-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_162080-395842

-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 Augustus_model.g33556.t1
Valid prediction for GeneMark_model.86652_t
Valid prediction for GeneMark_model.86650_t
Valid prediction for pasa_asmbl_29127.p1
Valid prediction for GeneMark_model.86646_t
Valid prediction for Augustus_model.g33555.t1
Couldn't classify 127129, 127221
Couldn't classify 129408, 129578
Sorry, prediction pasa_asmbl_29123.p1 fails validation.
(GAA)	 AG	127129-127221	GT	AGG
(CTC)	 AG	127548-127691	GT	AGG
(ATC)	 AG	128147-128329	GT	AGG
(GAC)	 AG	128575-128725	GT	AGG
(ACT)	 AG	128980-129077	GT	AGG
(GCT)	 AG	129408-129578	GC	CCG
add_exon() Sorry, pasa_asmbl_29123.p1 128575-128725-terminal-3 is invalid.
-recovered pasa_asmbl_29123.p1, terminal, 128575, 128725
-recovered pasa_asmbl_29123.p1, internal, 127129, 127221
-recovered pasa_asmbl_29123.p1, internal, 127548, 127691
-recovered pasa_asmbl_29123.p1, internal, 128147, 128329
-recovered pasa_asmbl_29123.p1, internal, 128575, 128725
-recovered pasa_asmbl_29123.p1, internal, 128980, 129077
-recovered pasa_asmbl_29123.p1, internal, 129408, 129578
Valid prediction for Augustus_model.g33552.t1
Valid prediction for Augustus_model.g33549.t1
Couldn't classify 154082, 154199
Sorry, prediction pasa_asmbl_29132.p1 fails validation.
(GCC)	 GG	154082-154199	GT	AGG
(ACC)	 AG	156342-156440	GT	AGG
(CCT)	 AG	156672-157441	GT	AGG
(GGA)	 AG	158752-158800	GT	AGG
(ACA)	 AG	160487-160575	GT	AGG
(ACA)	 AG	161359-161472	CT	AAC
-recovered pasa_asmbl_29132.p1, terminal, 161359, 161472
-recovered pasa_asmbl_29132.p1, internal, 156342, 156440
-recovered pasa_asmbl_29132.p1, internal, 156672, 157441
-recovered pasa_asmbl_29132.p1, internal, 158752, 158800
-recovered pasa_asmbl_29132.p1, internal, 160487, 160575
Valid prediction for Augustus_model.g33548.t1
Valid prediction for CodingQuarry_transcript_34007-T1
Valid prediction for GlimmerHMM_glimmerT_50022-T1
Valid prediction for GlimmerHMM_glimmerT_50007-T1
Valid prediction for snap_scaffold_22-snap.85-T1
Valid prediction for snap_scaffold_22-snap.63-T1
Valid prediction for GeneMark_model.86644_t
Valid prediction for GlimmerHMM_glimmerT_49996-T1
Couldn't classify 159459, 159824
Sorry, prediction pasa_asmbl_29135.p1 fails validation.
(AAG)	 GT	159459-159824	AC	GGA
Valid prediction for Augustus_model.g33551.t1
Valid prediction for snap_scaffold_22-snap.77-T1
Valid prediction for snap_scaffold_22-snap.54-T1
Valid prediction for GeneMark_model.86649_t
Valid prediction for Augustus_model.g33553.t1
Valid prediction for snap_scaffold_22-snap.75-T1
Valid prediction for pasa_asmbl_29122.p1
Valid prediction for GlimmerHMM_glimmerT_50006-T1
Valid prediction for GlimmerHMM_glimmerT_50024-T1
Valid prediction for snap_scaffold_22-snap.78-T1
Valid prediction for Augustus_model.g33531.t1
Couldn't classify 137356, 137667
Sorry, prediction pasa_asmbl_29128.p1 fails validation.
(GAG)	 CA	137356-137667	TC	GAT
Valid prediction for GeneMark_model.86653_t
Valid prediction for pasa_asmbl_29131.p1
Valid prediction for snap_scaffold_22-snap.47-T1
Valid prediction for CodingQuarry_transcript_33999-T1
Valid prediction for GeneMark_model.86648_t
Valid prediction for GlimmerHMM_glimmerT_50000-T1
Valid prediction for CodingQuarry_transcript_34004-T1
Valid prediction for snap_scaffold_22-snap.57-T1
Valid prediction for GeneMark_model.86643_t
Valid prediction for Augustus_model.g33543.t1
Valid prediction for snap_scaffold_22-snap.70-T1
Valid prediction for GeneMark_model.86628_t
Valid prediction for CodingQuarry_transcript_34010-T1
Valid prediction for CodingQuarry_transcript_33998-T1
Valid prediction for snap_scaffold_22-snap.82-T1
Valid prediction for GeneMark_model.86642_t
Valid prediction for CodingQuarry_transcript_33997-T1
Valid prediction for GlimmerHMM_glimmerT_50003-T1
Valid prediction for snap_scaffold_22-snap.72-T1
Valid prediction for Augustus_model.g33561.t1
Valid prediction for GlimmerHMM_glimmerT_50020-T1
Valid prediction for GlimmerHMM_glimmerT_50028-T1
Valid prediction for Augustus_model.g33538.t1
