-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_9551428-9853893

-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_56183-T1
Valid prediction for GeneMark_model.97806_t
Valid prediction for snap_scaffold_25-snap.2126-T1
Valid prediction for GlimmerHMM_glimmerT_56168-T1
Valid prediction for Augustus_model.g37462.t1
Valid prediction for snap_scaffold_25-snap.2128-T1
Valid prediction for Augustus_model.g37477.t1
Valid prediction for GeneMark_model.97817_t
Valid prediction for Augustus_model.g37458.t1
Valid prediction for Augustus_model.g37463.t1
Valid prediction for snap_scaffold_25-snap.2127-T1
Valid prediction for pasa_asmbl_33836.p1
Valid prediction for GlimmerHMM_glimmerT_56162-T1
Valid prediction for GlimmerHMM_glimmerT_56182-T1
Valid prediction for GeneMark_model.97829_t
Valid prediction for GeneMark_model.97820_t
Valid prediction for GlimmerHMM_glimmerT_56151-T1
Valid prediction for Augustus_model.g37453.t1
Valid prediction for snap_scaffold_25-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_56186-T1
Valid prediction for GeneMark_model.97805_t
Valid prediction for CodingQuarry_transcript_38751-T1
Valid prediction for GlimmerHMM_glimmerT_56163-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56180-T1
Valid prediction for GlimmerHMM_glimmerT_56156-T1
Valid prediction for GlimmerHMM_glimmerT_56164-T1
Valid prediction for GeneMark_model.97813_t
Valid prediction for snap_scaffold_25-snap.2108-T1
Couldn't classify 153340, 153430
Couldn't classify 155828, 155866
Sorry, prediction pasa_asmbl_33827.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_33827.p1, internal, 153340, 153430
-recovered pasa_asmbl_33827.p1, internal, 153596, 153695
-recovered pasa_asmbl_33827.p1, internal, 154877, 154981
-recovered pasa_asmbl_33827.p1, internal, 155193, 155328
-recovered pasa_asmbl_33827.p1, internal, 155409, 155471
Valid prediction for Augustus_model.g37466.t1
Valid prediction for Augustus_model.g37472.t1
Valid prediction for snap_scaffold_25-snap.2116-T1
Valid prediction for HiQ_model.g37478.t1
Valid prediction for snap_scaffold_25-snap.2113-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_56167-T1
Valid prediction for GeneMark_model.97828_t
Valid prediction for GeneMark_model.97812_t
Valid prediction for GeneMark_model.97819_t
Valid prediction for GlimmerHMM_glimmerT_56154-T1
Valid prediction for snap_scaffold_25-snap.2103-T1
Valid prediction for GeneMark_model.97816_t
Valid prediction for snap_scaffold_25-snap.2109-T1
Valid prediction for GlimmerHMM_glimmerT_56160-T1
Valid prediction for GlimmerHMM_glimmerT_56178-T1
Valid prediction for snap_scaffold_25-snap.2112-T1
Valid prediction for snap_scaffold_25-snap.2125-T1
Valid prediction for Augustus_model.g37459.t1
Valid prediction for GlimmerHMM_glimmerT_56173-T1
Valid prediction for GlimmerHMM_glimmerT_56188-T1
Valid prediction for snap_scaffold_25-snap.2124-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56171-T1
Valid prediction for snap_scaffold_25-snap.2115-T1
Valid prediction for GlimmerHMM_glimmerT_56159-T1
Valid prediction for Augustus_model.g37450.t1
Valid prediction for Augustus_model.g37460.t1
Valid prediction for snap_scaffold_25-snap.2110-T1
Valid prediction for GeneMark_model.97821_t
Valid prediction for GlimmerHMM_glimmerT_56187-T1
Valid prediction for Augustus_model.g37467.t1
Valid prediction for GeneMark_model.97826_t
Valid prediction for pasa_asmbl_33828.p1
Valid prediction for Augustus_model.g37473.t1
Valid prediction for snap_scaffold_25-snap.2101-T1
Valid prediction for Augustus_model.g37475.t1
Valid prediction for GeneMark_model.97814_t
Valid prediction for snap_scaffold_25-snap.2131-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.2129-T1
Valid prediction for GlimmerHMM_glimmerT_56161-T1
Valid prediction for HiQ_model.g37456.t1
Valid prediction for snap_scaffold_25-snap.2106-T1
Couldn't classify 7685, 8017
Sorry, prediction pasa_asmbl_33835.p1 fails validation.
