-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_11315018-11628974

-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_27899-T1
Valid prediction for Augustus_model.g18486.t1
Valid prediction for GlimmerHMM_glimmerT_27916-T1
Valid prediction for GlimmerHMM_glimmerT_27904-T1
Valid prediction for snap_scaffold_11-snap.2469-T1
Valid prediction for snap_scaffold_11-snap.2446-T1
Valid prediction for snap_scaffold_11-snap.2465-T1
Valid prediction for Augustus_model.g18482.t1
Valid prediction for snap_scaffold_11-snap.2456-T1
Valid prediction for GlimmerHMM_glimmerT_27900-T1
Valid prediction for GlimmerHMM_glimmerT_27895-T1
Valid prediction for snap_scaffold_11-snap.2444-T1
Couldn't classify 266503, 266582
Sorry, prediction pasa_asmbl_5974.p1 fails validation.
(ATA)	 AT	266503-266582	GT	AAG
(TAT)	 AG	266679-266881	GT	AGG
(AGA)	 AG	267006-267086	GT	AGG
(CAT)	 AG	267166-267200	GT	AGG
-recovered pasa_asmbl_5974.p1, terminal, 267166, 267200
-recovered pasa_asmbl_5974.p1, internal, 266679, 266881
-recovered pasa_asmbl_5974.p1, internal, 267006, 267086
-recovered pasa_asmbl_5974.p1, internal, 267166, 267200
Valid prediction for GlimmerHMM_glimmerT_27903-T1
Valid prediction for snap_scaffold_11-snap.2463-T1
Valid prediction for snap_scaffold_11-snap.2447-T1
Couldn't classify 14875, 15002
Sorry, prediction pasa_asmbl_5968.p1 fails validation.
(ATG)	 AG	12716-12904	GT	AGG
(GTG)	 AG	14226-14361	GT	CGG
(GAA)	 AG	14875-15002	AA	GTA
-recovered pasa_asmbl_5968.p1, initial, 12716, 12904
-recovered pasa_asmbl_5968.p1, internal, 12716, 12904
-recovered pasa_asmbl_5968.p1, internal, 14226, 14361
Valid prediction for Augustus_model.g18487.t1
Valid prediction for GlimmerHMM_glimmerT_27898-T1
Valid prediction for snap_scaffold_11-snap.2462-T1
Valid prediction for HiQ_model.g18484.t1
Couldn't classify 6425, 6504
Sorry, prediction pasa_asmbl_5965.p1 fails validation.
(ATG)	 AC	2114-2141	GT	GAG
(GCC)	 AG	2910-3053	GT	CGG
(AGT)	 AG	4788-4927	GT	AGG
(ATT)	 AG	5384-5477	GT	TGG
(GTG)	 AG	5680-5841	GT	TGG
(AGG)	 AG	6425-6504	AA	TCA
-recovered pasa_asmbl_5965.p1, initial, 2114, 2141
-recovered pasa_asmbl_5965.p1, internal, 2910, 3053
-recovered pasa_asmbl_5965.p1, internal, 4788, 4927
-recovered pasa_asmbl_5965.p1, internal, 5384, 5477
-recovered pasa_asmbl_5965.p1, internal, 5680, 5841
Valid prediction for snap_scaffold_11-snap.2470-T1
Valid prediction for snap_scaffold_11-snap.2472-T1
Valid prediction for GlimmerHMM_glimmerT_27910-T1
Valid prediction for snap_scaffold_11-snap.2449-T1
Couldn't classify 266145, 266323
Sorry, prediction pasa_asmbl_5973.p1 fails validation.
(ATG)	 TC	264768-265619	GT	AGG
(GAT)	 AG	265812-265914	GT	CGG
(TGG)	 AG	266145-266323	GG	GGG
-recovered pasa_asmbl_5973.p1, initial, 264768, 265619
-recovered pasa_asmbl_5973.p1, internal, 265812, 265914
Couldn't classify 311528, 311529
Couldn't classify 313213, 313239
Sorry, prediction pasa_asmbl_5977.p1 fails validation.
(ATG)	 AC	311528-311529	GT	ATG
(GGG)	 AG	311963-312008	GT	CAG
(ATA)	 AG	312107-312142	GT	TGG
(GGT)	 AG	312248-312302	GT	TGG
(ACT)	 AG	312572-312642	GT	ACG
(TTC)	 AG	312738-312816	GT	AGG
(GTT)	 AG	313002-313030	GT	AGG
(AAC)	 AG	313213-313239	AA	TGA
add_exon() Sorry, pasa_asmbl_5977.p1 312738-312816-terminal-3 is invalid.
