-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_12772555-12974141

-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_2-snap.2443-T1
Valid prediction for snap_scaffold_2-snap.2458-T1
Valid prediction for snap_scaffold_2-snap.2475-T1
Valid prediction for snap_scaffold_2-snap.2485-T1
Valid prediction for snap_scaffold_2-snap.2486-T1
Valid prediction for snap_scaffold_2-snap.2462-T1
Valid prediction for snap_scaffold_2-snap.2463-T1
Valid prediction for snap_scaffold_2-snap.2478-T1
Valid prediction for Augustus_model.g3161.t1
Valid prediction for GlimmerHMM_glimmerT_4718-T1
Valid prediction for GlimmerHMM_glimmerT_4700-T1
Valid prediction for GlimmerHMM_glimmerT_4699-T1
Valid prediction for GlimmerHMM_glimmerT_4695-T1
Valid prediction for snap_scaffold_2-snap.2438-T1
Valid prediction for snap_scaffold_2-snap.2450-T1
Valid prediction for GlimmerHMM_glimmerT_4707-T1
Valid prediction for GlimmerHMM_glimmerT_4698-T1
Valid prediction for Augustus_model.g3155.t1
Valid prediction for Augustus_model.g3157.t1
Valid prediction for snap_scaffold_2-snap.2471-T1
Valid prediction for snap_scaffold_2-snap.2481-T1
Valid prediction for Augustus_model.g3163.t1
Valid prediction for snap_scaffold_2-snap.2454-T1
Valid prediction for snap_scaffold_2-snap.2452-T1
Valid prediction for GlimmerHMM_glimmerT_4704-T1
Valid prediction for GlimmerHMM_glimmerT_4706-T1
Valid prediction for Augustus_model.g3162.t1
Valid prediction for snap_scaffold_2-snap.2457-T1
Valid prediction for snap_scaffold_2-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_4705-T1
Valid prediction for snap_scaffold_2-snap.2479-T1
Valid prediction for GlimmerHMM_glimmerT_4709-T1
Valid prediction for snap_scaffold_2-snap.2468-T1
Valid prediction for Augustus_model.g3160.t1
Valid prediction for snap_scaffold_2-snap.2469-T1
Valid prediction for snap_scaffold_2-snap.2477-T1
Valid prediction for snap_scaffold_2-snap.2444-T1
Valid prediction for GlimmerHMM_glimmerT_4703-T1
Valid prediction for Augustus_model.g3154.t1
Valid prediction for snap_scaffold_2-snap.2442-T1
Valid prediction for GlimmerHMM_glimmerT_4714-T1
Valid prediction for snap_scaffold_2-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_4713-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_2-snap.2455-T1
Valid prediction for snap_scaffold_2-snap.2459-T1
Valid prediction for snap_scaffold_2-snap.2445-T1
Valid prediction for Augustus_model.g3169.t1
Valid prediction for snap_scaffold_2-snap.2461-T1
Valid prediction for Augustus_model.g3165.t1
Valid prediction for Augustus_model.g3151.t1
Valid prediction for Augustus_model.g3156.t1
Valid prediction for GlimmerHMM_glimmerT_4712-T1
Valid prediction for snap_scaffold_2-snap.2441-T1
Valid prediction for GlimmerHMM_glimmerT_4688-T1
Valid prediction for GlimmerHMM_glimmerT_4687-T1
Valid prediction for Augustus_model.g3166.t1
Valid prediction for Augustus_model.g3164.t1
Valid prediction for GlimmerHMM_glimmerT_4690-T1
Valid prediction for snap_scaffold_2-snap.2487-T1
Valid prediction for snap_scaffold_2-snap.2464-T1
Valid prediction for GlimmerHMM_glimmerT_4701-T1
Valid prediction for GlimmerHMM_glimmerT_4696-T1
Valid prediction for snap_scaffold_2-snap.2488-T1
Valid prediction for GlimmerHMM_glimmerT_4689-T1
Valid prediction for snap_scaffold_2-snap.2446-T1
Valid prediction for snap_scaffold_2-snap.2451-T1
Valid prediction for Augustus_model.g3167.t1
Valid prediction for GlimmerHMM_glimmerT_4711-T1
Valid prediction for GlimmerHMM_glimmerT_4693-T1
Valid prediction for snap_scaffold_2-snap.2470-T1
Valid prediction for snap_scaffold_2-snap.2480-T1
Valid prediction for snap_scaffold_2-snap.2460-T1
Valid prediction for GlimmerHMM_glimmerT_4715-T1
Valid prediction for snap_scaffold_2-snap.2467-T1
Valid prediction for GlimmerHMM_glimmerT_4710-T1
Valid prediction for GlimmerHMM_glimmerT_4708-T1
Valid prediction for Augustus_model.g3153.t1
Valid prediction for snap_scaffold_2-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_4716-T1
Valid prediction for Augustus_model.g3152.t1
Valid prediction for GlimmerHMM_glimmerT_4720-T1
Valid prediction for Augustus_model.g3168.t1
Valid prediction for snap_scaffold_2-snap.2453-T1
Valid prediction for Augustus_model.g3159.t1
Valid prediction for snap_scaffold_2-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_4686-T1
Valid prediction for GlimmerHMM_glimmerT_4694-T1
Valid prediction for Augustus_model.g3150.t1
Valid prediction for snap_scaffold_2-snap.2466-T1
Valid prediction for snap_scaffold_2-snap.2447-T1
Valid prediction for snap_scaffold_2-snap.2449-T1
Valid prediction for Augustus_model.g3158.t1
Valid prediction for snap_scaffold_2-snap.2440-T1
Valid prediction for snap_scaffold_2-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_4697-T1
Valid prediction for GlimmerHMM_glimmerT_4692-T1
Valid prediction for GlimmerHMM_glimmerT_4702-T1
Valid prediction for GlimmerHMM_glimmerT_4719-T1
Valid prediction for Augustus_model.g3170.t1
Valid prediction for GlimmerHMM_glimmerT_4717-T1
Valid prediction for snap_scaffold_2-snap.2472-T1
Valid prediction for snap_scaffold_2-snap.2439-T1
Valid prediction for snap_scaffold_2-snap.2474-T1
Valid prediction for snap_scaffold_2-snap.2456-T1
Valid prediction for snap_scaffold_2-snap.2476-T1
Valid prediction for snap_scaffold_2-snap.2465-T1
Couldn't classify 85785, 85860
Sorry, prediction pasa_asmbl_23481.p1 fails validation.
(ATT)	 CC	85785-85860	GT	GGG
(ACC)	 AG	86012-86114	GT	AGG
(GTT)	 AG	86333-86414	GT	AGG
(ATG)	 AG	87067-87135	GT	AGG
(CTG)	 AG	87288-87401	GT	AGG
(GCC)	 AG	87609-87824	GG	GAG
-recovered pasa_asmbl_23481.p1, initial, 87067, 87135
-recovered pasa_asmbl_23481.p1, terminal, 87609, 87824
-recovered pasa_asmbl_23481.p1, internal, 86012, 86114
-recovered pasa_asmbl_23481.p1, internal, 86333, 86414
-recovered pasa_asmbl_23481.p1, internal, 87067, 87135
-recovered pasa_asmbl_23481.p1, internal, 87288, 87401
Valid prediction for GlimmerHMM_glimmerT_4691-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12497, rend_intergenic: 1741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36163, rend_intergenic: 13159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47622, rend_intergenic: 38708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51496, rend_intergenic: 47818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55867, rend_intergenic: 51996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58329, rend_intergenic: 55891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60026, rend_intergenic: 58681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64361, rend_intergenic: 62790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71022, rend_intergenic: 64404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83439, rend_intergenic: 76337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91719, rend_intergenic: 83507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109569, rend_intergenic: 92100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119573, rend_intergenic: 115141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127722, rend_intergenic: 119599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128478, rend_intergenic: 128298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147641, rend_intergenic: 131439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149960, rend_intergenic: 147792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171205, rend_intergenic: 157511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177981, rend_intergenic: 171675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184925, rend_intergenic: 178699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192117, rend_intergenic: 185990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194024, rend_intergenic: 192621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201587
-exon list size: 470


