-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_10123832-10325124

-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: +)Couldn't classify 13650, 13699
Sorry, prediction pasa_asmbl_11234.p1 fails validation.
(TCA)	 TC	13650-13699	GT	ATG
(GCC)	 AG	14702-14814	GT	AGG
(AGT)	 AG	15000-15079	GT	AGG
(CCA)	 AG	15181-15243	GT	AGG
(GCT)	 AG	15408-15605	GT	CGG
(TGG)	 AG	16176-16337	GT	AGG
(GCC)	 AG	16489-16623	GT	TGG
(ATT)	 AG	16841-16941	GT	CGG
(GGA)	 AG	17284-17350	GT	AGG
(GAG)	 AG	17492-17656	CT	AAC
-recovered pasa_asmbl_11234.p1, terminal, 17492, 17656
-recovered pasa_asmbl_11234.p1, internal, 14702, 14814
-recovered pasa_asmbl_11234.p1, internal, 15000, 15079
-recovered pasa_asmbl_11234.p1, internal, 15181, 15243
-recovered pasa_asmbl_11234.p1, internal, 15408, 15605
-recovered pasa_asmbl_11234.p1, internal, 16176, 16337
-recovered pasa_asmbl_11234.p1, internal, 16489, 16623
-recovered pasa_asmbl_11234.p1, internal, 16841, 16941
-recovered pasa_asmbl_11234.p1, internal, 17284, 17350
Valid prediction for GlimmerHMM_glimmerT_32235-T1
Valid prediction for CodingQuarry_transcript_13222-T1
Valid prediction for snap_scaffold_13-snap.1881-T1
Valid prediction for snap_scaffold_13-snap.1858-T1
Valid prediction for Augustus_model.g21529.t1
Valid prediction for GlimmerHMM_glimmerT_32229-T1
Valid prediction for snap_scaffold_13-snap.1874-T1
Valid prediction for GlimmerHMM_glimmerT_32236-T1
Valid prediction for pasa_asmbl_11235.p1
Valid prediction for Augustus_model.g21512.t1
Valid prediction for GlimmerHMM_glimmerT_32233-T1
Valid prediction for snap_scaffold_13-snap.1847-T1
Valid prediction for snap_scaffold_13-snap.1850-T1
Valid prediction for snap_scaffold_13-snap.1873-T1
Valid prediction for snap_scaffold_13-snap.1889-T1
Valid prediction for pasa_asmbl_11232.p1
Valid prediction for GlimmerHMM_glimmerT_32223-T1
Valid prediction for snap_scaffold_13-snap.1853-T1
Valid prediction for snap_scaffold_13-snap.1865-T1
Valid prediction for snap_scaffold_13-snap.1887-T1
Valid prediction for Augustus_model.g21528.t1
Valid prediction for GlimmerHMM_glimmerT_32215-T1
Valid prediction for snap_scaffold_13-snap.1879-T1
Valid prediction for GlimmerHMM_glimmerT_32227-T1
Valid prediction for CodingQuarry_transcript_13225-T1
Valid prediction for Augustus_model.g21519.t1
Valid prediction for Augustus_model.g21517.t1
Valid prediction for GlimmerHMM_glimmerT_32217-T1
Valid prediction for snap_scaffold_13-snap.1861-T1
Valid prediction for snap_scaffold_13-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_32231-T1
Valid prediction for snap_scaffold_13-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_32241-T1
Valid prediction for HiQ_model.g21510.t1
Valid prediction for snap_scaffold_13-snap.1877-T1
Couldn't classify 120181, 120567
Sorry, prediction pasa_asmbl_11236.p1 fails validation.
(AAT)	 CC	120181-120567	TG	AGT
Valid prediction for GlimmerHMM_glimmerT_32214-T1
Valid prediction for snap_scaffold_13-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_32240-T1
Valid prediction for snap_scaffold_13-snap.1883-T1
Valid prediction for Augustus_model.g21527.t1
Valid prediction for snap_scaffold_13-snap.1893-T1
Valid prediction for Augustus_model.g21509.t1
Valid prediction for snap_scaffold_13-snap.1857-T1
Valid prediction for GlimmerHMM_glimmerT_32219-T1
Valid prediction for snap_scaffold_13-snap.1880-T1
Valid prediction for snap_scaffold_13-snap.1860-T1
Valid prediction for snap_scaffold_13-snap.1871-T1
Valid prediction for Augustus_model.g21520.t1
Valid prediction for HiQ_model.g21525.t1
Valid prediction for snap_scaffold_13-snap.1854-T1
Valid prediction for snap_scaffold_13-snap.1885-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.g21511.t1
Valid prediction for snap_scaffold_13-snap.1882-T1
Valid prediction for snap_scaffold_13-snap.1878-T1
Valid prediction for snap_scaffold_13-snap.1856-T1
Valid prediction for snap_scaffold_13-snap.1891-T1
Valid prediction for Augustus_model.g21515.t1
Valid prediction for GlimmerHMM_glimmerT_32230-T1
Valid prediction for snap_scaffold_13-snap.1859-T1
Valid prediction for snap_scaffold_13-snap.1864-T1
Valid prediction for CodingQuarry_transcript_13223-T1
Valid prediction for GlimmerHMM_glimmerT_32239-T1
Valid prediction for Augustus_model.g21516.t1
Valid prediction for snap_scaffold_13-snap.1866-T1
Valid prediction for CodingQuarry_transcript_13226-T1
Valid prediction for GlimmerHMM_glimmerT_32242-T1
Valid prediction for snap_scaffold_13-snap.1869-T1
Valid prediction for snap_scaffold_13-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_32243-T1
Couldn't classify 123589, 123630
Sorry, prediction Augustus_model.g21518.t1 fails validation.
(CTG)	 AG	123589-123630	GT	CTG
(CCC)	 AG	124493-124618	GT	AGG
(TGC)	 AG	124737-124828	AT	AAA
-recovered Augustus_model.g21518.t1, terminal, 124737, 124828
-recovered Augustus_model.g21518.t1, internal, 123589, 123630
-recovered Augustus_model.g21518.t1, internal, 124493, 124618
Valid prediction for GlimmerHMM_glimmerT_32232-T1
Valid prediction for GlimmerHMM_glimmerT_32237-T1
Valid prediction for GlimmerHMM_glimmerT_32226-T1
Valid prediction for pasa_asmbl_10053.p1
Valid prediction for snap_scaffold_13-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_32218-T1
Valid prediction for snap_scaffold_13-snap.1867-T1
Valid prediction for CodingQuarry_transcript_13227-T1
Valid prediction for GlimmerHMM_glimmerT_32228-T1
Valid prediction for snap_scaffold_13-snap.1884-T1
Valid prediction for snap_scaffold_13-snap.1876-T1
Valid prediction for snap_scaffold_13-snap.1888-T1
Valid prediction for snap_scaffold_13-snap.1868-T1
Valid prediction for snap_scaffold_13-snap.1870-T1
Valid prediction for Augustus_model.g21524.t1
Valid prediction for Augustus_model.g21530.t1
Valid prediction for GlimmerHMM_glimmerT_32225-T1
Valid prediction for snap_scaffold_13-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_32234-T1
Valid prediction for GlimmerHMM_glimmerT_32221-T1
Valid prediction for snap_scaffold_13-snap.1892-T1
Valid prediction for CodingQuarry_transcript_13224-T1
Valid prediction for GlimmerHMM_glimmerT_32216-T1
Valid prediction for snap_scaffold_13-snap.1855-T1
Valid prediction for snap_scaffold_13-snap.1875-T1
Valid prediction for Augustus_model.g21523.t1
Valid prediction for pasa_asmbl_10051.p1
Valid prediction for Augustus_model.g21521.t1
Valid prediction for GlimmerHMM_glimmerT_32238-T1
Valid prediction for Augustus_model.g21513.t1
Valid prediction for GlimmerHMM_glimmerT_32224-T1
Valid prediction for snap_scaffold_13-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_32220-T1
Valid prediction for snap_scaffold_13-snap.1851-T1
Valid prediction for Augustus_model.g21514.t1
Valid prediction for GlimmerHMM_glimmerT_32222-T1
Valid prediction for snap_scaffold_13-snap.1862-T1
Valid prediction for Augustus_model.g21531.t1
Valid prediction for Augustus_model.g21522.t1
Valid prediction for HiQ_model.g21526.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40002, rend_intergenic: 25838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59733, rend_intergenic: 45475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81551, rend_intergenic: 69170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86135, rend_intergenic: 82630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115833, rend_intergenic: 104511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129243, rend_intergenic: 127561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140336, rend_intergenic: 134958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141711, rend_intergenic: 140339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158699, rend_intergenic: 141731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172745, rend_intergenic: 159001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177275, rend_intergenic: 173014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178884, rend_intergenic: 177331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179441, rend_intergenic: 179112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185805, rend_intergenic: 179566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189663, rend_intergenic: 185875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196903, rend_intergenic: 194211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201293
-exon list size: 401


