-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_14706824-15022084

-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_10637-T1
Valid prediction for snap_scaffold_4-snap.2981-T1
Valid prediction for CodingQuarry_transcript_49241-T1
Valid prediction for snap_scaffold_4-snap.2980-T1
Valid prediction for GlimmerHMM_glimmerT_10621-T1
Valid prediction for snap_scaffold_4-snap.2990-T1
Valid prediction for GlimmerHMM_glimmerT_10632-T1
Valid prediction for GlimmerHMM_glimmerT_10641-T1
Valid prediction for GlimmerHMM_glimmerT_10630-T1
Valid prediction for HiQ_model.g6989.t1
Valid prediction for Augustus_model.g6980.t1
Valid prediction for Augustus_model.g6979.t1
Valid prediction for Augustus_model.g6986.t1
Valid prediction for GlimmerHMM_glimmerT_10635-T1
Couldn't classify 226074, 226427
Sorry, prediction pasa_asmbl_41903.p1 fails validation.
(ATG)	 GA	226074-226427	AG	TGA
Valid prediction for GlimmerHMM_glimmerT_10638-T1
Valid prediction for snap_scaffold_4-snap.2983-T1
Valid prediction for snap_scaffold_4-snap.2977-T1
Valid prediction for pasa_asmbl_41909.p1
Valid prediction for GlimmerHMM_glimmerT_10639-T1
Valid prediction for CodingQuarry_transcript_49247-T1
Valid prediction for snap_scaffold_4-snap.2992-T1
Valid prediction for pasa_asmbl_41920.p1
Valid prediction for pasa_asmbl_41921.p1
Couldn't classify 273764, 273899
Sorry, prediction pasa_asmbl_41916.p1 fails validation.
(TCA)	 AA	273764-273899	GT	AGG
(ATG)	 AG	274229-274424	GT	AAG
(GTA)	 AG	274663-274777	GT	CGG
(CTG)	 AG	274985-275104	GT	ACG
(GAA)	 AG	275361-275491	GT	TGG
(TGC)	 AG	275702-275771	GG	GAG
add_exon() Sorry, pasa_asmbl_41916.p1 274229-274424-initial-1 is invalid.
-recovered pasa_asmbl_41916.p1, initial, 274229, 274424
add_exon() Sorry, pasa_asmbl_41916.p1 274229-274424-terminal-3 is invalid.
-recovered pasa_asmbl_41916.p1, terminal, 274229, 274424
-recovered pasa_asmbl_41916.p1, terminal, 275702, 275771
-recovered pasa_asmbl_41916.p1, internal, 274229, 274424
-recovered pasa_asmbl_41916.p1, internal, 274663, 274777
-recovered pasa_asmbl_41916.p1, internal, 274985, 275104
-recovered pasa_asmbl_41916.p1, internal, 275361, 275491
Valid prediction for snap_scaffold_4-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_10617-T1
Valid prediction for CodingQuarry_transcript_49243-T1
Valid prediction for GlimmerHMM_glimmerT_10614-T1
Valid prediction for HiQ_model.g6983.t1
Valid prediction for snap_scaffold_4-snap.2978-T1
Valid prediction for GlimmerHMM_glimmerT_10625-T1
Valid prediction for snap_scaffold_4-snap.2966-T1
Valid prediction for HiQ_model.g6981.t1
Valid prediction for CodingQuarry_transcript_49244-T1
Valid prediction for CodingQuarry_transcript_49245-T1
Valid prediction for CodingQuarry_transcript_49242-T1
Valid prediction for snap_scaffold_4-snap.2985-T1
Valid prediction for GlimmerHMM_glimmerT_10633-T1
Valid prediction for pasa_asmbl_41904.p1
Valid prediction for HiQ_model.g6987.t1
Valid prediction for snap_scaffold_4-snap.2982-T1
Valid prediction for Augustus_model.g6977.t1
Valid prediction for GlimmerHMM_glimmerT_10618-T1
Valid prediction for GlimmerHMM_glimmerT_10627-T1
Valid prediction for snap_scaffold_4-snap.2989-T1
Valid prediction for Augustus_model.g6982.t1
Valid prediction for CodingQuarry_transcript_49246-T1
Valid prediction for snap_scaffold_4-snap.2987-T1
Valid prediction for snap_scaffold_4-snap.2975-T1
Valid prediction for GlimmerHMM_glimmerT_10629-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 Augustus_model.g6972.t1
Valid prediction for Augustus_model.g6975.t1
Valid prediction for GlimmerHMM_glimmerT_10636-T1
Valid prediction for Augustus_model.g6976.t1
Valid prediction for Augustus_model.g6974.t1
Valid prediction for snap_scaffold_4-snap.2973-T1
Valid prediction for snap_scaffold_4-snap.2968-T1
Valid prediction for GlimmerHMM_glimmerT_10626-T1
Couldn't classify 4567, 5226
Sorry, prediction pasa_asmbl_43084.p1 fails validation.
(CGG)	 TC	4567-5226	CC	CAC
Valid prediction for snap_scaffold_4-snap.2967-T1
Valid prediction for snap_scaffold_4-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_10628-T1
Valid prediction for GlimmerHMM_glimmerT_10622-T1
Valid prediction for snap_scaffold_4-snap.2974-T1
Valid prediction for snap_scaffold_4-snap.2991-T1
Valid prediction for snap_scaffold_4-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_10620-T1
Valid prediction for snap_scaffold_4-snap.2972-T1
Valid prediction for GlimmerHMM_glimmerT_10616-T1
Valid prediction for Augustus_model.g6984.t1
Valid prediction for Augustus_model.g6985.t1
Valid prediction for snap_scaffold_4-snap.2970-T1
Valid prediction for Augustus_model.g6971.t1
Valid prediction for Augustus_model.g6988.t1
Valid prediction for Augustus_model.g6990.t1
Valid prediction for snap_scaffold_4-snap.2976-T1
Valid prediction for GlimmerHMM_glimmerT_10631-T1
Valid prediction for snap_scaffold_4-snap.2969-T1
Valid prediction for GlimmerHMM_glimmerT_10619-T1
Valid prediction for GlimmerHMM_glimmerT_10634-T1
Valid prediction for GlimmerHMM_glimmerT_10642-T1
Valid prediction for GlimmerHMM_glimmerT_10615-T1
Valid prediction for Augustus_model.g6973.t1
Valid prediction for snap_scaffold_4-snap.2988-T1
Valid prediction for GlimmerHMM_glimmerT_10640-T1
Valid prediction for GlimmerHMM_glimmerT_10623-T1
Valid prediction for snap_scaffold_4-snap.2986-T1
Valid prediction for GlimmerHMM_glimmerT_10624-T1
Valid prediction for snap_scaffold_4-snap.2979-T1
Valid prediction for Augustus_model.g6978.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 88797, rend_intergenic: 88794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 269156, rend_intergenic: 269153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283400, rend_intergenic: 281675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 315261
-exon list size: 281


