)	 GT	13800-13917	GT	TAG
(CCA)	 AG	14572-14654	GT	TAG
(CTT)	 AG	15227-15341	GT	AGG
(GTA)	 AG	18219-18349	TA	AAT
-recovered pasa_asmbl_16098.p1, initial, 13800, 13917
add_exon() Sorry, pasa_asmbl_16098.p1 15227-15341-terminal-3 is invalid.
-recovered pasa_asmbl_16098.p1, terminal, 15227, 15341
-recovered pasa_asmbl_16098.p1, internal, 14572, 14654
-recovered pasa_asmbl_16098.p1, internal, 15227, 15341
Valid prediction for snap_scaffold_16-snap.168-T1
Valid prediction for Augustus_model.g25907.t1
Valid prediction for snap_scaffold_16-snap.178-T1
Valid prediction for GeneMark_model.66031_t
Valid prediction for snap_scaffold_16-snap.167-T1
Couldn't classify 190416, 190745
Sorry, prediction pasa_asmbl_16090.p1 fails validation.
(GGC)	 CA	190416-190745	GA	GAG
Valid prediction for snap_scaffold_16-snap.188-T1
Valid prediction for HiQ_model.g25906.t1
Valid prediction for GlimmerHMM_glimmerT_38602-T1
Valid prediction for snap_scaffold_16-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_38596-T1
Valid prediction for snap_scaffold_16-snap.163-T1
Valid prediction for GeneMark_model.66034_t
Valid prediction for GeneMark_model.66030_t
Valid prediction for snap_scaffold_16-snap.169-T1
Valid prediction for snap_scaffold_16-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_38586-T1
Valid prediction for GlimmerHMM_glimmerT_38606-T1
Valid prediction for Augustus_model.g25911.t1
Valid prediction for GeneMark_model.66029_t
Valid prediction for snap_scaffold_16-snap.173-T1
Valid prediction for GeneMark_model.66049_t
Valid prediction for CodingQuarry_transcript_19858-T1
Valid prediction for Augustus_model.g25893.t1
Valid prediction for snap_scaffold_16-snap.182-T1
Valid prediction for snap_scaffold_16-snap.187-T1
Valid prediction for snap_scaffold_16-snap.181-T1
Valid prediction for Augustus_model.g25905.t1
Valid prediction for GeneMark_model.66051_t
Valid prediction for snap_scaffold_16-snap.179-T1
Valid prediction for snap_scaffold_16-snap.186-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g25894.t1
Valid prediction for snap_scaffold_16-snap.185-T1
Valid prediction for GlimmerHMM_glimmerT_38598-T1
Couldn't classify 177212, 177359
Sorry, prediction pasa_asmbl_16092.p1 fails validation.
(TTT)	 CC	177212-177359	GT	AGG
(GGA)	 AG	179505-179655	GT	AGG
(GTA)	 AG	179764-179879	GT	TGG
(ATA)	 AG	180596-180702	AT	AAA
-recovered pasa_asmbl_16092.p1, terminal, 180596, 180702
-recovered pasa_asmbl_16092.p1, internal, 179505, 179655
-recovered pasa_asmbl_16092.p1, internal, 179764, 179879
Valid prediction for snap_scaffold_16-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_38603-T1
Valid prediction for GlimmerHMM_glimmerT_38593-T1
Valid prediction for Augustus_model.g25910.t1
Valid prediction for GeneMark_model.66044_t
Valid prediction for snap_scaffold_16-snap.184-T1
Valid prediction for Augustus_model.g25912.t1
Valid prediction for GlimmerHMM_glimmerT_38587-T1
Valid prediction for GlimmerHMM_glimmerT_38607-T1
Valid prediction for GeneMark_model.66041_t
Valid prediction for snap_scaffold_16-snap.189-T1
Valid prediction for snap_scaffold_16-snap.172-T1
Valid prediction for GeneMark_model.66047_t
Valid prediction for GlimmerHMM_glimmerT_38600-T1

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

-building trellis in range 1 - 212339
-exon list size: 259


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.1    
3.4    
3.8    
4.2    
4.6    
5.0    
5.4    
5.7    
6.1    
6.5    
6.9    
7.3    
7.7    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.3    
10.7    
11.1    
11.5    
11.9    
12.3    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.2    
17.6    
18.0    
18.4    
18.8    
19.2    
19.5    
19.9    
20.3    
20.7    
21.1    
21.5    
21.8    
22.2    
22.6    
23.0    
23.4    
23.8    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.4    
26.8    
27.2    
27.6    
28.0    
28.4    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.0    
31.4    
31.8    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.5    
34.9    
35.2    
35.6    
36.0    
36.4    
36.8    
37.2    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.1    
42.5    
42.9    
43.3    
43.7    
44.1    
44.4    
44.8    
45.2    
45.6    
46.0    
46.4    
46.7    
47.1    
47.5    
47.9    
48.3    
48.7    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.3    
51.7    
52.1    
52.5    
52.9    
53.3    
53.6    
54.0    
54.4    
54.8    
55.2    
55.6    
55.9    
56.3    
56.7    
57.1    
57.5    
57.9    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.1    
65.5    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.2    
68.6    
69.0    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.6    
72.0    
72.4    
72.8    
73.2    
73.6    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.2    
76.6    
77.0    
77.4    
77.8    
78.2    
78.5    
78.9    
79.3    
79.7    
80.1    
80.5    
80.8    
81.2    
81.6    
82.0    
82.4    
82.8    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.7    
88.1    
88.5    
88.9    
89.3    
89.7    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.3    
92.7    
93.1    
93.5    
93.9    
94.3    
94.6    
95.0    
95.4    
95.8    
96.2    
96.6    
96.9    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 24 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21594
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 3500 - 21594
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 6184 - 21594
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 6184 - 17599
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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