-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_16065592-16254364

-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_8158.p1
Valid prediction for Augustus_model.g20360.t1
Valid prediction for snap_scaffold_12-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_30764-T1
Valid prediction for Augustus_model.g20356.t1
Valid prediction for snap_scaffold_12-snap.3096-T1
Valid prediction for GlimmerHMM_glimmerT_30763-T1
Valid prediction for GlimmerHMM_glimmerT_30772-T1
Valid prediction for Augustus_model.g20368.t1
Valid prediction for snap_scaffold_12-snap.3093-T1
Valid prediction for snap_scaffold_12-snap.3082-T1
Valid prediction for snap_scaffold_12-snap.3084-T1
Valid prediction for snap_scaffold_12-snap.3090-T1
Valid prediction for snap_scaffold_12-snap.3095-T1
Valid prediction for GlimmerHMM_glimmerT_30773-T1
Valid prediction for snap_scaffold_12-snap.3097-T1
Couldn't classify 165507, 165782
Sorry, prediction pasa_asmbl_9110.p1 fails validation.
(ATG)	 CT	165507-165782	GG	GTG
Valid prediction for Augustus_model.g20379.t1
Valid prediction for snap_scaffold_12-snap.3102-T1
Valid prediction for snap_scaffold_12-snap.3094-T1
Valid prediction for GlimmerHMM_glimmerT_30774-T1
Valid prediction for snap_scaffold_12-snap.3077-T1
Valid prediction for snap_scaffold_12-snap.3112-T1
Valid prediction for Augustus_model.g20358.t1
Valid prediction for Augustus_model.g20369.t1
Valid prediction for Augustus_model.g20357.t1
Valid prediction for Augustus_model.g20385.t1
Valid prediction for GlimmerHMM_glimmerT_30782-T1
Valid prediction for Augustus_model.g20380.t1
Valid prediction for Augustus_model.g20361.t1
Valid prediction for Augustus_model.g20366.t1
Valid prediction for snap_scaffold_12-snap.3110-T1
Couldn't classify 156130, 156534
Sorry, prediction pasa_asmbl_9109.p1 fails validation.
(GCT)	 TG	156130-156534	GA	ATG
Valid prediction for snap_scaffold_12-snap.3089-T1
Valid prediction for snap_scaffold_12-snap.3091-T1
Valid prediction for Augustus_model.g20383.t1
Valid prediction for GlimmerHMM_glimmerT_30770-T1
Valid prediction for snap_scaffold_12-snap.3107-T1
Valid prediction for snap_scaffold_12-snap.3104-T1
Valid prediction for snap_scaffold_12-snap.3079-T1
Valid prediction for GlimmerHMM_glimmerT_30767-T1
Valid prediction for GlimmerHMM_glimmerT_30766-T1
Valid prediction for GlimmerHMM_glimmerT_30779-T1
Valid prediction for Augustus_model.g20381.t1
Valid prediction for snap_scaffold_12-snap.3080-T1
Valid prediction for Augustus_model.g20376.t1
Valid prediction for Augustus_model.g20359.t1
Valid prediction for snap_scaffold_12-snap.3100-T1
Valid prediction for snap_scaffold_12-snap.3083-T1
Valid prediction for Augustus_model.g20370.t1
Valid prediction for snap_scaffold_12-snap.3092-T1
Valid prediction for GlimmerHMM_glimmerT_30781-T1
Valid prediction for Augustus_model.g20367.t1
Valid prediction for GlimmerHMM_glimmerT_30785-T1
Valid prediction for GlimmerHMM_glimmerT_30765-T1
Valid prediction for GlimmerHMM_glimmerT_30783-T1
Valid prediction for Augustus_model.g20365.t1
Valid prediction for GlimmerHMM_glimmerT_30771-T1
Valid prediction for GlimmerHMM_glimmerT_30762-T1
Couldn't classify 45283, 45339
Sorry, prediction pasa_asmbl_8143.p1 fails validation.
