-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_14089974-14331408

-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_7890-T1
Valid prediction for GlimmerHMM_glimmerT_7895-T1
Valid prediction for snap_scaffold_3-snap.2734-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g5210.t1
Valid prediction for GlimmerHMM_glimmerT_7873-T1
Valid prediction for GlimmerHMM_glimmerT_7865-T1
Valid prediction for snap_scaffold_3-snap.2730-T1
Valid prediction for Augustus_model.g5227.t1
Valid prediction for GlimmerHMM_glimmerT_7864-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7892-T1
Valid prediction for GlimmerHMM_glimmerT_7898-T1
Valid prediction for CodingQuarry_transcript_46242-T1
Valid prediction for GeneMark_model.12875_t
Valid prediction for GlimmerHMM_glimmerT_7899-T1
Valid prediction for GeneMark_model.12869_t
Valid prediction for Augustus_model.g5221.t1
Valid prediction for GlimmerHMM_glimmerT_7903-T1
Valid prediction for snap_scaffold_3-snap.2711-T1
Valid prediction for snap_scaffold_3-snap.2713-T1
Valid prediction for GeneMark_model.12857_t
Valid prediction for snap_scaffold_3-snap.2738-T1
Valid prediction for Augustus_model.g5225.t1
Valid prediction for snap_scaffold_3-snap.2726-T1
Valid prediction for GeneMark_model.12878_t
Valid prediction for Augustus_model.g5219.t1
Valid prediction for Augustus_model.g5203.t1
Valid prediction for snap_scaffold_3-snap.2725-T1
Valid prediction for Augustus_model.g5232.t1
Valid prediction for GlimmerHMM_glimmerT_7878-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2719-T1
Valid prediction for Augustus_model.g5237.t1
Valid prediction for Augustus_model.g5211.t1
Valid prediction for Augustus_model.g5229.t1
Valid prediction for snap_scaffold_3-snap.2716-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2733-T1
Valid prediction for GlimmerHMM_glimmerT_7882-T1
Valid prediction for GeneMark_model.12849_t
Valid prediction for GlimmerHMM_glimmerT_7885-T1
Valid prediction for GeneMark_model.12858_t
Valid prediction for snap_scaffold_3-snap.2739-T1
Valid prediction for snap_scaffold_3-snap.2709-T1
Valid prediction for snap_scaffold_3-snap.2742-T1
Valid prediction for GlimmerHMM_glimmerT_7868-T1
Valid prediction for GeneMark_model.12848_t
Valid prediction for GeneMark_model.12877_t
Valid prediction for Augustus_model.g5205.t1
Valid prediction for Augustus_model.g5213.t1
Valid prediction for Augustus_model.g5206.t1
Valid prediction for GlimmerHMM_glimmerT_7897-T1
Valid prediction for GlimmerHMM_glimmerT_7902-T1
Valid prediction for Augustus_model.g5222.t1
Valid prediction for GlimmerHMM_glimmerT_7871-T1
Valid prediction for GeneMark_model.12871_t
Valid prediction for GeneMark_model.12856_t
Couldn't classify 136435, 138291
Sorry, prediction pasa_asmbl_40460.p1 fails validation.
(ATG)	 AA	136435-138291	CT	GGC
Couldn't classify 166758, 166896
Sorry, prediction pasa_asmbl_40463.p1 fails validation.
(TAT)	 GG	166758-166896	GT	CGG
(CAA)	 AG	167176-167370	GT	AGG
(GAA)	 AG	169282-169345	GT	ATG
(AAC)	 AG	169437-169609	GT	AAG
(ACC)	 AG	169905-170022	GT	AGG
(ACT)	 AG	170273-170525	GA	AAG
-recovered pasa_asmbl_40463.p1, terminal, 170273, 170525
-recovered pasa_asmbl_40463.p1, internal, 167176, 167370
-recovered pasa_asmbl_40463.p1, internal, 169282, 169345
-recovered pasa_asmbl_40463.p1, internal, 169437, 169609
-recovered pasa_asmbl_40463.p1, internal, 169905, 170022
Valid prediction for GeneMark_model.12853_t
Couldn't classify 157571, 157891
Sorry, prediction pasa_asmbl_40461.p1 fails validation.
