-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_12933934-13131771

-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: +)Couldn't classify 146704, 146890
Sorry, prediction pasa_asmbl_47471.p1 fails validation.
(AGA)	 TC	146704-146890	GT	GGG
(CTC)	 AG	147599-147708	GT	AGG
(CCA)	 AG	148189-148308	AA	GAA
-recovered pasa_asmbl_47471.p1, terminal, 148189, 148308
-recovered pasa_asmbl_47471.p1, internal, 147599, 147708
Valid prediction for snap_scaffold_6-snap.2723-T1
Valid prediction for Augustus_model.g10545.t1
Valid prediction for HiQ_model.g10547.t1
Valid prediction for snap_scaffold_6-snap.2703-T1
Valid prediction for GlimmerHMM_glimmerT_15725-T1
Valid prediction for Augustus_model.g10532.t1
Valid prediction for snap_scaffold_6-snap.2739-T1
Valid prediction for HiQ_model.g10534.t1
Valid prediction for snap_scaffold_6-snap.2733-T1
Valid prediction for Augustus_model.g10533.t1
Valid prediction for snap_scaffold_6-snap.2720-T1
Valid prediction for GlimmerHMM_glimmerT_15703-T1
Couldn't classify 3678, 3794
Couldn't classify 6709, 6918
Sorry, prediction pasa_asmbl_47456.p1 fails validation.
(CCT)	 AT	3678-3794	GT	ATG
(GTG)	 AG	3989-4044	GT	ATG
(CTA)	 AG	5973-6079	GT	AGG
(GAC)	 AG	6347-6432	GT	AGG
(ATC)	 AG	6709-6918	GT	AGG
-recovered pasa_asmbl_47456.p1, internal, 3989, 4044
-recovered pasa_asmbl_47456.p1, internal, 5973, 6079
-recovered pasa_asmbl_47456.p1, internal, 6347, 6432
-recovered pasa_asmbl_47456.p1, internal, 6709, 6918
Valid prediction for Augustus_model.g10550.t1
Valid prediction for GlimmerHMM_glimmerT_15708-T1
Valid prediction for snap_scaffold_6-snap.2735-T1
Valid prediction for snap_scaffold_6-snap.2727-T1
Couldn't classify 140814, 140930
Sorry, prediction pasa_asmbl_47469.p1 fails validation.
(ATG)	 AC	134773-134984	GT	TGG
(CTC)	 AG	136402-136584	GT	GTG
(TTA)	 AG	137125-137314	GT	AGG
(ATC)	 AG	138275-138391	GT	AGG
(GGC)	 AG	140814-140930	AA	GTA
-recovered pasa_asmbl_47469.p1, initial, 134773, 134984
-recovered pasa_asmbl_47469.p1, internal, 136402, 136584
-recovered pasa_asmbl_47469.p1, internal, 137125, 137314
-recovered pasa_asmbl_47469.p1, internal, 138275, 138391
Valid prediction for snap_scaffold_6-snap.2719-T1
Valid prediction for CodingQuarry_transcript_55271-T1
Valid prediction for GlimmerHMM_glimmerT_15720-T1
Valid prediction for snap_scaffold_6-snap.2708-T1
Valid prediction for Augustus_model.g10546.t1
Valid prediction for GlimmerHMM_glimmerT_15723-T1
Valid prediction for CodingQuarry_transcript_55274-T1
Valid prediction for Augustus_model.g10541.t1
Valid prediction for CodingQuarry_transcript_55272-T1
Valid prediction for snap_scaffold_6-snap.2717-T1
Valid prediction for GlimmerHMM_glimmerT_15722-T1
Couldn't classify 14648, 14749
Sorry, prediction pasa_asmbl_47458.p1 fails validation.
(TTG)	 AG	14648-14749	GT	CGG
(CCC)	 AG	14943-15029	GT	CTG
(TCT)	 AG	15142-15340	GT	AGG
(AGC)	 AG	15564-15657	GT	AGG
(GTC)	 AG	15759-15807	GA	GAG