Valid prediction for CodingQuarry_transcript_34006-T1
Valid prediction for GeneMark_model.86656_t
Valid prediction for snap_scaffold_22-snap.69-T1
Valid prediction for pasa_asmbl_29140.p1
Valid prediction for CodingQuarry_transcript_34009-T1
Valid prediction for snap_scaffold_22-snap.88-T1
Valid prediction for HiQ_model.g33554.t1
Valid prediction for GlimmerHMM_glimmerT_50014-T1
Valid prediction for snap_scaffold_22-snap.56-T1
Valid prediction for Augustus_model.g33532.t1
Couldn't classify 54228, 54229
Sorry, prediction CodingQuarry_transcript_34000-T1 fails validation.
(ATG)	 CA	52235-52526	GT	AGG
(ATG)	 AG	52645-52752	GT	CTG
(GAC)	 AG	54228-54229	CT	GAC
-recovered CodingQuarry_transcript_34000-T1, initial, 52235, 52526
-recovered CodingQuarry_transcript_34000-T1, initial, 52645, 52752
-recovered CodingQuarry_transcript_34000-T1, internal, 52645, 52752
Valid prediction for snap_scaffold_22-snap.73-T1
Valid prediction for snap_scaffold_22-snap.83-T1
Valid prediction for CodingQuarry_transcript_34008-T1
Valid prediction for GeneMark_model.86639_t
Valid prediction for snap_scaffold_22-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_50021-T1
Valid prediction for Augustus_model.g33557.t1
Valid prediction for snap_scaffold_22-snap.50-T1
Valid prediction for snap_scaffold_22-snap.86-T1
Couldn't classify 37558, 37572
Sorry, prediction pasa_asmbl_29110.p1 fails validation.
(TCA)	 GC	37558-37572	GT	AGG
(GTT)	 AG	37747-37830	GT	TGG
(GAA)	 AG	39426-39590	GT	AGG
(ATG)	 AG	39708-39813	GT	AGG
(ATG)	 AG	39985-40263	GT	AGG
(ATA)	 AG	40875-41007	GT	AAG
(GCA)	 AG	41741-41886	GT	ACG
(TTG)	 AG	42060-42172	GT	AGG
(GAG)	 AG	43096-43255	GT	TGG
(GGG)	 AG	44143-44234	GT	AGG
(CTG)	 AG	44320-44397	TT	GAT
-recovered pasa_asmbl_29110.p1, initial, 39708, 39813
add_exon() Sorry, pasa_asmbl_29110.p1 39985-40263-initial-1 is invalid.
-recovered pasa_asmbl_29110.p1, initial, 39985, 40263
-recovered pasa_asmbl_29110.p1, terminal, 44320, 44397
-recovered pasa_asmbl_29110.p1, internal, 37747, 37830
-recovered pasa_asmbl_29110.p1, internal, 39426, 39590
-recovered pasa_asmbl_29110.p1, internal, 39708, 39813
-recovered pasa_asmbl_29110.p1, internal, 39985, 40263
-recovered pasa_asmbl_29110.p1, internal, 40875, 41007
-recovered pasa_asmbl_29110.p1, internal, 41741, 41886
-recovered pasa_asmbl_29110.p1, internal, 42060, 42172
-recovered pasa_asmbl_29110.p1, internal, 43096, 43255
-recovered pasa_asmbl_29110.p1, internal, 44143, 44234
Valid prediction for snap_scaffold_22-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_50023-T1
Valid prediction for GlimmerHMM_glimmerT_50019-T1
Valid prediction for CodingQuarry_transcript_34003-T1
Valid prediction for snap_scaffold_22-snap.62-T1
Valid prediction for snap_scaffold_22-snap.81-T1
Valid prediction for snap_scaffold_22-snap.53-T1
Valid prediction for GeneMark_model.86637_t
Valid prediction for snap_scaffold_22-snap.84-T1
Valid prediction for snap_scaffold_22-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_50012-T1
Valid prediction for Augustus_model.g33546.t1
Valid prediction for HiQ_model.g33550.t1
Valid prediction for HiQ_model.g33539.t1
Valid prediction for Augustus_model.g33560.t1
Valid prediction for GlimmerHMM_glimmerT_50001-T1
Valid prediction for GlimmerHMM_glimmerT_50018-T1
Valid prediction for snap_scaffold_22-snap.74-T1
Valid prediction for HiQ_model.g33536.t1
Valid prediction for snap_scaffold_22-snap.90-T1
Valid prediction for snap_scaffold_22-snap.68-T1
Valid prediction for snap_scaffold_22-snap.89-T1
Valid prediction for GlimmerHMM_glimmerT_50011-T1
Valid prediction for snap_scaffold_22-snap.71-T1
Couldn't classify 144435, 144466
Sorry, prediction pasa_asmbl_29130.p1 fails validation.
(GTG)	 GG	144435-144466	GT	AGG
(CCC)	 AG	145123-145262	GT	CGG
(TCC)	 AG	145795-145935	GT	CAG
(AGG)	 AG	146198-146340	GT	AGG
(GGG)	 AG	146646-146816	TG	AAT
-recovered pasa_asmbl_29130.p1, terminal, 146646, 146816
-recovered pasa_asmbl_29130.p1, internal, 145123, 145262
-recovered pasa_asmbl_29130.p1, internal, 145795, 145935
-recovered pasa_asmbl_29130.p1, internal, 146198, 146340