(AAA)	 CC	7685-8017	GG	GTG
Valid prediction for snap_scaffold_25-snap.2117-T1
Valid prediction for GeneMark_model.97827_t
Valid prediction for snap_scaffold_25-snap.2123-T1
Valid prediction for snap_scaffold_25-snap.2114-T1
Valid prediction for Augustus_model.g37474.t1
Valid prediction for GlimmerHMM_glimmerT_56184-T1
Valid prediction for Augustus_model.g37464.t1
Couldn't classify 229006, 229154
Sorry, prediction pasa_asmbl_34487.p2 fails validation.
(ATG)	 AC	226775-226787	GT	AGG
(GAA)	 AG	227816-228022	GT	AGG
(TCC)	 AG	229006-229154	GT	AGG
-recovered pasa_asmbl_34487.p2, initial, 226775, 226787
-recovered pasa_asmbl_34487.p2, internal, 227816, 228022
-recovered pasa_asmbl_34487.p2, internal, 229006, 229154
Valid prediction for snap_scaffold_25-snap.2098-T1
Valid prediction for snap_scaffold_25-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_56169-T1
Valid prediction for GlimmerHMM_glimmerT_56152-T1
Valid prediction for GeneMark_model.97825_t
Couldn't classify 245142, 245342
Couldn't classify 247738, 247877
Sorry, prediction pasa_asmbl_34486.p1 fails validation.
(GAG)	 GA	245142-245342	GT	AGG
(ACA)	 AG	246167-246353	GT	TGG
(GCC)	 AG	247453-247581	GT	AGG
(GGA)	 AG	247738-247877	AG	TTA
-recovered pasa_asmbl_34486.p1, internal, 246167, 246353
-recovered pasa_asmbl_34486.p1, internal, 247453, 247581
Valid prediction for snap_scaffold_25-snap.2118-T1
Valid prediction for Augustus_model.g37451.t1
Valid prediction for GeneMark_model.97824_t
Valid prediction for GlimmerHMM_glimmerT_56166-T1
Valid prediction for GlimmerHMM_glimmerT_56174-T1
Valid prediction for GlimmerHMM_glimmerT_56153-T1
Valid prediction for snap_scaffold_25-snap.2099-T1
Valid prediction for GlimmerHMM_glimmerT_56150-T1
Valid prediction for GlimmerHMM_glimmerT_56172-T1
Valid prediction for GlimmerHMM_glimmerT_56158-T1
Valid prediction for Augustus_model.g37452.t1
Valid prediction for snap_scaffold_25-snap.2122-T1
Valid prediction for GlimmerHMM_glimmerT_56155-T1
Valid prediction for snap_scaffold_25-snap.2121-T1
Valid prediction for Augustus_model.g37455.t1
Valid prediction for GlimmerHMM_glimmerT_56170-T1
Valid prediction for GlimmerHMM_glimmerT_56185-T1
Valid prediction for GlimmerHMM_glimmerT_56181-T1
Valid prediction for Augustus_model.g37471.t1
Valid prediction for GeneMark_model.97811_t
Valid prediction for GlimmerHMM_glimmerT_56177-T1
Valid prediction for snap_scaffold_25-snap.2105-T1
Valid prediction for Augustus_model.g37476.t1
Valid prediction for HiQ_model.g37457.t1
Valid prediction for Augustus_model.g37449.t1
Valid prediction for Augustus_model.g37469.t1
Valid prediction for CodingQuarry_transcript_38750-T1
Valid prediction for snap_scaffold_25-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_56165-T1
Valid prediction for GeneMark_model.97809_t
Couldn't classify 286934, 286999
Sorry, prediction pasa_asmbl_34484.p1 fails validation.
(ACT)	 GT	286934-286999	GT	CTG
(GTT)	 AG	287561-287623	GT	AGG
(GTG)	 AG	288214-288283	GT	AGG
(GAC)	 AG	288381-288487	GT	AGG
(GCA)	 AG	288592-288759	GC	AGG
(GTT)	 AG	289224-289296	GT	AAG
(GCA)	 AG	292013-292087	GT	AGG
(ATC)	 AG	292914-293298	GT	GAG
(AAC)	 AG	293815-293992	GG	GAG
-recovered pasa_asmbl_34484.p1, terminal, 289224, 289296
add_exon() Sorry, pasa_asmbl_34484.p1 292914-293298-terminal-3 is invalid.
