-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_8345536-8563372

-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_37371-T1
Valid prediction for snap_scaffold_15-snap.1760-T1
Valid prediction for snap_scaffold_15-snap.1783-T1
Valid prediction for snap_scaffold_15-snap.1763-T1
Valid prediction for snap_scaffold_15-snap.1756-T1
Valid prediction for GlimmerHMM_glimmerT_37381-T1
Valid prediction for GeneMark_model.64307_t
Valid prediction for GlimmerHMM_glimmerT_37383-T1
Valid prediction for GlimmerHMM_glimmerT_37378-T1
Valid prediction for snap_scaffold_15-snap.1786-T1
Valid prediction for snap_scaffold_15-snap.1771-T1
Valid prediction for GeneMark_model.64308_t
Valid prediction for snap_scaffold_15-snap.1764-T1
Valid prediction for GeneMark_model.64315_t
Valid prediction for Augustus_model.g25050.t1
Valid prediction for GeneMark_model.64310_t
Valid prediction for snap_scaffold_15-snap.1781-T1
Valid prediction for CodingQuarry_transcript_18027-T1
Valid prediction for snap_scaffold_15-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_37377-T1
Valid prediction for snap_scaffold_15-snap.1776-T1
Couldn't classify 4627, 4648
Couldn't classify 5644, 6014
Sorry, prediction pasa_asmbl_14863.p1 fails validation.
(GAC)	 CT	4627-4648	GT	AGG
(CTC)	 AG	4836-4972	GC	AGG
(GAA)	 AG	5281-5440	GT	AGG
(TCA)	 AG	5644-6014	GG	GAG
-recovered pasa_asmbl_14863.p1, internal, 4836, 4972
-recovered pasa_asmbl_14863.p1, internal, 5281, 5440
Valid prediction for snap_scaffold_15-snap.1773-T1
Valid prediction for snap_scaffold_15-snap.1765-T1
Valid prediction for snap_scaffold_15-snap.1766-T1
Couldn't classify 95001, 95037
Couldn't classify 97028, 97116
Sorry, prediction pasa_asmbl_14276.p1 fails validation.
(TGT)	 CA	95001-95037	GT	ACG
(CCC)	 AG	95471-95580	GT	AGG
(GGA)	 AG	96047-96139	GT	AGG
(GAC)	 AG	96411-96492	GT	AGG
(AGC)	 AG	97028-97116	GG	AGG
-recovered pasa_asmbl_14276.p1, internal, 95471, 95580
-recovered pasa_asmbl_14276.p1, internal, 96047, 96139
-recovered pasa_asmbl_14276.p1, internal, 96411, 96492
Valid prediction for GeneMark_model.64317_t
Couldn't classify 74120, 74178
Couldn't classify 75389, 75449
Sorry, prediction pasa_asmbl_14272.p1 fails validation.
(GGG)	 GC	74120-74178	GT	AGG
(GTC)	 AG	74349-74510	GT	AGG
(GGA)	 AG	74700-74841	GT	AGG
(GCC)	 AG	74965-75185	GT	AGG
(GGC)	 AG	75389-75449	GA	AGG
-recovered pasa_asmbl_14272.p1, internal, 74349, 74510
-recovered pasa_asmbl_14272.p1, internal, 74700, 74841
-recovered pasa_asmbl_14272.p1, internal, 74965, 75185
Valid prediction for CodingQuarry_transcript_18029-T1
Valid prediction for GlimmerHMM_glimmerT_37373-T1
Valid prediction for Augustus_model.g25044.t1
Valid prediction for snap_scaffold_15-snap.1767-T1
Valid prediction for Augustus_model.g25062.t1
Valid prediction for Augustus_model.g25058.t1
Valid prediction for GeneMark_model.64330_t
Valid prediction for snap_scaffold_15-snap.1754-T1
Valid prediction for GeneMark_model.64324_t
Valid prediction for pasa_asmbl_14278.p1
Valid prediction for snap_scaffold_15-snap.1775-T1
Valid prediction for GeneMark_model.64329_t
Valid prediction for GlimmerHMM_glimmerT_37369-T1
Valid prediction for GlimmerHMM_glimmerT_37380-T1
Valid prediction for GeneMark_model.64312_t
Valid prediction for GeneMark_model.64323_t
Valid prediction for Augustus_model.g25060.t1
Valid prediction for snap_scaffold_15-snap.1769-T1
Valid prediction for snap_scaffold_15-snap.1772-T1
Valid prediction for snap_scaffold_15-snap.1758-T1
Valid prediction for Augustus_model.g25052.t1
Valid prediction for Augustus_model.g25056.t1
Valid prediction for GeneMark_model.64326_t
Valid prediction for GlimmerHMM_glimmerT_37362-T1
Valid prediction for snap_scaffold_15-snap.1777-T1
Valid prediction for GlimmerHMM_glimmerT_37379-T1
Valid prediction for GeneMark_model.64314_t
Valid prediction for HiQ_model.g25051.t1
Valid prediction for snap_scaffold_15-snap.1780-T1
Valid prediction for HiQ_model.g25057.t1
Valid prediction for GeneMark_model.64327_t
Valid prediction for GeneMark_model.64313_t
Valid prediction for Augustus_model.g25045.t1
Valid prediction for GeneMark_model.64333_t
Valid prediction for snap_scaffold_15-snap.1768-T1
Valid prediction for Augustus_model.g25061.t1
Valid prediction for GlimmerHMM_glimmerT_37366-T1
Valid prediction for GeneMark_model.64325_t
Valid prediction for GlimmerHMM_glimmerT_37384-T1
Valid prediction for GeneMark_model.64328_t
Valid prediction for GlimmerHMM_glimmerT_37363-T1
Valid prediction for snap_scaffold_15-snap.1762-T1
Valid prediction for Augustus_model.g25059.t1
Valid prediction for GeneMark_model.64319_t
Valid prediction for GlimmerHMM_glimmerT_37364-T1
Valid prediction for pasa_asmbl_14279.p1
Valid prediction for GlimmerHMM_glimmerT_37372-T1
Valid prediction for GeneMark_model.64332_t
