-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_13126478-13282467

-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_6-snap.2743-T1
Couldn't classify 90929, 91166
Sorry, prediction pasa_asmbl_47493.p1 fails validation.
(ATG)	 AC	88920-88932	GT	TGG
(ATT)	 AG	89668-89692	GT	GGG
(GTA)	 AG	89780-89940	GT	TGG
(GAG)	 AG	90139-90307	GT	AAG
(CTA)	 AG	90929-91166	AA	GTA
-recovered pasa_asmbl_47493.p1, initial, 88920, 88932
-recovered pasa_asmbl_47493.p1, internal, 89668, 89692
-recovered pasa_asmbl_47493.p1, internal, 89780, 89940
-recovered pasa_asmbl_47493.p1, internal, 90139, 90307
Valid prediction for CodingQuarry_transcript_55291-T1
Valid prediction for HiQ_model.g10567.t1
Valid prediction for snap_scaffold_6-snap.2764-T1
Valid prediction for snap_scaffold_6-snap.2763-T1
Valid prediction for snap_scaffold_6-snap.2774-T1
Valid prediction for pasa_asmbl_47512.p1
Valid prediction for snap_scaffold_6-snap.2761-T1
Valid prediction for GlimmerHMM_glimmerT_15743-T1
Valid prediction for Augustus_model.g10563.t1
Valid prediction for snap_scaffold_6-snap.2772-T1
Valid prediction for HiQ_model.g10579.t1
Valid prediction for snap_scaffold_6-snap.2754-T1
Valid prediction for snap_scaffold_6-snap.2762-T1
Valid prediction for snap_scaffold_6-snap.2755-T1
Valid prediction for CodingQuarry_transcript_55300-T1
Valid prediction for snap_scaffold_6-snap.2758-T1
Valid prediction for snap_scaffold_6-snap.2773-T1
Valid prediction for CodingQuarry_transcript_55286-T1
Valid prediction for CodingQuarry_transcript_55292-T1
Valid prediction for HiQ_model.g10574.t1
Valid prediction for CodingQuarry_transcript_55289-T1
Valid prediction for GlimmerHMM_glimmerT_15735-T1
Couldn't classify 101247, 101247
Sorry, prediction CodingQuarry_transcript_55296-T1 fails validation.
(AGT)	 CC	101247-101247	GT	CAG
(TGC)	 AG	101496-101605	GT	AGG
(ATC)	 AG	101865-101994	GT	CGG
(GCC)	 AG	102907-103021	GT	ACG
(GGA)	 AG	103146-103246	GT	AGG
(GTT)	 AG	103630-103762	GT	AGG
(GGG)	 AG	103911-103950	TC	GAT
-recovered CodingQuarry_transcript_55296-T1, terminal, 103911, 103950
-recovered CodingQuarry_transcript_55296-T1, internal, 101496, 101605
-recovered CodingQuarry_transcript_55296-T1, internal, 101865, 101994
-recovered CodingQuarry_transcript_55296-T1, internal, 102907, 103021
-recovered CodingQuarry_transcript_55296-T1, internal, 103146, 103246
-recovered CodingQuarry_transcript_55296-T1, internal, 103630, 103762
Valid prediction for CodingQuarry_transcript_55298-T1
Valid prediction for snap_scaffold_6-snap.2771-T1
Valid prediction for GlimmerHMM_glimmerT_15745-T1
Valid prediction for pasa_asmbl_47509.p1
Couldn't classify 101247, 101247
Sorry, prediction CodingQuarry_transcript_55295-T1 fails validation.
