-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_8550091-8783403

-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_3-snap.1768-T1
Valid prediction for GeneMark_model.11791_t
Valid prediction for GlimmerHMM_glimmerT_7133-T1
Valid prediction for GlimmerHMM_glimmerT_7149-T1
Valid prediction for snap_scaffold_3-snap.1756-T1
Valid prediction for GeneMark_model.11810_t
Valid prediction for Augustus_model.g4692.t1
Valid prediction for GeneMark_model.11801_t
Valid prediction for GeneMark_model.11820_t
Valid prediction for GeneMark_model.11794_t
Valid prediction for GeneMark_model.11807_t
Valid prediction for GlimmerHMM_glimmerT_7143-T1
Valid prediction for snap_scaffold_3-snap.1772-T1
Valid prediction for snap_scaffold_3-snap.1778-T1
Valid prediction for HiQ_model.g4700.t1
Valid prediction for Augustus_model.g4690.t1
Valid prediction for GeneMark_model.11799_t
Valid prediction for snap_scaffold_3-snap.1763-T1
Valid prediction for snap_scaffold_3-snap.1774-T1
Valid prediction for GeneMark_model.11789_t
Valid prediction for snap_scaffold_3-snap.1752-T1
Valid prediction for GeneMark_model.11793_t
Valid prediction for GlimmerHMM_glimmerT_7136-T1
Valid prediction for GeneMark_model.11803_t
Valid prediction for snap_scaffold_3-snap.1766-T1
Valid prediction for CodingQuarry_transcript_46124-T1
Valid prediction for snap_scaffold_3-snap.1760-T1
Valid prediction for snap_scaffold_3-snap.1757-T1
Valid prediction for GlimmerHMM_glimmerT_7150-T1
Valid prediction for GlimmerHMM_glimmerT_7130-T1
Valid prediction for snap_scaffold_3-snap.1771-T1
Valid prediction for Augustus_model.g4689.t1
Valid prediction for snap_scaffold_3-snap.1762-T1
Valid prediction for GeneMark_model.11797_t
Valid prediction for GlimmerHMM_glimmerT_7126-T1
Valid prediction for pasa_asmbl_40182.p1
Valid prediction for GlimmerHMM_glimmerT_7131-T1
Valid prediction for GeneMark_model.11812_t
Valid prediction for GlimmerHMM_glimmerT_7134-T1
Valid prediction for snap_scaffold_3-snap.1755-T1
Valid prediction for snap_scaffold_3-snap.1769-T1
Valid prediction for GeneMark_model.11809_t
Valid prediction for Augustus_model.g4699.t1
Valid prediction for snap_scaffold_3-snap.1775-T1
Couldn't classify 37303, 37441
Couldn't classify 40278, 40313
Sorry, prediction pasa_asmbl_40178.p1 fails validation.
(ACC)	 AC	37303-37441	GT	CTG
(GCC)	 AG	38333-38389	GT	TGG
(TTC)	 AG	39083-39273	GT	ACG
(CAC)	 AG	39372-39500	GT	AGG
(GTG)	 AG	39650-39856	GT	AGG
(GGC)	 AG	40278-40313	AG	CCA
-recovered pasa_asmbl_40178.p1, internal, 38333, 38389
-recovered pasa_asmbl_40178.p1, internal, 39083, 39273
-recovered pasa_asmbl_40178.p1, internal, 39372, 39500
-recovered pasa_asmbl_40178.p1, internal, 39650, 39856
Valid prediction for Augustus_model.g4687.t1
Valid prediction for GlimmerHMM_glimmerT_7129-T1
Valid prediction for snap_scaffold_3-snap.1751-T1
Valid prediction for GlimmerHMM_glimmerT_7132-T1
Valid prediction for GlimmerHMM_glimmerT_7153-T1
Valid prediction for GlimmerHMM_glimmerT_7148-T1
Valid prediction for snap_scaffold_3-snap.1773-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_3-snap.1754-T1
Valid prediction for GeneMark_model.11815_t
Valid prediction for snap_scaffold_3-snap.1780-T1
Valid prediction for HiQ_model.g4698.t1
Valid prediction for GeneMark_model.11818_t
Valid prediction for GeneMark_model.11798_t
Valid prediction for snap_scaffold_3-snap.1765-T1
Valid prediction for Augustus_model.g4697.t1
Valid prediction for GeneMark_model.11795_t
Valid prediction for GlimmerHMM_glimmerT_7154-T1
Valid prediction for pasa_asmbl_38999.p1
Valid prediction for snap_scaffold_3-snap.1759-T1
Valid prediction for GlimmerHMM_glimmerT_7137-T1
Valid prediction for GlimmerHMM_glimmerT_7152-T1
Valid prediction for GlimmerHMM_glimmerT_7139-T1
Valid prediction for snap_scaffold_3-snap.1776-T1
Valid prediction for GeneMark_model.11805_t
Valid prediction for GlimmerHMM_glimmerT_7142-T1
Valid prediction for Augustus_model.g4693.t1
Valid prediction for Augustus_model.g4695.t1
Valid prediction for snap_scaffold_3-snap.1750-T1
Valid prediction for snap_scaffold_3-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_7127-T1
Valid prediction for snap_scaffold_3-snap.1770-T1
Valid prediction for snap_scaffold_3-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_7145-T1
Valid prediction for GlimmerHMM_glimmerT_7128-T1
Valid prediction for GeneMark_model.11800_t
Valid prediction for GeneMark_model.11819_t
Valid prediction for GlimmerHMM_glimmerT_7140-T1
Valid prediction for GlimmerHMM_glimmerT_7138-T1
Valid prediction for snap_scaffold_3-snap.1779-T1
Valid prediction for Augustus_model.g4688.t1
Valid prediction for GlimmerHMM_glimmerT_7147-T1
Valid prediction for GeneMark_model.11804_t
Valid prediction for GeneMark_model.11821_t