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    
5.7    
6.0    
6.4    
6.7    
7.1    
7.4    
7.8    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
11.0    
11.3    
11.7    
12.0    
12.4    
12.7    
13.1    
13.4    
13.8    
14.1    
14.5    
14.8    
15.2    
15.5    
15.9    
16.3    
16.6    
17.0    
17.3    
17.7    
18.0    
18.4    
18.7    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.6    
21.9    
22.3    
22.6    
23.0    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.9    
27.2    
27.6    
27.9    
28.3    
28.6    
29.0    
29.3    
29.7    
30.0    
30.4    
30.7    
31.1    
31.4    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.6    
35.0    
35.3    
35.7    
36.0    
36.4    
36.7    
37.1    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.7    
42.0    
42.4    
42.8    
43.1    
43.5    
43.8    
44.2    
44.5    
44.9    
45.2    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.8    
55.1    
55.5    
55.8    
56.2    
56.5    
56.9    
57.2    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.9    
63.3    
63.6    
64.0    
64.3    
64.7    
65.0    
65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.6    
68.9    
69.3    
69.6    
70.0    
70.3    
70.7    
71.0    
71.4    
71.7    
72.1    
72.4    
72.8    
73.1    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.0    
77.4    
77.7    
78.1    
78.4    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.3    
81.6    
82.0    
82.3    
82.7    
83.0    
83.4    
83.7    
84.1    
84.5    
84.8    
85.2    
85.5    
85.9    
86.2    
86.6    
86.9    
87.3    
87.6    
88.0    
88.3    
88.7    
89.0    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.2    
92.6    
92.9    
93.3    
93.6    
94.0    
94.3    
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 24 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 88797, rend_intergenic: 88794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 269156, rend_intergenic: 269153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283400, rend_intergenic: 281675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 95323
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-found 2 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 47718
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 - 16598
-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 1 - 11246

-building DP trellis

-building trellis in range 16643 - 47718
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 16643 - 33969
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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

-building DP trellis

-building trellis in range 34032 - 47718
-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 34032 - 44045