(ATG)	 TC	157571-157891	TA	GGT
Valid prediction for snap_scaffold_3-snap.2712-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g5234.t1
Valid prediction for GlimmerHMM_glimmerT_7870-T1
Valid prediction for GeneMark_model.12864_t
Valid prediction for GlimmerHMM_glimmerT_7886-T1
Valid prediction for Augustus_model.g5204.t1
Valid prediction for GeneMark_model.12863_t

-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_3-snap.2710-T1
Valid prediction for HiQ_model.g5235.t1
Valid prediction for Augustus_model.g5207.t1
Valid prediction for snap_scaffold_3-snap.2744-T1
Valid prediction for GeneMark_model.12850_t
Valid prediction for GeneMark_model.12859_t
Valid prediction for Augustus_model.g5217.t1
Valid prediction for GeneMark_model.12868_t
Couldn't classify 177791, 177957
Sorry, prediction pasa_asmbl_39272.p1 fails validation.
(ATG)	 AA	168524-168575	GT	TGG
(TGT)	 AG	168919-169010	GT	TGG
(AAC)	 AG	170390-170576	GT	TGG
(GAA)	 AG	170671-170841	GT	AGG
(GTT)	 AG	170934-171175	GT	GGG
(GAT)	 AG	173854-174012	GT	TGG
(GAC)	 AG	174123-174218	GT	TGG
(GAT)	 AG	174351-174440	GT	ATG
(AAG)	 AG	174562-174699	GT	TGG
(ATT)	 AG	174795-174985	GT	AGG
(TTG)	 AG	175190-175422	GT	AGG
(GTA)	 AG	175794-176013	GT	GGG
(GAA)	 AG	177361-177569	GT	GGG
(AAT)	 AG	177791-177957	GT	AGG
-recovered pasa_asmbl_39272.p1, initial, 168524, 168575
add_exon() Sorry, pasa_asmbl_39272.p1 170671-170841-terminal-1 is invalid.
-recovered pasa_asmbl_39272.p1, terminal, 170671, 170841
-recovered pasa_asmbl_39272.p1, internal, 168919, 169010
-recovered pasa_asmbl_39272.p1, internal, 170390, 170576
-recovered pasa_asmbl_39272.p1, internal, 170671, 170841
-recovered pasa_asmbl_39272.p1, internal, 170934, 171175
-recovered pasa_asmbl_39272.p1, internal, 173854, 174012
-recovered pasa_asmbl_39272.p1, internal, 174123, 174218
-recovered pasa_asmbl_39272.p1, internal, 174351, 174440
-recovered pasa_asmbl_39272.p1, internal, 174562, 174699
-recovered pasa_asmbl_39272.p1, internal, 174795, 174985
-recovered pasa_asmbl_39272.p1, internal, 175190, 175422
-recovered pasa_asmbl_39272.p1, internal, 175794, 176013
-recovered pasa_asmbl_39272.p1, internal, 177361, 177569
-recovered pasa_asmbl_39272.p1, internal, 177791, 177957
Valid prediction for GeneMark_model.12860_t
Valid prediction for GlimmerHMM_glimmerT_7891-T1
Valid prediction for Augustus_model.g5208.t1
Valid prediction for pasa_asmbl_39277.p1
Valid prediction for GeneMark_model.12855_t
Valid prediction for HiQ_model.g5230.t1
Couldn't classify 11268, 11413
Couldn't classify 14228, 14294
Sorry, prediction pasa_asmbl_39302.p1 fails validation.
