-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_10578068-10847521

-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 pasa_asmbl_7941.p1
Valid prediction for snap_scaffold_12-snap.2000-T1
Valid prediction for Augustus_model.g19845.t1
Valid prediction for snap_scaffold_12-snap.2001-T1
Valid prediction for pasa_asmbl_7952.p1
Valid prediction for snap_scaffold_12-snap.1999-T1
Valid prediction for snap_scaffold_12-snap.2027-T1
Valid prediction for snap_scaffold_12-snap.2014-T1
Valid prediction for Augustus_model.g19858.t1
Valid prediction for GlimmerHMM_glimmerT_29993-T1
Valid prediction for pasa_asmbl_7939.p1
Valid prediction for snap_scaffold_12-snap.2017-T1
Couldn't classify 9582, 9622
Sorry, prediction CodingQuarry_transcript_10381-T1 fails validation.
(ATG)	 CT	8110-8220	GT	AGG
(ATT)	 AG	8789-8895	GT	AGG
(CAT)	 AG	8975-9081	GT	AGG
(GAC)	 AG	9201-9299	GT	AGG
(ATC)	 AG	9376-9486	GT	AGG
(GCC)	 CA	9582-9622	AC	AAA
-recovered CodingQuarry_transcript_10381-T1, initial, 8110, 8220
add_exon() Sorry, CodingQuarry_transcript_10381-T1 9376-9486-terminal-1 is invalid.
-recovered CodingQuarry_transcript_10381-T1, terminal, 9376, 9486
-recovered CodingQuarry_transcript_10381-T1, internal, 8789, 8895
-recovered CodingQuarry_transcript_10381-T1, internal, 8975, 9081
-recovered CodingQuarry_transcript_10381-T1, internal, 9201, 9299
-recovered CodingQuarry_transcript_10381-T1, internal, 9376, 9486
Couldn't classify 71397, 71996
Sorry, prediction pasa_asmbl_7955.p1 fails validation.
(TCT)	 CC	71397-71996	GT	AAG
Valid prediction for snap_scaffold_12-snap.1998-T1
Valid prediction for Augustus_model.g19851.t1
Valid prediction for Augustus_model.g19843.t1
Valid prediction for HiQ_model.g19839.t1
Valid prediction for GlimmerHMM_glimmerT_30003-T1
Couldn't classify 67205, 67301
Couldn't classify 67893, 68035
Sorry, prediction pasa_asmbl_7954.p1 fails validation.
(GGC)	 CT	67205-67301	GT	AGG
(AAA)	 AG	67609-67713	GT	GAG
(TTC)	 AG	67893-68035	CG	AGC
-recovered pasa_asmbl_7954.p1, terminal, 67609, 67713
-recovered pasa_asmbl_7954.p1, internal, 67609, 67713
Valid prediction for GlimmerHMM_glimmerT_29992-T1
Valid prediction for Augustus_model.g19853.t1
Valid prediction for GlimmerHMM_glimmerT_30010-T1
Valid prediction for snap_scaffold_12-snap.2002-T1
Valid prediction for snap_scaffold_12-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_29989-T1
Valid prediction for snap_scaffold_12-snap.2009-T1
Valid prediction for HiQ_model.g19840.t1
Valid prediction for snap_scaffold_12-snap.2030-T1
Valid prediction for Augustus_model.g19857.t1
Valid prediction for CodingQuarry_transcript_10379-T1
Valid prediction for HiQ_model.g19842.t1
Valid prediction for GlimmerHMM_glimmerT_30007-T1
Valid prediction for snap_scaffold_12-snap.2008-T1
Valid prediction for snap_scaffold_12-snap.2020-T1
Valid prediction for CodingQuarry_transcript_10383-T1
Valid prediction for GlimmerHMM_glimmerT_30008-T1
Valid prediction for CodingQuarry_transcript_10384-T1
Valid prediction for snap_scaffold_12-snap.2005-T1
Valid prediction for snap_scaffold_12-snap.2004-T1
Valid prediction for CodingQuarry_transcript_10382-T1
Valid prediction for GlimmerHMM_glimmerT_29995-T1
Valid prediction for snap_scaffold_12-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_30014-T1
Valid prediction for CodingQuarry_transcript_10378-T1
Valid prediction for Augustus_model.g19852.t1
Valid prediction for GlimmerHMM_glimmerT_30002-T1
Valid prediction for Augustus_model.g19856.t1
Couldn't classify 225757, 226146
Sorry, prediction pasa_asmbl_7956.p1 fails validation.
(ACC)	 GC	225757-226146	CA	AAC
Valid prediction for GlimmerHMM_glimmerT_29988-T1
Valid prediction for pasa_asmbl_7949.p1
Valid prediction for GlimmerHMM_glimmerT_29990-T1
Valid prediction for snap_scaffold_12-snap.2024-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_12-snap.2015-T1
Valid prediction for Augustus_model.g19846.t1
Couldn't classify 252410, 252437
Sorry, prediction pasa_asmbl_8765.p1 fails validation.
(AAC)	 CA	252410-252437	GT	CGG
(ATC)	 AG	252775-252870	GT	AGG
(ACG)	 AG	252990-253126	GT	GGG
(GAA)	 AG	253306-253387	GT	AGG
(ACT)	 AG	253477-253632	GT	AGG