(AAA)	 TG	45283-45339	GT	AGG
(GAC)	 AG	46819-47064	GG	AAG
-recovered pasa_asmbl_8143.p1, terminal, 46819, 47064
Valid prediction for snap_scaffold_12-snap.3113-T1
Valid prediction for Augustus_model.g20364.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 CodingQuarry_transcript_10513-T1
Valid prediction for GlimmerHMM_glimmerT_30761-T1
Valid prediction for snap_scaffold_12-snap.3114-T1
Valid prediction for GlimmerHMM_glimmerT_30780-T1
Valid prediction for CodingQuarry_transcript_10514-T1
Valid prediction for GlimmerHMM_glimmerT_30775-T1
Valid prediction for snap_scaffold_12-snap.3086-T1
Valid prediction for Augustus_model.g20378.t1
Valid prediction for snap_scaffold_12-snap.3087-T1
Valid prediction for snap_scaffold_12-snap.3106-T1
Valid prediction for snap_scaffold_12-snap.3108-T1
Valid prediction for snap_scaffold_12-snap.3115-T1
Valid prediction for snap_scaffold_12-snap.3116-T1
Valid prediction for snap_scaffold_12-snap.3081-T1
Valid prediction for HiQ_model.g20371.t1
Valid prediction for snap_scaffold_12-snap.3103-T1
Valid prediction for GlimmerHMM_glimmerT_30784-T1
Valid prediction for GlimmerHMM_glimmerT_30769-T1
Valid prediction for GlimmerHMM_glimmerT_30786-T1
Valid prediction for snap_scaffold_12-snap.3105-T1
Valid prediction for snap_scaffold_12-snap.3085-T1
Valid prediction for Augustus_model.g20377.t1
Valid prediction for Augustus_model.g20372.t1
Valid prediction for GlimmerHMM_glimmerT_30778-T1
Couldn't classify 47251, 47358
Sorry, prediction pasa_asmbl_9106.p1 fails validation.
(TCA)	 TT	47251-47358	GT	AGG
(AAC)	 AG	48548-48655	GT	AGG
(GGT)	 AG	49232-49456	GA	GAG
-recovered pasa_asmbl_9106.p1, terminal, 49232, 49456
-recovered pasa_asmbl_9106.p1, internal, 48548, 48655
Valid prediction for snap_scaffold_12-snap.3078-T1
Valid prediction for Augustus_model.g20384.t1
Valid prediction for Augustus_model.g20363.t1
Couldn't classify 20725, 20882
Sorry, prediction pasa_asmbl_9111.p1 fails validation.
(ATG)	 CA	17521-17553	GT	TGG
(TAT)	 AG	18169-18257	GT	AGG
(GAC)	 AG	18482-18569	GT	AAG
(TAT)	 AG	20313-20487	GT	TGG
(GGA)	 AG	20725-20882	GT	AGG
-recovered pasa_asmbl_9111.p1, initial, 17521, 17553
-recovered pasa_asmbl_9111.p1, internal, 18169, 18257
-recovered pasa_asmbl_9111.p1, internal, 18482, 18569
-recovered pasa_asmbl_9111.p1, internal, 20313, 20487
-recovered pasa_asmbl_9111.p1, internal, 20725, 20882
Valid prediction for Augustus_model.g20374.t1
Valid prediction for snap_scaffold_12-snap.3111-T1
Valid prediction for Augustus_model.g20373.t1
Valid prediction for snap_scaffold_12-snap.3099-T1
Valid prediction for CodingQuarry_transcript_10512-T1
Valid prediction for snap_scaffold_12-snap.3088-T1
Valid prediction for snap_scaffold_12-snap.3101-T1
Valid prediction for Augustus_model.g20382.t1
Couldn't classify 39498, 39661
Couldn't classify 43184, 43402
Sorry, prediction pasa_asmbl_9107.p1 fails validation.
