-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_1044091-1386643

-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_16-snap.185-T1
Valid prediction for GlimmerHMM_glimmerT_37798-T1
Valid prediction for GlimmerHMM_glimmerT_37780-T1
Valid prediction for snap_scaffold_16-snap.208-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_37787-T1
Valid prediction for GlimmerHMM_glimmerT_37791-T1
Valid prediction for Augustus_model.g25204.t1
Valid prediction for snap_scaffold_16-snap.194-T1
Valid prediction for snap_scaffold_16-snap.210-T1
Valid prediction for GlimmerHMM_glimmerT_37777-T1
Valid prediction for snap_scaffold_16-snap.209-T1
Valid prediction for snap_scaffold_16-snap.207-T1
Valid prediction for Augustus_model.g25198.t1
Valid prediction for snap_scaffold_16-snap.197-T1
Valid prediction for snap_scaffold_16-snap.193-T1
Valid prediction for snap_scaffold_16-snap.189-T1
Couldn't classify 113146, 113323
Sorry, prediction pasa_asmbl_16070.p1 fails validation.
(GTA)	 CA	113146-113323	GT	AAG
(CCA)	 AG	113933-114195	GT	AGG
(CTG)	 AG	114300-114602	GT	AGG
(ATG)	 AG	114809-115900	CG	AAC
-recovered pasa_asmbl_16070.p1, terminal, 114809, 115900
-recovered pasa_asmbl_16070.p1, internal, 113933, 114195
-recovered pasa_asmbl_16070.p1, internal, 114300, 114602
Valid prediction for snap_scaffold_16-snap.187-T1
Valid prediction for Augustus_model.g25199.t1
Valid prediction for snap_scaffold_16-snap.192-T1
Valid prediction for snap_scaffold_16-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_37796-T1
Valid prediction for GlimmerHMM_glimmerT_37784-T1
Valid prediction for snap_scaffold_16-snap.184-T1
Valid prediction for Augustus_model.g25194.t1
Valid prediction for GlimmerHMM_glimmerT_37785-T1
Valid prediction for pasa_asmbl_16073.p1
Valid prediction for snap_scaffold_16-snap.186-T1
Valid prediction for snap_scaffold_16-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_37779-T1
Valid prediction for Augustus_model.g25213.t1
Valid prediction for Augustus_model.g25203.t1
Valid prediction for GlimmerHMM_glimmerT_37789-T1
Valid prediction for snap_scaffold_16-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_37807-T1
Valid prediction for HiQ_model.g25201.t1
Valid prediction for GlimmerHMM_glimmerT_37805-T1
Valid prediction for GlimmerHMM_glimmerT_37793-T1
Valid prediction for HiQ_model.g25205.t1
Valid prediction for GlimmerHMM_glimmerT_37783-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 HiQ_model.g25207.t1
Valid prediction for GlimmerHMM_glimmerT_37803-T1
Valid prediction for snap_scaffold_16-snap.201-T1
Valid prediction for Augustus_model.g25208.t1
Valid prediction for Augustus_model.g25192.t1
Valid prediction for CodingQuarry_transcript_19899-T1
Valid prediction for GlimmerHMM_glimmerT_37790-T1
Valid prediction for GlimmerHMM_glimmerT_37808-T1
Valid prediction for HiQ_model.g25215.t1
Valid prediction for snap_scaffold_16-snap.198-T1
Valid prediction for snap_scaffold_16-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_37778-T1
Valid prediction for snap_scaffold_16-snap.204-T1
Valid prediction for CodingQuarry_transcript_19897-T1
Valid prediction for GlimmerHMM_glimmerT_37794-T1
Valid prediction for Augustus_model.g25200.t1
Valid prediction for GlimmerHMM_glimmerT_37795-T1
Valid prediction for Augustus_model.g25209.t1
Valid prediction for snap_scaffold_16-snap.176-T1
Valid prediction for snap_scaffold_16-snap.196-T1
Valid prediction for GlimmerHMM_glimmerT_37801-T1
Valid prediction for Augustus_model.g25195.t1
Valid prediction for Augustus_model.g25196.t1
Valid prediction for GlimmerHMM_glimmerT_37799-T1
Valid prediction for snap_scaffold_16-snap.180-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_16939.p1
Valid prediction for snap_scaffold_16-snap.206-T1
Valid prediction for GlimmerHMM_glimmerT_37786-T1
Valid prediction for snap_scaffold_16-snap.181-T1
Couldn't classify 122192, 122278
Sorry, prediction pasa_asmbl_17560.p1 fails validation.
(GCG)	 AG	122192-122278	GT	TGG
(ATG)	 AG	122637-122721	GT	CTG
(ATC)	 AG	123096-123283	AG	AAA
-recovered pasa_asmbl_17560.p1, initial, 122637, 122721
-recovered pasa_asmbl_17560.p1, terminal, 123096, 123283
-recovered pasa_asmbl_17560.p1, internal, 122192, 122278
-recovered pasa_asmbl_17560.p1, internal, 122637, 122721
Valid prediction for GlimmerHMM_glimmerT_37797-T1
Valid prediction for snap_scaffold_16-snap.199-T1
Valid prediction for snap_scaffold_16-snap.202-T1
Valid prediction for snap_scaffold_16-snap.211-T1
Valid prediction for snap_scaffold_16-snap.188-T1
Valid prediction for Augustus_model.g25193.t1
Valid prediction for snap_scaffold_16-snap.179-T1
Valid prediction for snap_scaffold_16-snap.203-T1
Couldn't classify 279272, 279402
Sorry, prediction pasa_asmbl_16923.p1 fails validation.
(ATG)	 GT	274853-274970	GT	TAG
(CCA)	 AG	275625-275707	GT	TAG
(CTT)	 AG	276280-276394	GT	AGG
(GTA)	 AG	279272-279402	TA	AAT
-recovered pasa_asmbl_16923.p1, initial, 274853, 274970
add_exon() Sorry, pasa_asmbl_16923.p1 276280-276394-terminal-3 is invalid.
-recovered pasa_asmbl_16923.p1, terminal, 276280, 276394
-recovered pasa_asmbl_16923.p1, internal, 275625, 275707
-recovered pasa_asmbl_16923.p1, internal, 276280, 276394
Valid prediction for Augustus_model.g25202.t1
Valid prediction for Augustus_model.g25210.t1
Valid prediction for snap_scaffold_16-snap.178-T1
Valid prediction for GlimmerHMM_glimmerT_37782-T1
Valid prediction for Augustus_model.g25206.t1
Valid prediction for pasa_asmbl_16928.p1
Valid prediction for Augustus_model.g25214.t1
Valid prediction for GlimmerHMM_glimmerT_37788-T1
Valid prediction for GlimmerHMM_glimmerT_37781-T1
Valid prediction for snap_scaffold_16-snap.177-T1
Valid prediction for GlimmerHMM_glimmerT_37804-T1
Valid prediction for Augustus_model.g25212.t1
Valid prediction for Augustus_model.g25211.t1
Valid prediction for Augustus_model.g25190.t1
Valid prediction for HiQ_model.g25191.t1
Valid prediction for Augustus_model.g25197.t1
Valid prediction for GlimmerHMM_glimmerT_37802-T1
Valid prediction for GlimmerHMM_glimmerT_37806-T1
Valid prediction for snap_scaffold_16-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_37800-T1
Valid prediction for snap_scaffold_16-snap.200-T1
Valid prediction for GlimmerHMM_glimmerT_37792-T1
Valid prediction for snap_scaffold_16-snap.205-T1
Valid prediction for CodingQuarry_transcript_19898-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 109374, rend_intergenic: 108221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 342553
-exon list size: 256