building trellis

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29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
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37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
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40.7    
40.9    
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41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
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43.4    
43.6    
43.9    
44.1    
44.3    
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44.7    
44.9    
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45.6    
45.8    
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46.2    
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46.8    
47.0    
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47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
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48.9    
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52.8    
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68.9    
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70.8    
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78.6    
78.8    
79.0    
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83.7    
83.9    
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84.5    
84.7    
85.0    
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85.6    
85.8    
86.0    
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86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
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90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
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94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 12497, rend_intergenic: 1741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36163, rend_intergenic: 13159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47622, rend_intergenic: 38708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51496, rend_intergenic: 47818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55867, rend_intergenic: 51996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58329, rend_intergenic: 55891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60026, rend_intergenic: 58681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64361, rend_intergenic: 62790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71022, rend_intergenic: 64404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83439, rend_intergenic: 76337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91719, rend_intergenic: 83507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109569, rend_intergenic: 92100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119573, rend_intergenic: 115141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127722, rend_intergenic: 119599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128478, rend_intergenic: 128298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147641, rend_intergenic: 131439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149960, rend_intergenic: 147792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171205, rend_intergenic: 157511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177981, rend_intergenic: 171675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184925, rend_intergenic: 178699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192117, rend_intergenic: 185990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194024, rend_intergenic: 192621  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

-building DP trellis

-building trellis in range 1 - 13865
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 1572 - 13865
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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 2993 - 13865
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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