(TTG)	 CT	11268-11413	GT	GGG
(TAT)	 AG	11511-11755	GT	AAG
(TGC)	 AG	11970-12199	GC	AGG
(GAA)	 AG	12281-12381	GT	AAG
(TGA)	 AG	12907-13038	GT	AGG
(GAG)	 AG	13262-13375	GT	CAG
(GTT)	 AG	13593-13745	GC	AGG
(GTG)	 AG	13864-14061	GT	AGG
(ATT)	 AG	14228-14294	AA	TGA
-recovered pasa_asmbl_39302.p1, internal, 11511, 11755
-recovered pasa_asmbl_39302.p1, internal, 11970, 12199
-recovered pasa_asmbl_39302.p1, internal, 12281, 12381
-recovered pasa_asmbl_39302.p1, internal, 12907, 13038
-recovered pasa_asmbl_39302.p1, internal, 13262, 13375
-recovered pasa_asmbl_39302.p1, internal, 13593, 13745
-recovered pasa_asmbl_39302.p1, internal, 13864, 14061
Valid prediction for GlimmerHMM_glimmerT_7876-T1
Valid prediction for snap_scaffold_3-snap.2731-T1
Valid prediction for Augustus_model.g5223.t1
Valid prediction for GlimmerHMM_glimmerT_7901-T1
Valid prediction for GeneMark_model.12879_t
Valid prediction for Augustus_model.g5224.t1
Valid prediction for snap_scaffold_3-snap.2741-T1
Valid prediction for GlimmerHMM_glimmerT_7896-T1
Valid prediction for GeneMark_model.12866_t
Valid prediction for GlimmerHMM_glimmerT_7881-T1
Valid prediction for snap_scaffold_3-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_7900-T1
Valid prediction for Augustus_model.g5202.t1
Valid prediction for GeneMark_model.12865_t
Valid prediction for GeneMark_model.12854_t
Valid prediction for GlimmerHMM_glimmerT_7889-T1
Valid prediction for snap_scaffold_3-snap.2714-T1
Valid prediction for snap_scaffold_3-snap.2722-T1
Valid prediction for GlimmerHMM_glimmerT_7874-T1
Couldn't classify 40009, 40089
Couldn't classify 40682, 40805
Sorry, prediction pasa_asmbl_39291.p1 fails validation.
(CAG)	 GG	40009-40089	GT	CGG
(AGC)	 AG	40195-40333	GT	AGG
(GTC)	 AG	40465-40573	GT	CTG
(ACA)	 AG	40682-40805	GA	GTG
-recovered pasa_asmbl_39291.p1, internal, 40195, 40333
-recovered pasa_asmbl_39291.p1, internal, 40465, 40573
Valid prediction for Augustus_model.g5226.t1
Valid prediction for GlimmerHMM_glimmerT_7880-T1
Valid prediction for snap_scaffold_3-snap.2743-T1
Valid prediction for snap_scaffold_3-snap.2721-T1
Valid prediction for snap_scaffold_3-snap.2720-T1
Valid prediction for CodingQuarry_transcript_46238-T1
Valid prediction for GeneMark_model.12862_t
Valid prediction for GeneMark_model.12861_t
Valid prediction for Augustus_model.g5214.t1
Valid prediction for GlimmerHMM_glimmerT_7869-T1
Valid prediction for snap_scaffold_3-snap.2724-T1
Valid prediction for GlimmerHMM_glimmerT_7906-T1
Valid prediction for snap_scaffold_3-snap.2717-T1
Valid prediction for snap_scaffold_3-snap.2745-T1
Valid prediction for GlimmerHMM_glimmerT_7879-T1
Valid prediction for GeneMark_model.12872_t
Valid prediction for Augustus_model.g5212.t1
Valid prediction for GlimmerHMM_glimmerT_7877-T1
Valid prediction for CodingQuarry_transcript_46244-T1
Valid prediction for snap_scaffold_3-snap.2729-T1
Valid prediction for Augustus_model.g5220.t1
Valid prediction for HiQ_model.g5215.t1
Couldn't classify 2792, 4223
Couldn't classify 7368, 7530
Sorry, prediction pasa_asmbl_39307.p1 fails validation.
(TTT)	 CC	2792-4223	GT	AGG
(GGT)	 AG	4612-4859	GT	ATG
(ACA)	 AG	5063-5144	GT	AAG
(ATA)	 AG	5290-5410	GT	AGG
(TTC)	 AG	5515-5705	GT	AGG
(GGC)	 AG	6056-6195	GT	TGG
(GTG)	 AG	6383-6580	GT	AGG
(GAT)	 AG	6994-7262	GT	CGG
(GGA)	 AG	7368-7530	GT	AGG
-recovered pasa_asmbl_39307.p1, internal, 4612, 4859
-recovered pasa_asmbl_39307.p1, internal, 5063, 5144
-recovered pasa_asmbl_39307.p1, internal, 5290, 5410
-recovered pasa_asmbl_39307.p1, internal, 5515, 5705
-recovered pasa_asmbl_39307.p1, internal, 6056, 6195
-recovered pasa_asmbl_39307.p1, internal, 6383, 6580
-recovered pasa_asmbl_39307.p1, internal, 6994, 7262
-recovered pasa_asmbl_39307.p1, internal, 7368, 7530
Valid prediction for snap_scaffold_3-snap.2718-T1
Valid prediction for snap_scaffold_3-snap.2715-T1
Valid prediction for Augustus_model.g5231.t1
Valid prediction for GlimmerHMM_glimmerT_7887-T1
Valid prediction for snap_scaffold_3-snap.2740-T1
Valid prediction for GlimmerHMM_glimmerT_7867-T1
Valid prediction for Augustus_model.g5218.t1
Valid prediction for GlimmerHMM_glimmerT_7875-T1
Couldn't classify 21155, 21544
Sorry, prediction pasa_asmbl_39301.p1 fails validation.