-recovered pasa_asmbl_5977.p1, terminal, 312738, 312816
-recovered pasa_asmbl_5977.p1, internal, 311963, 312008
-recovered pasa_asmbl_5977.p1, internal, 312107, 312142
-recovered pasa_asmbl_5977.p1, internal, 312248, 312302
-recovered pasa_asmbl_5977.p1, internal, 312572, 312642
-recovered pasa_asmbl_5977.p1, internal, 312738, 312816
-recovered pasa_asmbl_5977.p1, internal, 313002, 313030
Valid prediction for snap_scaffold_11-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_27913-T1
Valid prediction for GlimmerHMM_glimmerT_27912-T1
Valid prediction for Augustus_model.g18473.t1
Valid prediction for CodingQuarry_transcript_8245-T1
Valid prediction for snap_scaffold_11-snap.2468-T1
Valid prediction for snap_scaffold_11-snap.2448-T1
Couldn't classify 25269, 25395
Sorry, prediction pasa_asmbl_5972.p1 fails validation.
(TGC)	 AT	25269-25395	GT	TGG
(GGA)	 AG	25562-25637	GT	AGG
(GAC)	 AG	26157-26547	GA	GAG
-recovered pasa_asmbl_5972.p1, terminal, 26157, 26547
-recovered pasa_asmbl_5972.p1, internal, 25562, 25637
Valid prediction for snap_scaffold_11-snap.2467-T1
Valid prediction for Augustus_model.g18472.t1
Valid prediction for GlimmerHMM_glimmerT_27894-T1
Valid prediction for GlimmerHMM_glimmerT_27914-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_11-snap.2455-T1
Valid prediction for GlimmerHMM_glimmerT_27906-T1
Valid prediction for GlimmerHMM_glimmerT_27902-T1
Valid prediction for GlimmerHMM_glimmerT_27915-T1
Valid prediction for Augustus_model.g18477.t1
Valid prediction for snap_scaffold_11-snap.2450-T1
Valid prediction for GlimmerHMM_glimmerT_27896-T1
Valid prediction for Augustus_model.g18485.t1
Valid prediction for GlimmerHMM_glimmerT_27911-T1
Valid prediction for snap_scaffold_11-snap.2458-T1
Valid prediction for GlimmerHMM_glimmerT_27905-T1
Valid prediction for GlimmerHMM_glimmerT_27917-T1
Valid prediction for GlimmerHMM_glimmerT_27907-T1
Valid prediction for GlimmerHMM_glimmerT_27908-T1
Valid prediction for snap_scaffold_11-snap.2451-T1
Valid prediction for Augustus_model.g18474.t1
Valid prediction for snap_scaffold_11-snap.2454-T1
Valid prediction for Augustus_model.g18480.t1
Valid prediction for snap_scaffold_11-snap.2457-T1
Valid prediction for Augustus_model.g18479.t1
Valid prediction for snap_scaffold_11-snap.2459-T1
Valid prediction for GlimmerHMM_glimmerT_27909-T1
Valid prediction for snap_scaffold_11-snap.2475-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_7022.p1
Valid prediction for Augustus_model.g18476.t1
Valid prediction for snap_scaffold_11-snap.2471-T1
Valid prediction for Augustus_model.g18475.t1
Valid prediction for snap_scaffold_11-snap.2460-T1
Valid prediction for snap_scaffold_11-snap.2474-T1
Valid prediction for snap_scaffold_11-snap.2466-T1
Valid prediction for HiQ_model.g18481.t1
Valid prediction for snap_scaffold_11-snap.2445-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g18483.t1
Valid prediction for GlimmerHMM_glimmerT_27897-T1
Valid prediction for snap_scaffold_11-snap.2464-T1
Valid prediction for snap_scaffold_11-snap.2453-T1
Valid prediction for snap_scaffold_11-snap.2452-T1
Valid prediction for GlimmerHMM_glimmerT_27901-T1
Valid prediction for Augustus_model.g18478.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 290795, rend_intergenic: 289622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 313957
-exon list size: 282


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 290795, rend_intergenic: 289622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support