-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_1669523-1965650

-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_244-T1
Valid prediction for GlimmerHMM_glimmerT_234-T1
Valid prediction for Augustus_model.g190.t1
Couldn't classify 235331, 235398
Couldn't classify 240717, 240869
Sorry, prediction pasa_asmbl_1517.p1 fails validation.
(GTA)	 AG	235331-235398	GT	TGG
(TGA)	 AG	237710-237860	GT	CGG
(AGT)	 AG	238490-238582	GT	GTG
(TTG)	 AG	238696-238775	GT	AGG
(TAA)	 AG	238927-239007	GT	GGG
(GGT)	 AG	240256-240361	GT	AGG
(TTG)	 AG	240717-240869	CT	AGC
-recovered pasa_asmbl_1517.p1, internal, 235331, 235398
-recovered pasa_asmbl_1517.p1, internal, 237710, 237860
-recovered pasa_asmbl_1517.p1, internal, 238490, 238582
-recovered pasa_asmbl_1517.p1, internal, 238696, 238775
-recovered pasa_asmbl_1517.p1, internal, 238927, 239007
-recovered pasa_asmbl_1517.p1, internal, 240256, 240361
Valid prediction for Augustus_model.g170.t1
Couldn't classify 76873, 78120
Sorry, prediction pasa_asmbl_1506.p1 fails validation.
(ATG)	 GG	76873-78120	AG	GGA
Valid prediction for snap_scaffold_1-snap.318-T1
Valid prediction for GlimmerHMM_glimmerT_241-T1
Valid prediction for GlimmerHMM_glimmerT_235-T1
Valid prediction for GlimmerHMM_glimmerT_216-T1
Valid prediction for snap_scaffold_1-snap.297-T1
Valid prediction for snap_scaffold_1-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_239-T1
Valid prediction for Augustus_model.g182.t1
Valid prediction for snap_scaffold_1-snap.290-T1
Valid prediction for snap_scaffold_1-snap.315-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.309-T1
Valid prediction for snap_scaffold_1-snap.296-T1
Valid prediction for Augustus_model.g181.t1
Valid prediction for snap_scaffold_1-snap.291-T1
Valid prediction for pasa_asmbl_1509.p1
Valid prediction for snap_scaffold_1-snap.320-T1
Valid prediction for snap_scaffold_1-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_217-T1
Valid prediction for snap_scaffold_1-snap.292-T1
Valid prediction for snap_scaffold_1-snap.299-T1
Valid prediction for Augustus_model.g192.t1
Valid prediction for GlimmerHMM_glimmerT_215-T1
Valid prediction for CodingQuarry_transcript_2540-T1
Valid prediction for GlimmerHMM_glimmerT_220-T1
Valid prediction for HiQ_model.g173.t1
Valid prediction for snap_scaffold_1-snap.310-T1
Valid prediction for pasa_asmbl_1505.p1
Valid prediction for GlimmerHMM_glimmerT_226-T1
Couldn't classify 221738, 221831
Couldn't classify 231575, 231712
Sorry, prediction pasa_asmbl_1515.p1 fails validation.
(GAA)	 CT	221738-221831	GT	AGG
(AGA)	 AG	222033-222094	GT	AGG
(GAT)	 AG	222827-222872	GT	AGG
(GCC)	 AG	223655-223780	GT	GGG
(GAT)	 AG	223961-224005	GT	GGG
(ATT)	 AG	224357-224400	GT	TAG
(GTG)	 AG	224602-224658	GT	AGG
(ATG)	 AG	225608-225660	GT	GGG
(TCT)	 AG	226665-226867	GT	TGG
(ATG)	 AG	227795-227986	GT	TGG
(ATC)	 AG	228076-228121	GT	AGG
(AGC)	 AG	228296-228409	GT	TGG
(TGC)	 AG	229781-229836	GT	AGG
(GGT)	 AG	231014-231171	GT	GAG
(GGA)	 AG	231575-231712	GT	AAG
-recovered pasa_asmbl_1515.p1, initial, 225608, 225660
add_exon() Sorry, pasa_asmbl_1515.p1 227795-227986-initial-1 is invalid.
-recovered pasa_asmbl_1515.p1, initial, 227795, 227986
-recovered pasa_asmbl_1515.p1, terminal, 229781, 229836
-recovered pasa_asmbl_1515.p1, internal, 222033, 222094
-recovered pasa_asmbl_1515.p1, internal, 222827, 222872
-recovered pasa_asmbl_1515.p1, internal, 223655, 223780
-recovered pasa_asmbl_1515.p1, internal, 223961, 224005
-recovered pasa_asmbl_1515.p1, internal, 224357, 224400
-recovered pasa_asmbl_1515.p1, internal, 224602, 224658
-recovered pasa_asmbl_1515.p1, internal, 225608, 225660
-recovered pasa_asmbl_1515.p1, internal, 226665, 226867
-recovered pasa_asmbl_1515.p1, internal, 227795, 227986
-recovered pasa_asmbl_1515.p1, internal, 228076, 228121
-recovered pasa_asmbl_1515.p1, internal, 228296, 228409
-recovered pasa_asmbl_1515.p1, internal, 229781, 229836
-recovered pasa_asmbl_1515.p1, internal, 231014, 231171
-recovered pasa_asmbl_1515.p1, internal, 231575, 231712
Valid prediction for snap_scaffold_1-snap.319-T1
Valid prediction for snap_scaffold_1-snap.308-T1
Valid prediction for CodingQuarry_transcript_2539-T1
Valid prediction for Augustus_model.g175.t1
Valid prediction for Augustus_model.g184.t1
Valid prediction for Augustus_model.g195.t1
Valid prediction for Augustus_model.g172.t1