(AGT)	 CC	101247-101247	GT	CAG
(TGC)	 AG	101496-101605	GT	AGG
(ATC)	 AG	101865-101994	GT	CGG
(GCC)	 AG	102907-103021	GT	ACG
(GGA)	 AG	103146-103246	GT	AGG
(GAG)	 AG	103627-103762	GT	AGG
(GGG)	 AG	103911-103950	TC	GAT
-recovered CodingQuarry_transcript_55295-T1, terminal, 103911, 103950
-recovered CodingQuarry_transcript_55295-T1, internal, 101496, 101605
-recovered CodingQuarry_transcript_55295-T1, internal, 101865, 101994
-recovered CodingQuarry_transcript_55295-T1, internal, 102907, 103021
-recovered CodingQuarry_transcript_55295-T1, internal, 103146, 103246
-recovered CodingQuarry_transcript_55295-T1, internal, 103627, 103762
Valid prediction for Augustus_model.g10575.t1
Valid prediction for snap_scaffold_6-snap.2757-T1
Valid prediction for Augustus_model.g10559.t1
Valid prediction for snap_scaffold_6-snap.2750-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2756-T1
Valid prediction for snap_scaffold_6-snap.2759-T1
Valid prediction for pasa_asmbl_47487.p1
Valid prediction for CodingQuarry_transcript_55290-T1
Valid prediction for snap_scaffold_6-snap.2765-T1
Valid prediction for CodingQuarry_transcript_55294-T1
Valid prediction for GlimmerHMM_glimmerT_15728-T1
Couldn't classify 66613, 66659
Couldn't classify 67174, 67180
Sorry, prediction CodingQuarry_transcript_55287-T1 fails validation.
(ATG)	 AG	61926-61942	GT	GAG
(CGT)	 AG	62454-62525	GT	GGG
(GGG)	 AG	63552-63648	GT	AGG
(AAA)	 AG	64895-64966	GT	AGG
(GAA)	 AG	65218-65361	GT	AGG
(GAG)	 AG	66326-66415	GT	AGG
(ATG)	 AG	66613-66659	AT	GAA
(ATA)	 TC	67174-67180	CG	GAC
-recovered CodingQuarry_transcript_55287-T1, initial, 61926, 61942
-recovered CodingQuarry_transcript_55287-T1, internal, 61926, 61942
-recovered CodingQuarry_transcript_55287-T1, internal, 62454, 62525
-recovered CodingQuarry_transcript_55287-T1, internal, 63552, 63648
-recovered CodingQuarry_transcript_55287-T1, internal, 64895, 64966
-recovered CodingQuarry_transcript_55287-T1, internal, 65218, 65361
-recovered CodingQuarry_transcript_55287-T1, internal, 66326, 66415
Valid prediction for Augustus_model.g10569.t1
Valid prediction for Augustus_model.g10554.t1
Valid prediction for snap_scaffold_6-snap.2742-T1
Valid prediction for GlimmerHMM_glimmerT_15739-T1
Valid prediction for HiQ_model.g10571.t1
Valid prediction for HiQ_model.g10568.t1
Valid prediction for CodingQuarry_transcript_55299-T1
Valid prediction for GlimmerHMM_glimmerT_15731-T1
Valid prediction for HiQ_model.g10580.t1
Valid prediction for snap_scaffold_6-snap.2766-T1
Valid prediction for pasa_asmbl_47514.p1
Valid prediction for snap_scaffold_6-snap.2747-T1
Valid prediction for snap_scaffold_6-snap.2740-T1
Valid prediction for GlimmerHMM_glimmerT_15737-T1
Valid prediction for GlimmerHMM_glimmerT_15742-T1
Valid prediction for pasa_asmbl_47484.p1
Valid prediction for Augustus_model.g10570.t1
Valid prediction for snap_scaffold_6-snap.2768-T1
Couldn't classify 101247, 101247
Sorry, prediction CodingQuarry_transcript_55293-T1 fails validation.
(AGT)	 CC	101247-101247	GT	CAG
(TGC)	 AG	101496-101605	GT	AGG
(ATC)	 AG	101865-101994	GT	CGG
(GGA)	 AG	102494-102616	GT	TGG
(GCC)	 AG	102907-103021	GT	ACG
(GGA)	 AG	103146-103246	GT	AGG
(GAG)	 AG	103627-103762	GT	AGG
(GGG)	 AG	103911-103950	TC	GAT
-recovered CodingQuarry_transcript_55293-T1, terminal, 103911, 103950
-recovered CodingQuarry_transcript_55293-T1, internal, 101496, 101605
-recovered CodingQuarry_transcript_55293-T1, internal, 101865, 101994
-recovered CodingQuarry_transcript_55293-T1, internal, 102494, 102616
-recovered CodingQuarry_transcript_55293-T1, internal, 102907, 103021
-recovered CodingQuarry_transcript_55293-T1, internal, 103146, 103246
-recovered CodingQuarry_transcript_55293-T1, internal, 103627, 103762
Valid prediction for snap_scaffold_6-snap.2760-T1
Valid prediction for GlimmerHMM_glimmerT_15750-T1
Valid prediction for snap_scaffold_6-snap.2739-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 pasa_asmbl_48881.p1
Valid prediction for snap_scaffold_6-snap.2744-T1
Valid prediction for GlimmerHMM_glimmerT_15738-T1
Valid prediction for HiQ_model.g10557.t1
Valid prediction for GlimmerHMM_glimmerT_15733-T1
Couldn't classify 112270, 112437
Sorry, prediction pasa_asmbl_48884.p1 fails validation.