-recovered pasa_asmbl_34484.p1, terminal, 292914, 293298
-recovered pasa_asmbl_34484.p1, terminal, 293815, 293992
-recovered pasa_asmbl_34484.p1, internal, 287561, 287623
-recovered pasa_asmbl_34484.p1, internal, 288214, 288283
-recovered pasa_asmbl_34484.p1, internal, 288381, 288487
-recovered pasa_asmbl_34484.p1, internal, 288592, 288759
-recovered pasa_asmbl_34484.p1, internal, 289224, 289296
-recovered pasa_asmbl_34484.p1, internal, 292013, 292087
-recovered pasa_asmbl_34484.p1, internal, 292914, 293298
Couldn't classify 232430, 232579
Couldn't classify 237925, 238067
Sorry, prediction pasa_asmbl_34595.p1 fails validation.
(GTC)	 TA	232430-232579	GT	AGG
(AAG)	 AG	233761-233865	GT	ATG
(ATG)	 AG	233989-234091	GT	AGG
(GTG)	 AG	235601-235761	GT	AGG
(GAG)	 AG	237556-237691	GT	AGG
(AGG)	 AG	237925-238067	GT	AGG
-recovered pasa_asmbl_34595.p1, initial, 233989, 234091
add_exon() Sorry, pasa_asmbl_34595.p1 233989-234091-terminal-3 is invalid.
-recovered pasa_asmbl_34595.p1, terminal, 233989, 234091
add_exon() Sorry, pasa_asmbl_34595.p1 237556-237691-terminal-3 is invalid.
-recovered pasa_asmbl_34595.p1, terminal, 237556, 237691
-recovered pasa_asmbl_34595.p1, internal, 233761, 233865
-recovered pasa_asmbl_34595.p1, internal, 233989, 234091
-recovered pasa_asmbl_34595.p1, internal, 235601, 235761
-recovered pasa_asmbl_34595.p1, internal, 237556, 237691
-recovered pasa_asmbl_34595.p1, internal, 237925, 238067
Valid prediction for Augustus_model.g37465.t1
Valid prediction for snap_scaffold_25-snap.2120-T1
Couldn't classify 29562, 29627
Couldn't classify 33397, 33479
Sorry, prediction pasa_asmbl_34494.p1 fails validation.
(GCT)	 TG	29562-29627	GT	AGG
(AGG)	 AG	30241-30373	GT	AGG
(GTC)	 AG	32147-32308	GT	GGG
(ACG)	 AG	32579-32629	GT	AGG
(GAG)	 AG	33397-33479	AT	TGA
-recovered pasa_asmbl_34494.p1, internal, 30241, 30373
-recovered pasa_asmbl_34494.p1, internal, 32147, 32308
-recovered pasa_asmbl_34494.p1, internal, 32579, 32629
Valid prediction for GlimmerHMM_glimmerT_56176-T1
Valid prediction for GeneMark_model.97815_t
Valid prediction for GlimmerHMM_glimmerT_56175-T1
Valid prediction for GeneMark_model.97804_t
Valid prediction for Augustus_model.g37454.t1
Valid prediction for GeneMark_model.97818_t
Valid prediction for Augustus_model.g37470.t1
Valid prediction for snap_scaffold_25-snap.2100-T1
Valid prediction for GeneMark_model.97810_t
Valid prediction for GlimmerHMM_glimmerT_56179-T1
Valid prediction for Augustus_model.g37468.t1
Valid prediction for snap_scaffold_25-snap.2111-T1
Valid prediction for snap_scaffold_25-snap.2104-T1
Valid prediction for GeneMark_model.97808_t
Valid prediction for GlimmerHMM_glimmerT_56157-T1
Valid prediction for GeneMark_model.97807_t
Valid prediction for Augustus_model.g37461.t1

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

-building trellis in range 1 - 302466
-exon list size: 411


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.5    
6.8    
7.0    
7.3    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 41 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support