Valid prediction for snap_scaffold_1-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_214-T1
Valid prediction for GlimmerHMM_glimmerT_245-T1
Valid prediction for snap_scaffold_1-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_243-T1
Valid prediction for snap_scaffold_1-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_236-T1
Valid prediction for snap_scaffold_1-snap.300-T1
Valid prediction for GlimmerHMM_glimmerT_247-T1
Valid prediction for GlimmerHMM_glimmerT_221-T1
Valid prediction for GlimmerHMM_glimmerT_246-T1
Valid prediction for GlimmerHMM_glimmerT_227-T1
Valid prediction for GlimmerHMM_glimmerT_225-T1
Valid prediction for Augustus_model.g196.t1
Valid prediction for GlimmerHMM_glimmerT_228-T1
Valid prediction for pasa_asmbl_1521.p1
Valid prediction for GlimmerHMM_glimmerT_232-T1
Valid prediction for Augustus_model.g197.t1
Valid prediction for GlimmerHMM_glimmerT_238-T1
Valid prediction for GlimmerHMM_glimmerT_219-T1
Valid prediction for CodingQuarry_transcript_2537-T1
Valid prediction for HiQ_model.g176.t1
Valid prediction for snap_scaffold_1-snap.305-T1
Valid prediction for HiQ_model.g193.t1
Valid prediction for snap_scaffold_1-snap.317-T1
Valid prediction for snap_scaffold_1-snap.324-T1
Valid prediction for GlimmerHMM_glimmerT_242-T1
Valid prediction for Augustus_model.g171.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_1-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_240-T1
Valid prediction for snap_scaffold_1-snap.306-T1
Valid prediction for HiQ_model.g179.t1
Valid prediction for GlimmerHMM_glimmerT_233-T1
Valid prediction for snap_scaffold_1-snap.295-T1
Valid prediction for GlimmerHMM_glimmerT_218-T1
Valid prediction for snap_scaffold_1-snap.321-T1
Valid prediction for snap_scaffold_1-snap.323-T1
Couldn't classify 148423, 149100
Sorry, prediction pasa_asmbl_87.p1 fails validation.
(TGC)	 CC	148423-149100	AG	GAA
Valid prediction for GlimmerHMM_glimmerT_231-T1
Valid prediction for snap_scaffold_1-snap.304-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_230-T1
Valid prediction for Augustus_model.g177.t1
Valid prediction for snap_scaffold_1-snap.303-T1
Valid prediction for Augustus_model.g191.t1
Couldn't classify 152948, 153262
Sorry, prediction pasa_asmbl_86.p1 fails validation.
(ATG)	 TG	152948-153262	AA	GAA
Valid prediction for Augustus_model.g188.t1
Valid prediction for GlimmerHMM_glimmerT_222-T1
Valid prediction for Augustus_model.g189.t1
Valid prediction for GlimmerHMM_glimmerT_229-T1
Valid prediction for snap_scaffold_1-snap.313-T1
Valid prediction for Augustus_model.g194.t1
Valid prediction for GlimmerHMM_glimmerT_223-T1
Valid prediction for GlimmerHMM_glimmerT_237-T1
Valid prediction for Augustus_model.g185.t1
Valid prediction for snap_scaffold_1-snap.298-T1
Valid prediction for Augustus_model.g183.t1
Couldn't classify 153396, 153737
Sorry, prediction pasa_asmbl_85.p1 fails validation.
(CAT)	 CT	153396-153737	TG	ACT
Valid prediction for HiQ_model.g187.t1
Valid prediction for snap_scaffold_1-snap.294-T1
Couldn't classify 133482, 133496
Sorry, prediction pasa_asmbl_88.p1 fails validation.
(GGA)	 AC	133482-133496	GT	AGG
(GCA)	 AG	133638-133723	GT	AGG
(CCG)	 AG	133903-133978	GT	TGG
(CTG)	 AG	134266-134348	GT	AGG
(TGG)	 AG	135455-136166	GT	AGG
(GTA)	 AG	139139-139225	GT	AGG
(CAG)	 AG	139616-139720	CA	AGC
-recovered pasa_asmbl_88.p1, terminal, 139616, 139720
-recovered pasa_asmbl_88.p1, internal, 133638, 133723
-recovered pasa_asmbl_88.p1, internal, 133903, 133978
-recovered pasa_asmbl_88.p1, internal, 134266, 134348
-recovered pasa_asmbl_88.p1, internal, 135455, 136166
-recovered pasa_asmbl_88.p1, internal, 139139, 139225
Valid prediction for Augustus_model.g186.t1
Valid prediction for Augustus_model.g180.t1
Valid prediction for Augustus_model.g174.t1
Valid prediction for GlimmerHMM_glimmerT_224-T1
Valid prediction for snap_scaffold_1-snap.322-T1
Valid prediction for snap_scaffold_1-snap.314-T1
Valid prediction for snap_scaffold_1-snap.312-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g178.t1
Valid prediction for snap_scaffold_1-snap.307-T1

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

-building trellis in range 1 - 296128
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19808
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 15103
-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
	-no exons in range 3927 - 15103