-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_123215-301176

-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 snap_scaffold_22-snap.66-T1
Valid prediction for Augustus_model.g32583.t1
Valid prediction for snap_scaffold_22-snap.47-T1
Valid prediction for snap_scaffold_22-snap.65-T1
Valid prediction for snap_scaffold_22-snap.42-T1
Valid prediction for snap_scaffold_22-snap.71-T1
Valid prediction for Augustus_model.g32560.t1
Couldn't classify 93093, 93094
Sorry, prediction CodingQuarry_transcript_34063-T1 fails validation.
(ATG)	 CA	91100-91391	GT	AGG
(ATG)	 AG	91510-91617	GT	CTG
(GAC)	 AG	93093-93094	CT	GAC
-recovered CodingQuarry_transcript_34063-T1, initial, 91100, 91391
-recovered CodingQuarry_transcript_34063-T1, initial, 91510, 91617
-recovered CodingQuarry_transcript_34063-T1, internal, 91510, 91617
Valid prediction for snap_scaffold_22-snap.72-T1
Valid prediction for snap_scaffold_22-snap.54-T1
Valid prediction for Augustus_model.g32578.t1
Valid prediction for Augustus_model.g32566.t1
Valid prediction for HiQ_model.g32585.t1
Valid prediction for GlimmerHMM_glimmerT_48791-T1
Valid prediction for CodingQuarry_transcript_34062-T1
Valid prediction for GlimmerHMM_glimmerT_48787-T1
Valid prediction for GlimmerHMM_glimmerT_48803-T1
Valid prediction for snap_scaffold_22-snap.62-T1
Valid prediction for GlimmerHMM_glimmerT_48795-T1
Valid prediction for CodingQuarry_transcript_34061-T1
Valid prediction for pasa_asmbl_29828.p1
Valid prediction for Augustus_model.g32577.t1
Couldn't classify 113250, 113315
Sorry, prediction pasa_asmbl_29825.p1 fails validation.
(ATC)	 CC	113250-113315	GT	AGG
(GTA)	 AG	113922-114041	GT	CGG
(AAG)	 AG	114153-114257	GT	AGG
(GGG)	 AG	114378-114523	GT	AGG
(ATT)	 AG	114643-114700	GT	AGG
(TCA)	 AG	114831-115163	GC	AGG
(GAG)	 AG	115366-115488	AG	GAA
-recovered pasa_asmbl_29825.p1, terminal, 115366, 115488
-recovered pasa_asmbl_29825.p1, internal, 113922, 114041
-recovered pasa_asmbl_29825.p1, internal, 114153, 114257
-recovered pasa_asmbl_29825.p1, internal, 114378, 114523
-recovered pasa_asmbl_29825.p1, internal, 114643, 114700
-recovered pasa_asmbl_29825.p1, internal, 114831, 115163
Valid prediction for Augustus_model.g32581.t1
Valid prediction for Augustus_model.g32565.t1
Valid prediction for snap_scaffold_22-snap.60-T1
Valid prediction for GlimmerHMM_glimmerT_48775-T1
Valid prediction for snap_scaffold_22-snap.48-T1
Valid prediction for CodingQuarry_transcript_34068-T1
Valid prediction for GlimmerHMM_glimmerT_48778-T1
Valid prediction for GlimmerHMM_glimmerT_48796-T1
Valid prediction for GlimmerHMM_glimmerT_48772-T1
Valid prediction for snap_scaffold_22-snap.50-T1
Valid prediction for snap_scaffold_22-snap.69-T1
Valid prediction for GlimmerHMM_glimmerT_48801-T1
Valid prediction for Augustus_model.g32567.t1
Valid prediction for GlimmerHMM_glimmerT_48773-T1
Valid prediction for GlimmerHMM_glimmerT_48784-T1
Valid prediction for snap_scaffold_22-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_48776-T1
Valid prediction for GlimmerHMM_glimmerT_48777-T1
Valid prediction for HiQ_model.g32573.t1
Couldn't classify 33628, 33768
Couldn't classify 34848, 34999
Sorry, prediction pasa_asmbl_30539.p1 fails validation.
