-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_12681934-12936029

-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_16077-T1
Valid prediction for snap_scaffold_6-snap.2691-T1
Valid prediction for GlimmerHMM_glimmerT_16065-T1
Valid prediction for GlimmerHMM_glimmerT_16082-T1
Valid prediction for snap_scaffold_6-snap.2657-T1
Valid prediction for GlimmerHMM_glimmerT_16076-T1
Valid prediction for snap_scaffold_6-snap.2695-T1
Valid prediction for CodingQuarry_transcript_55119-T1
Couldn't classify 243960, 244334
Sorry, prediction pasa_asmbl_47389.p1 fails validation.
(GTG)	 CA	243960-244334	GT	AGG
(AAT)	 AG	244527-244792	GT	CGG
(ACC)	 AG	244886-244949	GT	CGG
(ACC)	 AG	245070-245241	GT	CAG
(GTT)	 AG	245400-245716	CT	AGC
-recovered pasa_asmbl_47389.p1, terminal, 245400, 245716
-recovered pasa_asmbl_47389.p1, internal, 244527, 244792
-recovered pasa_asmbl_47389.p1, internal, 244886, 244949
-recovered pasa_asmbl_47389.p1, internal, 245070, 245241
Valid prediction for Augustus_model.g10816.t1
Valid prediction for snap_scaffold_6-snap.2689-T1
Valid prediction for Augustus_model.g10799.t1
Valid prediction for snap_scaffold_6-snap.2688-T1
Valid prediction for GlimmerHMM_glimmerT_16069-T1
Valid prediction for snap_scaffold_6-snap.2655-T1
Valid prediction for snap_scaffold_6-snap.2684-T1
Valid prediction for GlimmerHMM_glimmerT_16067-T1
Valid prediction for GlimmerHMM_glimmerT_16064-T1
Valid prediction for GeneMark_model.26880_t
Valid prediction for snap_scaffold_6-snap.2693-T1
Valid prediction for GlimmerHMM_glimmerT_16062-T1
Valid prediction for snap_scaffold_6-snap.2692-T1
Valid prediction for CodingQuarry_transcript_55121-T1
Valid prediction for Augustus_model.g10804.t1
Valid prediction for Augustus_model.g10796.t1
Valid prediction for HiQ_model.g10817.t1
Valid prediction for snap_scaffold_6-snap.2681-T1
Valid prediction for Augustus_model.g10820.t1
Valid prediction for snap_scaffold_6-snap.2696-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g10787.t1
Valid prediction for GeneMark_model.26888_t
Valid prediction for Augustus_model.g10788.t1
Valid prediction for GlimmerHMM_glimmerT_16054-T1
Valid prediction for Augustus_model.g10809.t1
Valid prediction for snap_scaffold_6-snap.2665-T1
Valid prediction for GeneMark_model.26887_t
Valid prediction for GlimmerHMM_glimmerT_16080-T1
Valid prediction for Augustus_model.g10813.t1
Valid prediction for snap_scaffold_6-snap.2697-T1
Valid prediction for Augustus_model.g10797.t1
Valid prediction for GeneMark_model.26872_t
Couldn't classify 183708, 183845
Sorry, prediction pasa_asmbl_47371.p1 fails validation.
(GCC)	 AG	183708-183845	GT	TTG
(GCT)	 AG	184101-184172	GT	AGG
(AAA)	 AG	184612-184713	GT	GGG
(CTG)	 AG	185549-185594	GT	AGG
(TTC)	 AG	185730-185826	GT	AGG
(GGA)	 AG	186328-186441	GT	TGG
(GAT)	 AG	186802-186893	GT	GGG
(CTG)	 AG	187371-187468	GA	GAG
-recovered pasa_asmbl_47371.p1, terminal, 187371, 187468
-recovered pasa_asmbl_47371.p1, internal, 183708, 183845
-recovered pasa_asmbl_47371.p1, internal, 184101, 184172
-recovered pasa_asmbl_47371.p1, internal, 184612, 184713
-recovered pasa_asmbl_47371.p1, internal, 185549, 185594
-recovered pasa_asmbl_47371.p1, internal, 185730, 185826
-recovered pasa_asmbl_47371.p1, internal, 186328, 186441
-recovered pasa_asmbl_47371.p1, internal, 186802, 186893
Valid prediction for Augustus_model.g10798.t1
Valid prediction for snap_scaffold_6-snap.2668-T1
Valid prediction for GeneMark_model.26877_t
Valid prediction for GeneMark_model.26895_t
Valid prediction for GeneMark_model.26896_t
Valid prediction for GeneMark_model.26900_t