building trellis

0.4    
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1.2    
1.6    
1.9    
2.3    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.0    
5.4    
5.8    
6.2    
6.6    
7.0    
7.4    
7.8    
8.1    
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9.3    
9.7    
10.1    
10.5    
10.9    
11.2    
11.6    
12.0    
12.4    
12.8    
13.2    
13.6    
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14.3    
14.7    
15.1    
15.5    
15.9    
16.3    
16.7    
17.1    
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17.8    
18.2    
18.6    
19.0    
19.4    
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20.2    
20.5    
20.9    
21.3    
21.7    
22.1    
22.5    
22.9    
23.3    
23.6    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.4    
26.7    
27.1    
27.5    
27.9    
28.3    
28.7    
29.1    
29.5    
29.8    
30.2    
30.6    
31.0    
31.4    
31.8    
32.2    
32.6    
32.9    
33.3    
33.7    
34.1    
34.5    
34.9    
35.3    
35.7    
36.0    
36.4    
36.8    
37.2    
37.6    
38.0    
38.4    
38.8    
39.1    
39.5    
39.9    
40.3    
40.7    
41.1    
41.5    
41.9    
42.2    
42.6    
43.0    
43.4    
43.8    
44.2    
44.6    
45.0    
45.3    
45.7    
46.1    
46.5    
46.9    
47.3    
47.7    
48.1    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
51.9    
52.3    
52.7    
53.1    
53.5    
53.9    
54.3    
54.7    
55.0    
55.4    
55.8    
56.2    
56.6    
57.0    
57.4    
57.8    
58.1    
58.5    
58.9    
59.3    
59.7    
60.1    
60.5    
60.9    
61.2    
61.6    
62.0    
62.4    
62.8    
63.2    
63.6    
64.0    
64.3    
64.7    
65.1    
65.5    
65.9    
66.3    
66.7    
67.1    
67.4    
67.8    
68.2    
68.6    
69.0    
69.4    
69.8    
70.2    
70.5    
70.9    
71.3    
71.7    
72.1    
72.5    
72.9    
73.3    
73.6    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.4    
76.7    
77.1    
77.5    
77.9    
78.3    
78.7    
79.1    
79.5    
79.8    
80.2    
80.6    
81.0    
81.4    
81.8    
82.2    
82.6    
82.9    
83.3    
83.7    
84.1    
84.5    
84.9    
85.3    
85.7    
86.0    
86.4    
86.8    
87.2    
87.6    
88.0    
88.4    
88.8    
89.1    
89.5    
89.9    
90.3    
90.7    
91.1    
91.5    
91.9    
92.2    
92.6    
93.0    
93.4    
93.8    
94.2    
94.6    
95.0    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.7    
98.1    
98.4    
98.8    
99.2    
99.6    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 109374, rend_intergenic: 108221  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