(CAG)	 AT	33628-33768	GT	AGG
(CTC)	 AG	34407-34524	GT	GTG
(GGG)	 AG	34848-34999	AG	AGA
-recovered pasa_asmbl_30539.p1, internal, 34407, 34524
Couldn't classify 76423, 76437
Sorry, prediction pasa_asmbl_29816.p1 fails validation.
(TCA)	 GC	76423-76437	GT	AGG
(GTT)	 AG	76612-76695	GT	TGG
(GAA)	 AG	78291-78455	GT	AGG
(ATG)	 AG	78573-78678	GT	AGG
(ATG)	 AG	78850-79128	GT	AGG
(ATA)	 AG	79740-79872	GT	AAG
(GCA)	 AG	80606-80751	GT	ACG
(TTG)	 AG	80925-81037	GT	AGG
(GAG)	 AG	81961-82120	GT	TGG
(GGG)	 AG	83008-83099	GT	AGG
(CTG)	 AG	83185-83262	TT	GAT
-recovered pasa_asmbl_29816.p1, initial, 78573, 78678
add_exon() Sorry, pasa_asmbl_29816.p1 78850-79128-initial-1 is invalid.
-recovered pasa_asmbl_29816.p1, initial, 78850, 79128
-recovered pasa_asmbl_29816.p1, terminal, 83185, 83262
-recovered pasa_asmbl_29816.p1, internal, 76612, 76695
-recovered pasa_asmbl_29816.p1, internal, 78291, 78455
-recovered pasa_asmbl_29816.p1, internal, 78573, 78678
-recovered pasa_asmbl_29816.p1, internal, 78850, 79128
-recovered pasa_asmbl_29816.p1, internal, 79740, 79872
-recovered pasa_asmbl_29816.p1, internal, 80606, 80751
-recovered pasa_asmbl_29816.p1, internal, 80925, 81037
-recovered pasa_asmbl_29816.p1, internal, 81961, 82120
-recovered pasa_asmbl_29816.p1, internal, 83008, 83099
Valid prediction for GlimmerHMM_glimmerT_48802-T1
Valid prediction for snap_scaffold_22-snap.61-T1
Valid prediction for snap_scaffold_22-snap.68-T1
Valid prediction for CodingQuarry_transcript_34069-T1
Valid prediction for GlimmerHMM_glimmerT_48798-T1
Valid prediction for Augustus_model.g32584.t1
Valid prediction for snap_scaffold_22-snap.67-T1
Valid prediction for Augustus_model.g32558.t1
Valid prediction for HiQ_model.g32574.t1
Valid prediction for CodingQuarry_transcript_34060-T1
Valid prediction for HiQ_model.g32582.t1
Couldn't classify 165994, 166086
Couldn't classify 168273, 168443
Sorry, prediction pasa_asmbl_29829.p1 fails validation.
(GAA)	 AG	165994-166086	GT	AGG
(CTC)	 AG	166413-166556	GT	AGG
(ATC)	 AG	167012-167194	GT	AGG
(GAC)	 AG	167440-167590	GT	AGG
(ACT)	 AG	167845-167942	GT	AGG
(GCT)	 AG	168273-168443	GC	CCG
add_exon() Sorry, pasa_asmbl_29829.p1 167440-167590-terminal-3 is invalid.
-recovered pasa_asmbl_29829.p1, terminal, 167440, 167590
-recovered pasa_asmbl_29829.p1, internal, 165994, 166086
-recovered pasa_asmbl_29829.p1, internal, 166413, 166556
-recovered pasa_asmbl_29829.p1, internal, 167012, 167194
-recovered pasa_asmbl_29829.p1, internal, 167440, 167590
-recovered pasa_asmbl_29829.p1, internal, 167845, 167942
-recovered pasa_asmbl_29829.p1, internal, 168273, 168443
Couldn't classify 16826, 17001
Couldn't classify 17285, 17456
Sorry, prediction pasa_asmbl_29808.p1 fails validation.
(GTA)	 AG	16826-17001	GT	GGG
(GTA)	 AG	17285-17456	AG	AGA
-recovered pasa_asmbl_29808.p1, internal, 16826, 17001
Valid prediction for Augustus_model.g32564.t1
Valid prediction for pasa_asmbl_29832.p1
Couldn't classify 176221, 176532
Sorry, prediction pasa_asmbl_29834.p1 fails validation.