Valid prediction for GeneMark_model.11813_t
Valid prediction for snap_scaffold_3-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_7141-T1
Valid prediction for GeneMark_model.11811_t
Valid prediction for snap_scaffold_3-snap.1777-T1
Valid prediction for GeneMark_model.11802_t
Valid prediction for GeneMark_model.11816_t
Valid prediction for snap_scaffold_3-snap.1767-T1
Valid prediction for GlimmerHMM_glimmerT_7135-T1
Valid prediction for GlimmerHMM_glimmerT_7146-T1
Valid prediction for CodingQuarry_transcript_46123-T1
Valid prediction for GeneMark_model.11790_t
Valid prediction for GeneMark_model.11817_t
Valid prediction for GeneMark_model.11792_t
Valid prediction for GlimmerHMM_glimmerT_7144-T1
Valid prediction for Augustus_model.g4696.t1
Valid prediction for GeneMark_model.11814_t
Valid prediction for GeneMark_model.11806_t
Valid prediction for GlimmerHMM_glimmerT_7151-T1
Valid prediction for Augustus_model.g4694.t1
Valid prediction for snap_scaffold_3-snap.1761-T1
Valid prediction for GeneMark_model.11808_t
Valid prediction for GeneMark_model.11822_t
Valid prediction for GeneMark_model.11823_t
Valid prediction for Augustus_model.g4691.t1
Valid prediction for GeneMark_model.11796_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41183, rend_intergenic: 21601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85865, rend_intergenic: 80432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135113, rend_intergenic: 130375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233313
-exon list size: 523


building trellis

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27.8    
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29.9    
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30.9    
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32.2    
32.4    
32.6    
32.8    
33.0    
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33.3    
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35.8    
36.0    
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36.4    
36.6    
36.8    
37.0    
37.1    
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37.5    
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37.9    
38.1    
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38.9    
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40.6    
40.8    
41.0    
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41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
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42.7    
42.9    
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43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
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45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
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46.9    
47.0    
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47.6    
47.8    
48.0    
48.2    
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48.6    
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49.0    
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49.3    
49.5    
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50.1    
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50.7    
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51.4    
51.6    
51.8    
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52.4    
52.6    
52.8    
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53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
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54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
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56.6    
56.8    
57.0    
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57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
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60.4    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
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62.9    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
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65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
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68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.8    
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72.2    
72.4    
72.6    
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73.0    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 41183, rend_intergenic: 21601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85865, rend_intergenic: 80432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135113, rend_intergenic: 130375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 221247 - 233313
-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 221247 - 232207