(AAT)	 TG	112270-112437	GT	AGG
(GTG)	 AG	113394-113465	GT	AGG
(GCA)	 AG	113603-113812	GT	TGG
(AGT)	 AG	114327-114490	GT	TCG
(GTC)	 AG	114617-114638	CC	AGC
-recovered pasa_asmbl_48884.p1, terminal, 114617, 114638
-recovered pasa_asmbl_48884.p1, internal, 113394, 113465
-recovered pasa_asmbl_48884.p1, internal, 113603, 113812
-recovered pasa_asmbl_48884.p1, internal, 114327, 114490
Valid prediction for pasa_asmbl_48903.p1
Valid prediction for snap_scaffold_6-snap.2767-T1
Valid prediction for snap_scaffold_6-snap.2775-T1
Valid prediction for pasa_asmbl_48905.p1
Valid prediction for Augustus_model.g10560.t1
Valid prediction for HiQ_model.g10576.t1
Valid prediction for CodingQuarry_transcript_55283-T1
Valid prediction for GlimmerHMM_glimmerT_15732-T1
Valid prediction for GlimmerHMM_glimmerT_15746-T1
Valid prediction for GlimmerHMM_glimmerT_15744-T1
Valid prediction for snap_scaffold_6-snap.2770-T1
Valid prediction for snap_scaffold_6-snap.2751-T1
Valid prediction for Augustus_model.g10556.t1
Valid prediction for Augustus_model.g10573.t1
Valid prediction for CodingQuarry_transcript_55297-T1
Valid prediction for GlimmerHMM_glimmerT_15736-T1
Valid prediction for GlimmerHMM_glimmerT_15749-T1
Valid prediction for Augustus_model.g10564.t1
Valid prediction for HiQ_model.g10562.t1
Valid prediction for GlimmerHMM_glimmerT_15734-T1
Valid prediction for snap_scaffold_6-snap.2749-T1
Valid prediction for Augustus_model.g10555.t1
Valid prediction for GlimmerHMM_glimmerT_15729-T1
Valid prediction for snap_scaffold_6-snap.2745-T1
Valid prediction for Augustus_model.g10572.t1
Valid prediction for Augustus_model.g10561.t1
Valid prediction for snap_scaffold_6-snap.2753-T1
Valid prediction for CodingQuarry_transcript_55285-T1
Valid prediction for snap_scaffold_6-snap.2769-T1
Valid prediction for HiQ_model.g10577.t1
Valid prediction for GlimmerHMM_glimmerT_15747-T1
Valid prediction for GlimmerHMM_glimmerT_15748-T1
Valid prediction for Augustus_model.g10578.t1
Valid prediction for Augustus_model.g10565.t1
Valid prediction for snap_scaffold_6-snap.2746-T1
Valid prediction for GlimmerHMM_glimmerT_15740-T1
Valid prediction for CodingQuarry_transcript_55281-T1
Valid prediction for pasa_asmbl_48895.p2
Valid prediction for snap_scaffold_6-snap.2752-T1
Valid prediction for Augustus_model.g10558.t1
Valid prediction for CodingQuarry_transcript_55282-T1
Valid prediction for snap_scaffold_6-snap.2741-T1
Valid prediction for snap_scaffold_6-snap.2748-T1
Valid prediction for HiQ_model.g10566.t1
Valid prediction for GlimmerHMM_glimmerT_15730-T1
Valid prediction for GlimmerHMM_glimmerT_15741-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 145274, rend_intergenic: 142565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155990
-exon list size: 357


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 145274, rend_intergenic: 142565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support