Valid prediction for HiQ_model.g10812.t1
Valid prediction for HiQ_model.g10814.t1
Valid prediction for Augustus_model.g10802.t1
Valid prediction for snap_scaffold_6-snap.2666-T1
Valid prediction for snap_scaffold_6-snap.2671-T1
Valid prediction for snap_scaffold_6-snap.2670-T1
Couldn't classify 201511, 201747
Couldn't classify 201965, 202093
Sorry, prediction pasa_asmbl_47890.p1 fails validation.
(GTG)	 AG	201511-201747	GT	AGG
(ACA)	 AG	201965-202093	GT	AGG
-recovered pasa_asmbl_47890.p1, internal, 201511, 201747
-recovered pasa_asmbl_47890.p1, internal, 201965, 202093
Valid prediction for GlimmerHMM_glimmerT_16070-T1
Valid prediction for Augustus_model.g10815.t1
Valid prediction for GeneMark_model.26899_t
Valid prediction for snap_scaffold_6-snap.2694-T1
Valid prediction for GlimmerHMM_glimmerT_16056-T1
Valid prediction for snap_scaffold_6-snap.2664-T1
Valid prediction for GlimmerHMM_glimmerT_16058-T1
Couldn't classify 191302, 191382
Couldn't classify 192488, 192583
Sorry, prediction pasa_asmbl_47375.p1 fails validation.
(TCA)	 GG	191302-191382	GT	ATG
(CAT)	 AG	191662-191829	GT	AGG
(GAG)	 AG	191997-192203	GT	CTG
(GGT)	 AG	192488-192583	GA	GAG
-recovered pasa_asmbl_47375.p1, internal, 191662, 191829
-recovered pasa_asmbl_47375.p1, internal, 191997, 192203
Valid prediction for GeneMark_model.26882_t
Valid prediction for snap_scaffold_6-snap.2686-T1
Valid prediction for GlimmerHMM_glimmerT_16081-T1
Valid prediction for snap_scaffold_6-snap.2667-T1
Valid prediction for snap_scaffold_6-snap.2687-T1
Valid prediction for GlimmerHMM_glimmerT_16066-T1
Valid prediction for GeneMark_model.26898_t
Valid prediction for snap_scaffold_6-snap.2685-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g10819.t1
Valid prediction for GlimmerHMM_glimmerT_16063-T1
Valid prediction for CodingQuarry_transcript_55120-T1
Couldn't classify 205545, 205748
Sorry, prediction pasa_asmbl_47376.p1 fails validation.
(GAG)	 AG	205545-205748	GT	AGG
(GAA)	 AG	205858-206097	GT	AGG
(TCC)	 AG	206311-206532	GC	AGG
(CTT)	 AG	206885-207067	GT	GGG
(ATA)	 AG	209674-210570	AG	AAA
-recovered pasa_asmbl_47376.p1, terminal, 209674, 210570
-recovered pasa_asmbl_47376.p1, internal, 205545, 205748
-recovered pasa_asmbl_47376.p1, internal, 205858, 206097
-recovered pasa_asmbl_47376.p1, internal, 206311, 206532
-recovered pasa_asmbl_47376.p1, internal, 206885, 207067
Valid prediction for Augustus_model.g10800.t1
Valid prediction for GlimmerHMM_glimmerT_16073-T1
Valid prediction for Augustus_model.g10818.t1
Valid prediction for GeneMark_model.26891_t
Valid prediction for GeneMark_model.26881_t
Valid prediction for snap_scaffold_6-snap.2690-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_16079-T1
Valid prediction for CodingQuarry_transcript_55118-T1
Valid prediction for snap_scaffold_6-snap.2674-T1
Valid prediction for snap_scaffold_6-snap.2672-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.26894_t
Valid prediction for Augustus_model.g10794.t1
Valid prediction for Augustus_model.g10795.t1
Valid prediction for Augustus_model.g10793.t1
Valid prediction for snap_scaffold_6-snap.2678-T1
Valid prediction for snap_scaffold_6-snap.2682-T1
Valid prediction for snap_scaffold_6-snap.2659-T1
Couldn't classify 1261, 1569
Sorry, prediction pasa_asmbl_47391.p1 fails validation.
(CCC)	 GC	1261-1569	CA	AGC
Valid prediction for snap_scaffold_6-snap.2673-T1
Valid prediction for GlimmerHMM_glimmerT_16055-T1
Valid prediction for GeneMark_model.26878_t
Valid prediction for snap_scaffold_6-snap.2669-T1
Valid prediction for snap_scaffold_6-snap.2683-T1
Valid prediction for GlimmerHMM_glimmerT_16057-T1
