-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_12171137-12412637

-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.g10439.t1
Valid prediction for GlimmerHMM_glimmerT_15623-T1
Valid prediction for Augustus_model.g10428.t1
Valid prediction for GlimmerHMM_glimmerT_15625-T1
Valid prediction for GlimmerHMM_glimmerT_15634-T1
Valid prediction for GlimmerHMM_glimmerT_15631-T1
Valid prediction for Augustus_model.g10446.t1
Valid prediction for HiQ_model.g10429.t1
Valid prediction for snap_scaffold_6-snap.2589-T1
Valid prediction for CodingQuarry_transcript_55249-T1
Valid prediction for snap_scaffold_6-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_15628-T1
Valid prediction for snap_scaffold_6-snap.2579-T1
Valid prediction for snap_scaffold_6-snap.2581-T1
Valid prediction for GlimmerHMM_glimmerT_15606-T1
Valid prediction for GlimmerHMM_glimmerT_15612-T1
Valid prediction for GlimmerHMM_glimmerT_15619-T1
Couldn't classify 55398, 55496
Couldn't classify 62132, 62194
Sorry, prediction pasa_asmbl_47387.p1 fails validation.
(GGG)	 TA	55398-55496	GT	AGG
(GAA)	 AG	55893-55922	GT	AGG
(AAT)	 AG	58121-58238	GT	TGG
(GAT)	 AG	60205-60254	GT	TGG
(AGT)	 AG	60362-60442	GT	CGG
(ATT)	 AG	60753-60845	GT	GGG
(AAC)	 AG	62132-62194	GT	AGG
-recovered pasa_asmbl_47387.p1, internal, 55893, 55922
-recovered pasa_asmbl_47387.p1, internal, 58121, 58238
-recovered pasa_asmbl_47387.p1, internal, 60205, 60254
-recovered pasa_asmbl_47387.p1, internal, 60362, 60442
-recovered pasa_asmbl_47387.p1, internal, 60753, 60845
-recovered pasa_asmbl_47387.p1, internal, 62132, 62194
Valid prediction for GlimmerHMM_glimmerT_15608-T1
Valid prediction for GlimmerHMM_glimmerT_15607-T1
Valid prediction for GlimmerHMM_glimmerT_15629-T1
Valid prediction for snap_scaffold_6-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_15613-T1
Valid prediction for HiQ_model.g10422.t1
Valid prediction for Augustus_model.g10441.t1
Valid prediction for snap_scaffold_6-snap.2577-T1
Valid prediction for snap_scaffold_6-snap.2582-T1
Valid prediction for GlimmerHMM_glimmerT_15627-T1
Couldn't classify 69591, 69654
Couldn't classify 70660, 70830
Sorry, prediction pasa_asmbl_47388.p1 fails validation.
(TCC)	 AG	69591-69654	GT	GGG
(GTT)	 AG	70195-70343	GT	AGG
(GTT)	 AG	70415-70552	GT	AGG
(CAT)	 AG	70660-70830	AT	TGA
-recovered pasa_asmbl_47388.p1, internal, 69591, 69654
-recovered pasa_asmbl_47388.p1, internal, 70195, 70343
-recovered pasa_asmbl_47388.p1, internal, 70415, 70552
Valid prediction for snap_scaffold_6-snap.2602-T1
Valid prediction for pasa_asmbl_47393.p1
Valid prediction for HiQ_model.g10445.t1
Valid prediction for snap_scaffold_6-snap.2597-T1
Valid prediction for Augustus_model.g10427.t1
Valid prediction for GlimmerHMM_glimmerT_15618-T1
Valid prediction for snap_scaffold_6-snap.2605-T1
Valid prediction for snap_scaffold_6-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_15615-T1
Valid prediction for GlimmerHMM_glimmerT_15610-T1
Valid prediction for snap_scaffold_6-snap.2569-T1
Couldn't classify 198272, 198430
Couldn't classify 199401, 199513
Sorry, prediction pasa_asmbl_47392.p1 fails validation.
(CCA)	 CT	198272-198430	GT	AGG
(GAC)	 AG	199106-199229	GT	TGG
(GGA)	 AG	199401-199513	GG	GAG
-recovered pasa_asmbl_47392.p1, internal, 199106, 199229
Valid prediction for GlimmerHMM_glimmerT_15622-T1
Valid prediction for Augustus_model.g10443.t1
Valid prediction for snap_scaffold_6-snap.2604-T1
Valid prediction for GlimmerHMM_glimmerT_15630-T1
Valid prediction for snap_scaffold_6-snap.2583-T1
Valid prediction for CodingQuarry_transcript_55248-T1
Valid prediction for GlimmerHMM_glimmerT_15603-T1
Valid prediction for Augustus_model.g10430.t1
Valid prediction for snap_scaffold_6-snap.2584-T1
Valid prediction for snap_scaffold_6-snap.2573-T1
Couldn't classify 14624, 14711
Sorry, prediction pasa_asmbl_47379.p1 fails validation.
(ATG)	 CA	7959-8064	GT	AGG
(TCT)	 AG	8717-8939	GT	AGG
(GCC)	 AG	9208-9338	GT	AGG
(AAC)	 AG	9559-9599	GT	AGG
(GTT)	 AG	10388-10532	GT	AGG
(ATA)	 AG	13220-13291	GT	AGG
(GTG)	 AG	13556-13609	GT	AGG
(ATG)	 AG	13789-13863	GT	TGG
(TGT)	 AG	14086-14188	GT	AGG