(ATG)	 AG	253777-253862	AT	AGA
-recovered pasa_asmbl_8765.p1, terminal, 253306, 253387
-recovered pasa_asmbl_8765.p1, terminal, 253777, 253862
-recovered pasa_asmbl_8765.p1, internal, 252775, 252870
-recovered pasa_asmbl_8765.p1, internal, 252990, 253126
-recovered pasa_asmbl_8765.p1, internal, 253306, 253387
-recovered pasa_asmbl_8765.p1, internal, 253477, 253632
Valid prediction for CodingQuarry_transcript_10380-T1
Valid prediction for GlimmerHMM_glimmerT_29987-T1
Valid prediction for snap_scaffold_12-snap.2012-T1
Valid prediction for snap_scaffold_12-snap.2019-T1
Valid prediction for snap_scaffold_12-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_30011-T1
Valid prediction for snap_scaffold_12-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_29991-T1
Valid prediction for snap_scaffold_12-snap.2029-T1
Valid prediction for snap_scaffold_12-snap.2018-T1
Valid prediction for snap_scaffold_12-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_30012-T1
Valid prediction for GlimmerHMM_glimmerT_29999-T1
Valid prediction for GlimmerHMM_glimmerT_29997-T1
Valid prediction for GlimmerHMM_glimmerT_30009-T1
Valid prediction for GlimmerHMM_glimmerT_29996-T1
Valid prediction for GlimmerHMM_glimmerT_29994-T1
Valid prediction for Augustus_model.g19848.t1
Valid prediction for Augustus_model.g19854.t1
Valid prediction for snap_scaffold_12-snap.2022-T1
Valid prediction for Augustus_model.g19847.t1
Valid prediction for GlimmerHMM_glimmerT_29998-T1
Valid prediction for Augustus_model.g19849.t1
Valid prediction for GlimmerHMM_glimmerT_30004-T1
Valid prediction for GlimmerHMM_glimmerT_30006-T1
Valid prediction for GlimmerHMM_glimmerT_30001-T1
Valid prediction for snap_scaffold_12-snap.1997-T1
Valid prediction for snap_scaffold_12-snap.2011-T1
Valid prediction for Augustus_model.g19850.t1
Valid prediction for HiQ_model.g19844.t1
Valid prediction for snap_scaffold_12-snap.2010-T1
Valid prediction for Augustus_model.g19855.t1
Valid prediction for Augustus_model.g19838.t1
Valid prediction for GlimmerHMM_glimmerT_30000-T1
Valid prediction for snap_scaffold_12-snap.2021-T1
Valid prediction for snap_scaffold_12-snap.2023-T1
Couldn't classify 254852, 255625
Sorry, prediction pasa_asmbl_8764.p1 fails validation.
(GCT)	 GC	254852-255625	GA	AGG
Valid prediction for snap_scaffold_12-snap.2007-T1
Valid prediction for snap_scaffold_12-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_30005-T1
Valid prediction for GlimmerHMM_glimmerT_30013-T1
Valid prediction for HiQ_model.g19841.t1
Valid prediction for snap_scaffold_12-snap.2013-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 63186, rend_intergenic: 60403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64422, rend_intergenic: 63543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 269454
-exon list size: 275


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.2    
2.5    
2.9    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.4    
5.8    
6.1    
6.5    
6.9    
7.2    
7.6    
7.9    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.5    
10.8    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.2    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.7    
22.0    
22.4    
22.7    
23.1    
23.5    
23.8    
24.2    
24.5    
24.9    
25.3    
25.6    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.8    
32.1    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.7    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.3    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
75.8    
76.2    
76.5    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.2    
89.5    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.1    
92.4    
92.8    
93.1    
93.5    
93.9    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 63186, rend_intergenic: 60403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64422, rend_intergenic: 63543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 255484 - 269454
-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 255484 - 269410
-exon list size: 1


building trellis

33.3    
66.7    
-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