Valid prediction for snap_scaffold_22-snap.67-T1
Valid prediction for HiQ_model.g33547.t1
Valid prediction for GeneMark_model.86645_t
Couldn't classify 74385, 74450
Sorry, prediction pasa_asmbl_29119.p1 fails validation.
(ATC)	 CC	74385-74450	GT	AGG
(GTA)	 AG	75057-75176	GT	CGG
(AAG)	 AG	75288-75392	GT	AGG
(GGG)	 AG	75513-75658	GT	AGG
(ATT)	 AG	75778-75835	GT	AGG
(TCA)	 AG	75966-76298	GC	AGG
(GAG)	 AG	76501-76623	AG	GAA
-recovered pasa_asmbl_29119.p1, terminal, 76501, 76623
-recovered pasa_asmbl_29119.p1, internal, 75057, 75176
-recovered pasa_asmbl_29119.p1, internal, 75288, 75392
-recovered pasa_asmbl_29119.p1, internal, 75513, 75658
-recovered pasa_asmbl_29119.p1, internal, 75778, 75835
-recovered pasa_asmbl_29119.p1, internal, 75966, 76298
Valid prediction for GlimmerHMM_glimmerT_50017-T1
Valid prediction for GlimmerHMM_glimmerT_50026-T1
Valid prediction for Augustus_model.g33542.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 Augustus_model.g33545.t1
Valid prediction for GlimmerHMM_glimmerT_50027-T1
Valid prediction for GlimmerHMM_glimmerT_50009-T1
Valid prediction for Augustus_model.g33534.t1
Valid prediction for Augustus_model.g33544.t1
Valid prediction for GeneMark_model.86636_t
Valid prediction for GlimmerHMM_glimmerT_49997-T1
Valid prediction for snap_scaffold_22-snap.48-T1
Valid prediction for GeneMark_model.86627_t
Valid prediction for GlimmerHMM_glimmerT_50015-T1
Valid prediction for GeneMark_model.86640_t
Valid prediction for GeneMark_model.86657_t
Valid prediction for GeneMark_model.86631_t
Valid prediction for GeneMark_model.86630_t
Valid prediction for GeneMark_model.86629_t
Valid prediction for snap_scaffold_22-snap.52-T1
Valid prediction for GeneMark_model.86634_t
Valid prediction for snap_scaffold_22-snap.61-T1
Valid prediction for GlimmerHMM_glimmerT_49999-T1
Valid prediction for CodingQuarry_transcript_34002-T1
Valid prediction for GlimmerHMM_glimmerT_50013-T1
Valid prediction for Augustus_model.g33559.t1
Valid prediction for snap_scaffold_22-snap.65-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49998-T1
Valid prediction for Augustus_model.g33533.t1
Valid prediction for snap_scaffold_22-snap.60-T1
Valid prediction for GeneMark_model.86654_t
Valid prediction for snap_scaffold_22-snap.49-T1
Valid prediction for snap_scaffold_22-snap.51-T1
Valid prediction for CodingQuarry_transcript_34001-T1
Valid prediction for GeneMark_model.86633_t
Valid prediction for GlimmerHMM_glimmerT_50005-T1
Valid prediction for HiQ_model.g33541.t1
Valid prediction for pasa_asmbl_29837.p1
Valid prediction for GeneMark_model.86635_t
Valid prediction for snap_scaffold_22-snap.55-T1
Valid prediction for snap_scaffold_22-snap.76-T1
Valid prediction for GlimmerHMM_glimmerT_50004-T1
Valid prediction for GlimmerHMM_glimmerT_50002-T1
Valid prediction for GlimmerHMM_glimmerT_50010-T1
Valid prediction for snap_scaffold_22-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_50008-T1
Valid prediction for snap_scaffold_22-snap.58-T1
Valid prediction for snap_scaffold_22-snap.59-T1
Valid prediction for snap_scaffold_22-snap.87-T1
Valid prediction for Augustus_model.g33535.t1
Valid prediction for Augustus_model.g33537.t1
Valid prediction for Augustus_model.g33558.t1
Valid prediction for GeneMark_model.86641_t
Valid prediction for GlimmerHMM_glimmerT_50016-T1
Valid prediction for Augustus_model.g33540.t1
Valid prediction for GlimmerHMM_glimmerT_50025-T1

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

-building trellis in range 1 - 233763
-exon list size: 449


building trellis

0.2    
0.4    
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0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.4    
2.7    
2.9    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.6    
8.9    
9.1    
9.3    
9.5    
9.8    
10.0    
10.2    
10.4    
10.6    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.5    
15.7    
16.0    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.5    
60.8    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 44 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support