(GAG)	 CA	176221-176532	TC	GAT
Couldn't classify 8509, 9573
Couldn't classify 13472, 13527
Sorry, prediction pasa_asmbl_29807.p1 fails validation.
(GGC)	 GT	8509-9573	GT	AGG
(GAT)	 AG	12335-12527	GT	ATG
(ATC)	 AG	13472-13527	TT	GGT
-recovered pasa_asmbl_29807.p1, internal, 12335, 12527
Valid prediction for snap_scaffold_22-snap.70-T1
Valid prediction for snap_scaffold_22-snap.43-T1
Valid prediction for HiQ_model.g32563.t1
Valid prediction for GlimmerHMM_glimmerT_48804-T1
Valid prediction for Augustus_model.g32586.t1
Valid prediction for Augustus_model.g32562.t1
Valid prediction for GlimmerHMM_glimmerT_48790-T1
Valid prediction for Augustus_model.g32557.t1
Valid prediction for GlimmerHMM_glimmerT_48771-T1
Valid prediction for GlimmerHMM_glimmerT_48779-T1
Valid prediction for GlimmerHMM_glimmerT_48783-T1
Valid prediction for HiQ_model.g32571.t1
Valid prediction for snap_scaffold_22-snap.55-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_48789-T1
Valid prediction for GlimmerHMM_glimmerT_48797-T1
Valid prediction for HiQ_model.g32576.t1
Valid prediction for snap_scaffold_22-snap.57-T1
Valid prediction for Augustus_model.g32575.t1
Valid prediction for snap_scaffold_22-snap.56-T1
Valid prediction for snap_scaffold_22-snap.51-T1
Valid prediction for snap_scaffold_22-snap.44-T1
Valid prediction for snap_scaffold_22-snap.59-T1
Couldn't classify 92950, 93384
Sorry, prediction pasa_asmbl_30478.p1 fails validation.
(GTG)	 TC	92950-93384	GT	CAG
Valid prediction for snap_scaffold_22-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_48780-T1
Valid prediction for GlimmerHMM_glimmerT_48788-T1
Valid prediction for snap_scaffold_22-snap.63-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48782-T1
Valid prediction for GlimmerHMM_glimmerT_48785-T1
Valid prediction for snap_scaffold_22-snap.40-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g32579.t1
Valid prediction for snap_scaffold_22-snap.37-T1
Valid prediction for Augustus_model.g32561.t1
Valid prediction for GlimmerHMM_glimmerT_48793-T1
Valid prediction for snap_scaffold_22-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_48792-T1
Valid prediction for snap_scaffold_22-snap.38-T1
Valid prediction for Augustus_model.g32580.t1
Valid prediction for CodingQuarry_transcript_34066-T1
Valid prediction for pasa_asmbl_29082.p1
Valid prediction for Augustus_model.g32568.t1
Valid prediction for Augustus_model.g32572.t1
Valid prediction for snap_scaffold_22-snap.58-T1
Valid prediction for GlimmerHMM_glimmerT_48799-T1
Valid prediction for GlimmerHMM_glimmerT_48774-T1
Valid prediction for snap_scaffold_22-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_48770-T1
Valid prediction for Augustus_model.g32559.t1
Valid prediction for GlimmerHMM_glimmerT_48800-T1
Valid prediction for GlimmerHMM_glimmerT_48786-T1
Valid prediction for GlimmerHMM_glimmerT_48794-T1
Valid prediction for snap_scaffold_22-snap.39-T1
Valid prediction for Augustus_model.g32556.t1
Valid prediction for snap_scaffold_22-snap.41-T1
Valid prediction for CodingQuarry_transcript_34067-T1
Valid prediction for snap_scaffold_22-snap.45-T1
Valid prediction for CodingQuarry_transcript_34065-T1
Valid prediction for Augustus_model.g32570.t1
Valid prediction for snap_scaffold_22-snap.46-T1
Valid prediction for snap_scaffold_22-snap.53-T1
Valid prediction for CodingQuarry_transcript_34064-T1
Valid prediction for Augustus_model.g32569.t1
Valid prediction for snap_scaffold_22-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_48781-T1

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

-building trellis in range 1 - 177962
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 38 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support