building trellis

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32.3    
32.5    
32.8    
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33.3    
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34.2    
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34.7    
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35.7    
36.0    
36.2    
36.5    
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37.0    
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37.5    
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39.5    
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41.9    
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42.9    
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44.2    
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44.7    
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46.9    
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47.4    
47.6    
47.9    
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48.6    
48.9    
49.1    
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49.6    
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59.6    
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61.3    
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66.3    
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66.7    
67.0    
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68.7    
69.0    
69.2    
69.5    
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70.0    
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71.0    
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71.5    
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72.0    
72.2    
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73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
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75.7    
75.9    
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76.4    
76.7    
76.9    
77.2    
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78.7    
78.9    
79.2    
79.4    
79.7    
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80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
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83.4    
83.6    
83.9    
84.1    
84.4    
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85.4    
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86.4    
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87.1    
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88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
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90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 40002, rend_intergenic: 25838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59733, rend_intergenic: 45475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81551, rend_intergenic: 69170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86135, rend_intergenic: 82630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115833, rend_intergenic: 104511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129243, rend_intergenic: 127561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140336, rend_intergenic: 134958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141711, rend_intergenic: 140339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158699, rend_intergenic: 141731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172745, rend_intergenic: 159001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177275, rend_intergenic: 173014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178884, rend_intergenic: 177331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179441, rend_intergenic: 179112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185805, rend_intergenic: 179566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189663, rend_intergenic: 185875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196903, rend_intergenic: 194211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 186649 - 201293
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support