(GAA)	 AG	39498-39661	GT	GGG
(GAA)	 AG	42558-42687	GT	AGG
(GAT)	 AG	43184-43402	AA	GGA
-recovered pasa_asmbl_9107.p1, internal, 39498, 39661
-recovered pasa_asmbl_9107.p1, internal, 42558, 42687
Valid prediction for GlimmerHMM_glimmerT_30777-T1
Valid prediction for snap_scaffold_12-snap.3076-T1
Valid prediction for Augustus_model.g20375.t1
Valid prediction for GlimmerHMM_glimmerT_30776-T1
Valid prediction for GlimmerHMM_glimmerT_30768-T1
Valid prediction for Augustus_model.g20386.t1
Valid prediction for snap_scaffold_12-snap.3098-T1
Valid prediction for Augustus_model.g20362.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26358, rend_intergenic: 22504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38463, rend_intergenic: 37894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188773
-exon list size: 262


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.0    
3.4    
3.8    
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4.5    
4.9    
5.3    
5.7    
6.1    
6.4    
6.8    
7.2    
7.6    
8.0    
8.3    
8.7    
9.1    
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10.6    
11.0    
11.4    
11.7    
12.1    
12.5    
12.9    
13.3    
13.6    
14.0    
14.4    
14.8    
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15.5    
15.9    
16.3    
16.7    
17.0    
17.4    
17.8    
18.2    
18.6    
18.9    
19.3    
19.7    
20.1    
20.5    
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21.6    
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22.3    
22.7    
23.1    
23.5    
23.9    
24.2    
24.6    
25.0    
25.4    
25.8    
26.1    
26.5    
26.9    
27.3    
27.7    
28.0    
28.4    
28.8    
29.2    
29.5    
29.9    
30.3    
30.7    
31.1    
31.4    
31.8    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.5    
34.8    
35.2    
35.6    
36.0    
36.4    
36.7    
37.1    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.8    
40.2    
40.5    
40.9    
41.3    
41.7    
42.0    
42.4    
42.8    
43.2    
43.6    
43.9    
44.3    
44.7    
45.1    
45.5    
45.8    
46.2    
46.6    
47.0    
47.3    
47.7    
48.1    
48.5    
48.9    
49.2    
49.6    
50.0    
50.4    
50.8    
51.1    
51.5    
51.9    
52.3    
52.7    
53.0    
53.4    
53.8    
54.2    
54.5    
54.9    
55.3    
55.7    
56.1    
56.4    
56.8    
57.2    
57.6    
58.0    
58.3    
58.7    
59.1    
59.5    
59.8    
60.2    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.9    
63.3    
63.6    
64.0    
64.4    
64.8    
65.2    
65.5    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.2    
68.6    
68.9    
69.3    
69.7    
70.1    
70.5    
70.8    
71.2    
71.6    
72.0    
72.3    
72.7    
73.1    
73.5    
73.9    
74.2    
74.6    
75.0    
75.4    
75.8    
76.1    
76.5    
76.9    
77.3    
77.7    
78.0    
78.4    
78.8    
79.2    
79.5    
79.9    
80.3    
80.7    
81.1    
81.4    
81.8    
82.2    
82.6    
83.0    
83.3    
83.7    
84.1    
84.5    
84.8    
85.2    
85.6    
86.0    
86.4    
86.7    
87.1    
87.5    
87.9    
88.3    
88.6    
89.0    
89.4    
89.8    
90.2    
90.5    
90.9    
91.3    
91.7    
92.0    
92.4    
92.8    
93.2    
93.6    
93.9    
94.3    
94.7    
95.1    
95.5    
95.8    
96.2    
96.6    
97.0    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 26358, rend_intergenic: 22504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38463, rend_intergenic: 37894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12669
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 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 - 12564
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 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 - 11690
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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