(ATG)	 TT	19234-19326	GT	AGG
(GTG)	 AG	21155-21544	GG	CAG
-recovered pasa_asmbl_39301.p1, initial, 19234, 19326
Valid prediction for snap_scaffold_3-snap.2736-T1
Valid prediction for Augustus_model.g5228.t1
Valid prediction for snap_scaffold_3-snap.2723-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for HiQ_model.g5238.t1
Valid prediction for GlimmerHMM_glimmerT_7888-T1
Valid prediction for snap_scaffold_3-snap.2727-T1
Valid prediction for GlimmerHMM_glimmerT_7884-T1
Valid prediction for GeneMark_model.12870_t
Valid prediction for Augustus_model.g5216.t1
Valid prediction for CodingQuarry_transcript_46243-T1
Valid prediction for snap_scaffold_3-snap.2735-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 28788, 28918
Sorry, prediction pasa_asmbl_39293.p1 fails validation.
(GAT)	 CA	28788-28918	GT	TGG
(TGA)	 AG	29054-29242	GT	AGG
(CTG)	 AG	29432-29585	GT	AGG
(GGG)	 AG	29763-29918	TG	GAT
-recovered pasa_asmbl_39293.p1, terminal, 29763, 29918
-recovered pasa_asmbl_39293.p1, internal, 29054, 29242
-recovered pasa_asmbl_39293.p1, internal, 29432, 29585
Valid prediction for GlimmerHMM_glimmerT_7872-T1
Valid prediction for GlimmerHMM_glimmerT_7893-T1
Valid prediction for GlimmerHMM_glimmerT_7866-T1
Valid prediction for Augustus_model.g5236.t1
Valid prediction for GlimmerHMM_glimmerT_7894-T1
Valid prediction for GlimmerHMM_glimmerT_7904-T1
Couldn't classify 59675, 59781
Sorry, prediction pasa_asmbl_39290.p1 fails validation.
(GGA)	 CA	59675-59781	GT	TGG
(GTC)	 AG	59994-60059	GT	GGG
(GTC)	 AG	62562-62642	GT	GGG
(TGG)	 AG	62781-62951	GT	AGG
(GCA)	 AG	65007-65085	GT	AAG
(GAG)	 AG	65204-65350	AA	GAA
-recovered pasa_asmbl_39290.p1, terminal, 65204, 65350
-recovered pasa_asmbl_39290.p1, internal, 59994, 60059
-recovered pasa_asmbl_39290.p1, internal, 62562, 62642
-recovered pasa_asmbl_39290.p1, internal, 62781, 62951
-recovered pasa_asmbl_39290.p1, internal, 65007, 65085
Valid prediction for GlimmerHMM_glimmerT_7883-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g5233.t1
Valid prediction for snap_scaffold_3-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_7905-T1
Valid prediction for GeneMark_model.12880_t
Valid prediction for Augustus_model.g5209.t1
Valid prediction for snap_scaffold_3-snap.2732-T1
Valid prediction for Augustus_model.g5239.t1
Valid prediction for CodingQuarry_transcript_46241-T1
Valid prediction for GeneMark_model.12876_t

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

-building trellis in range 1 - 241435
-exon list size: 510


building trellis

0.2    
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1.0    
1.2    
1.4    
1.6    
1.8    
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2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
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5.3    
5.5    
5.7    
5.9    
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6.6    
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8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
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16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 48 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 44 predictions persist after filtering for low support