Valid prediction for snap_scaffold_6-snap.2660-T1
Valid prediction for snap_scaffold_6-snap.2680-T1
Valid prediction for GlimmerHMM_glimmerT_16078-T1
Valid prediction for snap_scaffold_6-snap.2677-T1
Valid prediction for snap_scaffold_6-snap.2661-T1
Valid prediction for GlimmerHMM_glimmerT_16061-T1
Valid prediction for GeneMark_model.26876_t
Valid prediction for Augustus_model.g10807.t1
Valid prediction for GeneMark_model.26873_t
Valid prediction for Augustus_model.g10801.t1
Valid prediction for Augustus_model.g10791.t1
Valid prediction for GeneMark_model.26884_t
Valid prediction for pasa_asmbl_48784.p2
Valid prediction for GeneMark_model.26890_t
Valid prediction for GeneMark_model.26901_t
Valid prediction for Augustus_model.g10811.t1
Valid prediction for Augustus_model.g10806.t1
Valid prediction for GlimmerHMM_glimmerT_16068-T1
Valid prediction for snap_scaffold_6-snap.2658-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g10790.t1
Valid prediction for Augustus_model.g10805.t1
Valid prediction for GeneMark_model.26892_t
Couldn't classify 95507, 95608
Sorry, prediction pasa_asmbl_48789.p1 fails validation.
(ATG)	 GA	92996-94729	GT	AAG
(TCC)	 AG	95507-95608	GT	AGG
-recovered pasa_asmbl_48789.p1, initial, 92996, 94729
-recovered pasa_asmbl_48789.p1, internal, 95507, 95608
Valid prediction for Augustus_model.g10810.t1
Valid prediction for GeneMark_model.26889_t
Valid prediction for GeneMark_model.26885_t
Valid prediction for GlimmerHMM_glimmerT_16059-T1
Valid prediction for snap_scaffold_6-snap.2663-T1
Valid prediction for GlimmerHMM_glimmerT_16083-T1
Valid prediction for snap_scaffold_6-snap.2676-T1
Valid prediction for snap_scaffold_6-snap.2656-T1
Valid prediction for GeneMark_model.26874_t
Valid prediction for GlimmerHMM_glimmerT_16071-T1
Valid prediction for GeneMark_model.26879_t
Valid prediction for GlimmerHMM_glimmerT_16060-T1
Valid prediction for snap_scaffold_6-snap.2662-T1
Valid prediction for Augustus_model.g10821.t1
Valid prediction for Augustus_model.g10792.t1
Valid prediction for GlimmerHMM_glimmerT_16074-T1
Valid prediction for GeneMark_model.26886_t
Valid prediction for GlimmerHMM_glimmerT_16072-T1
Valid prediction for snap_scaffold_6-snap.2675-T1
Valid prediction for Augustus_model.g10789.t1
Valid prediction for Augustus_model.g10808.t1
Valid prediction for GlimmerHMM_glimmerT_16075-T1
Valid prediction for snap_scaffold_6-snap.2679-T1
Couldn't classify 101199, 101293
Couldn't classify 103269, 103495
Sorry, prediction pasa_asmbl_49245.p1 fails validation.
(CAG)	 CT	101199-101293	GT	AGG
(TGA)	 AG	101500-101576	GT	AGG
(TGT)	 AG	101738-101884	GT	AGG
(GTT)	 AG	103269-103495	GG	AAG
-recovered pasa_asmbl_49245.p1, internal, 101500, 101576
-recovered pasa_asmbl_49245.p1, internal, 101738, 101884
Valid prediction for Augustus_model.g10803.t1

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

-building trellis in range 1 - 254096
-exon list size: 379


building trellis

0.3    
0.5    
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6.8    
7.1    
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7.9    
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12.1    
12.3    
12.6    
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13.6    
13.9    
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14.7    
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15.2    
15.5    
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16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 12438
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11670
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support