add_exon() Sorry, pasa_asmbl_47458.p1 15564-15657-terminal-3 is invalid.
-recovered pasa_asmbl_47458.p1, terminal, 15564, 15657
-recovered pasa_asmbl_47458.p1, terminal, 15759, 15807
-recovered pasa_asmbl_47458.p1, internal, 14648, 14749
-recovered pasa_asmbl_47458.p1, internal, 14943, 15029
-recovered pasa_asmbl_47458.p1, internal, 15142, 15340
-recovered pasa_asmbl_47458.p1, internal, 15564, 15657
Valid prediction for snap_scaffold_6-snap.2737-T1
Valid prediction for snap_scaffold_6-snap.2729-T1
Valid prediction for snap_scaffold_6-snap.2718-T1
Valid prediction for snap_scaffold_6-snap.2728-T1
Couldn't classify 48756, 48798
Sorry, prediction pasa_asmbl_47466.p1 fails validation.
(GTA)	 TT	48756-48798	GT	TGG
(AGG)	 AG	48915-48926	GT	AGG
(TGC)	 AG	49230-49384	GT	AGG
(GCA)	 AG	49727-49843	GT	AGG
(GTT)	 AG	50527-50631	GG	GAG
-recovered pasa_asmbl_47466.p1, terminal, 50527, 50631
-recovered pasa_asmbl_47466.p1, internal, 48915, 48926
-recovered pasa_asmbl_47466.p1, internal, 49230, 49384
-recovered pasa_asmbl_47466.p1, internal, 49727, 49843
Valid prediction for GlimmerHMM_glimmerT_15719-T1
Valid prediction for CodingQuarry_transcript_55273-T1
Valid prediction for snap_scaffold_6-snap.2711-T1
Valid prediction for GlimmerHMM_glimmerT_15706-T1
Valid prediction for CodingQuarry_transcript_55280-T1
Valid prediction for Augustus_model.g10554.t1
Valid prediction for snap_scaffold_6-snap.2732-T1
Valid prediction for snap_scaffold_6-snap.2734-T1
Valid prediction for GlimmerHMM_glimmerT_15705-T1
Valid prediction for Augustus_model.g10531.t1
Valid prediction for Augustus_model.g10529.t1
Valid prediction for pasa_asmbl_47461.p1
Valid prediction for GlimmerHMM_glimmerT_15715-T1
Valid prediction for Augustus_model.g10549.t1
Valid prediction for GlimmerHMM_glimmerT_15721-T1
Valid prediction for Augustus_model.g10551.t1
Valid prediction for GlimmerHMM_glimmerT_15713-T1
Valid prediction for Augustus_model.g10548.t1
Valid prediction for GlimmerHMM_glimmerT_15711-T1
Valid prediction for GlimmerHMM_glimmerT_15727-T1
Valid prediction for snap_scaffold_6-snap.2736-T1
Valid prediction for Augustus_model.g10536.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_6-snap.2707-T1
Valid prediction for Augustus_model.g10530.t1
Valid prediction for GlimmerHMM_glimmerT_15726-T1
Couldn't classify 5297, 5380
Sorry, prediction pasa_asmbl_48875.p1 fails validation.
(CTG)	 AG	5297-5380	GT	TGG
(TTC)	 AG	5575-5688	GT	AGG
(CCT)	 AG	6225-6308	GT	AGG
(ATC)	 AG	6667-6735	CC	GAC
-recovered pasa_asmbl_48875.p1, terminal, 6667, 6735
-recovered pasa_asmbl_48875.p1, internal, 5297, 5380
-recovered pasa_asmbl_48875.p1, internal, 5575, 5688
-recovered pasa_asmbl_48875.p1, internal, 6225, 6308
Valid prediction for snap_scaffold_6-snap.2709-T1
Couldn't classify 84437, 84554
Couldn't classify 85997, 86135
Sorry, prediction pasa_asmbl_48869.p1 fails validation.
(GAG)	 CA	84437-84554	GT	GGG
(GGG)	 AG	85053-85213	GT	AGG
(AGA)	 AG	85376-85474	GT	AGG
