-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_14138026-14410509

-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 Augustus_model.g8918.t1
Valid prediction for Augustus_model.g8920.t1
Valid prediction for GlimmerHMM_glimmerT_13351-T1
Valid prediction for snap_scaffold_5-snap.2667-T1
Valid prediction for GeneMark_model.22448_t
Valid prediction for GeneMark_model.22427_t
Valid prediction for snap_scaffold_5-snap.2645-T1
Valid prediction for snap_scaffold_5-snap.2640-T1
Valid prediction for snap_scaffold_5-snap.2651-T1
Valid prediction for CodingQuarry_transcript_52218-T1
Valid prediction for Augustus_model.g8921.t1
Valid prediction for GeneMark_model.22441_t
Valid prediction for GeneMark_model.22450_t
Valid prediction for Augustus_model.g8922.t1
Valid prediction for snap_scaffold_5-snap.2636-T1
Valid prediction for Augustus_model.g8932.t1
Valid prediction for GlimmerHMM_glimmerT_13362-T1
Valid prediction for snap_scaffold_5-snap.2638-T1
Valid prediction for GlimmerHMM_glimmerT_13361-T1
Valid prediction for Augustus_model.g8937.t1
Valid prediction for GeneMark_model.22437_t
Valid prediction for GeneMark_model.22447_t
Valid prediction for snap_scaffold_5-snap.2635-T1
Valid prediction for pasa_asmbl_44590.p1
Valid prediction for Augustus_model.g8924.t1
Valid prediction for GlimmerHMM_glimmerT_13345-T1
Valid prediction for snap_scaffold_5-snap.2665-T1
Valid prediction for snap_scaffold_5-snap.2666-T1
Valid prediction for GeneMark_model.22436_t
Valid prediction for snap_scaffold_5-snap.2652-T1
Valid prediction for GeneMark_model.22431_t
Valid prediction for snap_scaffold_5-snap.2657-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2653-T1
Valid prediction for CodingQuarry_transcript_52217-T1
Valid prediction for Augustus_model.g8927.t1
Valid prediction for Augustus_model.g8928.t1
Valid prediction for Augustus_model.g8931.t1
Valid prediction for GeneMark_model.22423_t
Valid prediction for GlimmerHMM_glimmerT_13343-T1
Valid prediction for GeneMark_model.22454_t
Couldn't classify 240111, 241106
Sorry, prediction pasa_asmbl_44594.p1 fails validation.
(GGC)	 AA	240111-241106	CA	GAC
Valid prediction for snap_scaffold_5-snap.2637-T1
Valid prediction for Augustus_model.g8923.t1
Valid prediction for snap_scaffold_5-snap.2646-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2641-T1
Valid prediction for GlimmerHMM_glimmerT_13353-T1
Valid prediction for Augustus_model.g8926.t1
Valid prediction for GeneMark_model.22429_t
Valid prediction for snap_scaffold_5-snap.2658-T1
Valid prediction for GeneMark_model.22432_t
Valid prediction for GlimmerHMM_glimmerT_13357-T1
Valid prediction for snap_scaffold_5-snap.2642-T1
Valid prediction for GeneMark_model.22446_t
Valid prediction for Augustus_model.g8919.t1
Valid prediction for GeneMark_model.22442_t
Valid prediction for snap_scaffold_5-snap.2648-T1
Valid prediction for GlimmerHMM_glimmerT_13349-T1
Valid prediction for GlimmerHMM_glimmerT_13354-T1
Valid prediction for GlimmerHMM_glimmerT_13346-T1
Valid prediction for GeneMark_model.22438_t
Valid prediction for pasa_asmbl_45003.p1
Valid prediction for GeneMark_model.22433_t
Valid prediction for snap_scaffold_5-snap.2632-T1
Couldn't classify 25058, 25085
Couldn't classify 26842, 26908
Sorry, prediction pasa_asmbl_45050.p2 fails validation.