Valid prediction for snap_scaffold_15-snap.1782-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 GeneMark_model.64309_t
Valid prediction for GeneMark_model.64316_t
Valid prediction for GlimmerHMM_glimmerT_37374-T1
Valid prediction for snap_scaffold_15-snap.1759-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g25055.t1
Valid prediction for GeneMark_model.64320_t
Valid prediction for snap_scaffold_15-snap.1757-T1
Valid prediction for Augustus_model.g25063.t1
Valid prediction for Augustus_model.g25049.t1
Valid prediction for GeneMark_model.64321_t
Valid prediction for CodingQuarry_transcript_18025-T1
Valid prediction for Augustus_model.g25053.t1
Valid prediction for GeneMark_model.64335_t
Valid prediction for HiQ_model.g25046.t1
Valid prediction for GlimmerHMM_glimmerT_37376-T1
Valid prediction for snap_scaffold_15-snap.1784-T1
Valid prediction for Augustus_model.g25054.t1
Valid prediction for snap_scaffold_15-snap.1778-T1
Valid prediction for snap_scaffold_15-snap.1761-T1
Valid prediction for snap_scaffold_15-snap.1755-T1
Valid prediction for GlimmerHMM_glimmerT_37370-T1
Valid prediction for GlimmerHMM_glimmerT_37367-T1
Valid prediction for snap_scaffold_15-snap.1779-T1
Valid prediction for GeneMark_model.64318_t
Valid prediction for GlimmerHMM_glimmerT_37368-T1
Valid prediction for GlimmerHMM_glimmerT_37375-T1
Valid prediction for GlimmerHMM_glimmerT_37382-T1
Valid prediction for GlimmerHMM_glimmerT_37365-T1
Valid prediction for GeneMark_model.64334_t
Valid prediction for Augustus_model.g25048.t1
Valid prediction for snap_scaffold_15-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_37385-T1
Valid prediction for Augustus_model.g25047.t1
Valid prediction for GeneMark_model.64331_t
Valid prediction for pasa_asmbl_15358.p1
Valid prediction for GeneMark_model.64322_t
Valid prediction for GeneMark_model.64311_t
Couldn't classify 144318, 144713
Sorry, prediction pasa_asmbl_15363.p1 fails validation.
(CTA)	 AA	144318-144713	TG	GAT
Valid prediction for snap_scaffold_15-snap.1785-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6542, rend_intergenic: 2984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54613, rend_intergenic: 50143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148009, rend_intergenic: 147209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210458, rend_intergenic: 206270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217837
-exon list size: 389


building trellis

0.3    
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0.8    
1.0    
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3.1    
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5.4    
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10.7    
11.0    
11.3    
11.5    
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12.3    
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14.8    
15.1    
15.3    
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17.1    
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17.6    
17.9    
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18.4    
18.7    
18.9    
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19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
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22.0    
22.3    
22.5    
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23.0    
23.3    
23.5    
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24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
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29.9    
30.2    
30.4    
30.7    
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31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
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47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
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58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
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61.1    
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62.9    
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64.5    
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65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
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68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
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70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 6542, rend_intergenic: 2984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54613, rend_intergenic: 50143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148009, rend_intergenic: 147209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210458, rend_intergenic: 206270  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