(GCT)	 AG	14624-14711	GG	TGG
-recovered pasa_asmbl_47379.p1, initial, 7959, 8064
add_exon() Sorry, pasa_asmbl_47379.p1 13789-13863-initial-1 is invalid.
-recovered pasa_asmbl_47379.p1, initial, 13789, 13863
add_exon() Sorry, pasa_asmbl_47379.p1 9208-9338-terminal-2 is invalid.
-recovered pasa_asmbl_47379.p1, terminal, 9208, 9338
-recovered pasa_asmbl_47379.p1, internal, 8717, 8939
-recovered pasa_asmbl_47379.p1, internal, 9208, 9338
-recovered pasa_asmbl_47379.p1, internal, 9559, 9599
-recovered pasa_asmbl_47379.p1, internal, 10388, 10532
-recovered pasa_asmbl_47379.p1, internal, 13220, 13291
-recovered pasa_asmbl_47379.p1, internal, 13556, 13609
-recovered pasa_asmbl_47379.p1, internal, 13789, 13863
-recovered pasa_asmbl_47379.p1, internal, 14086, 14188
Valid prediction for snap_scaffold_6-snap.2607-T1
Valid prediction for Augustus_model.g10449.t1
Valid prediction for HiQ_model.g10431.t1
Valid prediction for snap_scaffold_6-snap.2600-T1
Valid prediction for Augustus_model.g10425.t1
Valid prediction for Augustus_model.g10434.t1
Valid prediction for snap_scaffold_6-snap.2588-T1
Couldn't classify 77854, 78000
Sorry, prediction pasa_asmbl_47390.p1 fails validation.
(GCA)	 AG	77854-78000	GT	AGG
(GCA)	 AG	78083-78194	GT	AGG
(GTG)	 AG	78442-78563	AA	AAA
-recovered pasa_asmbl_47390.p1, terminal, 78442, 78563
-recovered pasa_asmbl_47390.p1, internal, 77854, 78000
-recovered pasa_asmbl_47390.p1, internal, 78083, 78194
Valid prediction for GlimmerHMM_glimmerT_15616-T1
Valid prediction for snap_scaffold_6-snap.2576-T1
Valid prediction for Augustus_model.g10433.t1
Valid prediction for snap_scaffold_6-snap.2595-T1
Valid prediction for HiQ_model.g10448.t1
Valid prediction for snap_scaffold_6-snap.2592-T1
Valid prediction for Augustus_model.g10437.t1
Valid prediction for Augustus_model.g10440.t1
Valid prediction for Augustus_model.g10432.t1
Valid prediction for GlimmerHMM_glimmerT_15620-T1
Valid prediction for GlimmerHMM_glimmerT_15633-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.g10447.t1
Valid prediction for snap_scaffold_6-snap.2575-T1
Valid prediction for snap_scaffold_6-snap.2571-T1
Valid prediction for Augustus_model.g10421.t1
Valid prediction for snap_scaffold_6-snap.2568-T1
Valid prediction for snap_scaffold_6-snap.2591-T1
Valid prediction for Augustus_model.g10424.t1
Valid prediction for GlimmerHMM_glimmerT_15624-T1
Valid prediction for GlimmerHMM_glimmerT_15602-T1
Valid prediction for snap_scaffold_6-snap.2574-T1
Valid prediction for snap_scaffold_6-snap.2587-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2580-T1
Valid prediction for snap_scaffold_6-snap.2590-T1
Valid prediction for snap_scaffold_6-snap.2572-T1
Valid prediction for snap_scaffold_6-snap.2606-T1
Valid prediction for snap_scaffold_6-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_15617-T1
Valid prediction for Augustus_model.g10436.t1
Valid prediction for GlimmerHMM_glimmerT_15614-T1
Valid prediction for GlimmerHMM_glimmerT_15609-T1
Valid prediction for GlimmerHMM_glimmerT_15626-T1
Valid prediction for snap_scaffold_6-snap.2593-T1
Valid prediction for snap_scaffold_6-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_15605-T1
Valid prediction for snap_scaffold_6-snap.2578-T1
Valid prediction for snap_scaffold_6-snap.2598-T1
Valid prediction for Augustus_model.g10444.t1
Valid prediction for Augustus_model.g10438.t1
Valid prediction for snap_scaffold_6-snap.2594-T1
Valid prediction for snap_scaffold_6-snap.2586-T1
Valid prediction for GlimmerHMM_glimmerT_15621-T1
Valid prediction for Augustus_model.g10426.t1
Valid prediction for Augustus_model.g10435.t1
Valid prediction for GlimmerHMM_glimmerT_15632-T1
Valid prediction for Augustus_model.g10423.t1
Valid prediction for GlimmerHMM_glimmerT_15611-T1
Valid prediction for snap_scaffold_6-snap.2596-T1
Valid prediction for GlimmerHMM_glimmerT_15604-T1
Valid prediction for Augustus_model.g10442.t1

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

-building trellis in range 1 - 241501
-exon list size: 315


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 42 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support