(CAA)	 AG	85678-85823	GT	AGG
(GCA)	 AG	85997-86135	GA	GGG
-recovered pasa_asmbl_48869.p1, internal, 85053, 85213
-recovered pasa_asmbl_48869.p1, internal, 85376, 85474
-recovered pasa_asmbl_48869.p1, internal, 85678, 85823
Valid prediction for GlimmerHMM_glimmerT_15704-T1
Valid prediction for GlimmerHMM_glimmerT_15710-T1
Valid prediction for pasa_asmbl_48856.p1
Valid prediction for snap_scaffold_6-snap.2714-T1
Valid prediction for snap_scaffold_6-snap.2704-T1
Valid prediction for Augustus_model.g10540.t1
Valid prediction for Augustus_model.g10543.t1
Valid prediction for GlimmerHMM_glimmerT_15707-T1
Valid prediction for snap_scaffold_6-snap.2706-T1
Valid prediction for snap_scaffold_6-snap.2725-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g10537.t1
Valid prediction for GlimmerHMM_glimmerT_15709-T1
Valid prediction for snap_scaffold_6-snap.2713-T1
Valid prediction for GlimmerHMM_glimmerT_15714-T1
Valid prediction for Augustus_model.g10535.t1
Valid prediction for Augustus_model.g10544.t1
Valid prediction for snap_scaffold_6-snap.2705-T1
Valid prediction for HiQ_model.g10538.t1
Couldn't classify 197003, 197311
Sorry, prediction pasa_asmbl_47455.p1 fails validation.
(CCC)	 GC	197003-197311	CA	AGC
Valid prediction for CodingQuarry_transcript_55278-T1
Valid prediction for snap_scaffold_6-snap.2724-T1
Valid prediction for snap_scaffold_6-snap.2726-T1
Valid prediction for GlimmerHMM_glimmerT_15724-T1
Valid prediction for CodingQuarry_transcript_55275-T1
Valid prediction for snap_scaffold_6-snap.2710-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2721-T1
Valid prediction for snap_scaffold_6-snap.2712-T1
Valid prediction for Augustus_model.g10539.t1
Couldn't classify 100729, 101460
Sorry, prediction pasa_asmbl_47468.p1 fails validation.
(CCC)	 CN	100729-101460	GC	AAG
Valid prediction for GlimmerHMM_glimmerT_15712-T1
Valid prediction for Augustus_model.g10542.t1
Valid prediction for GlimmerHMM_glimmerT_15717-T1
Valid prediction for Augustus_model.g10552.t1
Valid prediction for snap_scaffold_6-snap.2716-T1
Valid prediction for snap_scaffold_6-snap.2731-T1
Valid prediction for GlimmerHMM_glimmerT_15702-T1
Valid prediction for HiQ_model.g10553.t1
Valid prediction for CodingQuarry_transcript_55279-T1
Valid prediction for CodingQuarry_transcript_55276-T1
Valid prediction for GlimmerHMM_glimmerT_15716-T1
Valid prediction for CodingQuarry_transcript_55277-T1
Valid prediction for pasa_asmbl_48870.p1
Valid prediction for snap_scaffold_6-snap.2738-T1
Valid prediction for snap_scaffold_6-snap.2730-T1
Valid prediction for snap_scaffold_6-snap.2722-T1
Valid prediction for GlimmerHMM_glimmerT_15718-T1
Valid prediction for snap_scaffold_6-snap.2715-T1

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

-building trellis in range 1 - 197838
-exon list size: 322


building trellis

0.3    
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1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support