(CAC)	 GG	25058-25085	GT	AGG
(GAT)	 AG	25496-25595	GT	GGG
(AGA)	 AG	25865-25925	GT	ATG
(GAT)	 AG	26324-26415	GT	AGG
(GGA)	 AG	26842-26908	CA	ACC
-recovered pasa_asmbl_45050.p2, internal, 25496, 25595
-recovered pasa_asmbl_45050.p2, internal, 25865, 25925
-recovered pasa_asmbl_45050.p2, internal, 26324, 26415
Valid prediction for GeneMark_model.22455_t
Valid prediction for GlimmerHMM_glimmerT_13341-T1
Couldn't classify 244043, 244057
Sorry, prediction GeneMark_model.22453_t fails validation.
(ATG)	 TT	239153-239447	GT	TGG
(GGG)	 AG	239674-241066	GT	CTG
(GAA)	 AG	244043-244057	GT	AAG
-recovered GeneMark_model.22453_t, initial, 239153, 239447
-recovered GeneMark_model.22453_t, internal, 239674, 241066
-recovered GeneMark_model.22453_t, internal, 244043, 244057
Valid prediction for GeneMark_model.22430_t
Couldn't classify 239333, 239447
Couldn't classify 239674, 239978
Sorry, prediction pasa_asmbl_44593.p1 fails validation.
(AGT)	 GC	239333-239447	GT	TGG
(GGG)	 AG	239674-239978	GC	GAG
-recovered pasa_asmbl_44593.p1, internal, 239674, 239978
Couldn't classify 137625, 138131
Sorry, prediction pasa_asmbl_44591.p1 fails validation.
(AGC)	 CC	137625-138131	TA	GCT
Valid prediction for snap_scaffold_5-snap.2663-T1
Valid prediction for GeneMark_model.22439_t
Valid prediction for Augustus_model.g8936.t1
Couldn't classify 35075, 35266
Couldn't classify 37790, 37900
Sorry, prediction pasa_asmbl_44991.p1 fails validation.
(GGT)	 AG	35075-35266	GT	AGG
(GAA)	 AG	36289-36453	GT	AGG
(ACA)	 AG	37098-37193	GT	ATG
(TTG)	 AG	37466-37666	GT	CGG
(TTT)	 AG	37790-37900	GT	CGG
-recovered pasa_asmbl_44991.p1, internal, 35075, 35266
-recovered pasa_asmbl_44991.p1, internal, 36289, 36453
-recovered pasa_asmbl_44991.p1, internal, 37098, 37193
-recovered pasa_asmbl_44991.p1, internal, 37466, 37666
-recovered pasa_asmbl_44991.p1, internal, 37790, 37900
Valid prediction for snap_scaffold_5-snap.2647-T1
Valid prediction for GlimmerHMM_glimmerT_13347-T1
Valid prediction for snap_scaffold_5-snap.2643-T1
Valid prediction for GlimmerHMM_glimmerT_13360-T1
Valid prediction for snap_scaffold_5-snap.2644-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 GlimmerHMM_glimmerT_13344-T1
Valid prediction for GlimmerHMM_glimmerT_13356-T1
Valid prediction for Augustus_model.g8935.t1
Valid prediction for snap_scaffold_5-snap.2661-T1
Valid prediction for GeneMark_model.22443_t
Valid prediction for Augustus_model.g8929.t1
Valid prediction for CodingQuarry_transcript_52216-T1
Valid prediction for snap_scaffold_5-snap.2662-T1
Valid prediction for snap_scaffold_5-snap.2659-T1
Valid prediction for GeneMark_model.22444_t
Valid prediction for HiQ_model.g8930.t1
Valid prediction for Augustus_model.g8934.t1
Valid prediction for snap_scaffold_5-snap.2654-T1
Valid prediction for snap_scaffold_5-snap.2650-T1
Valid prediction for GeneMark_model.22434_t
Valid prediction for GeneMark_model.22424_t
Valid prediction for Augustus_model.g8925.t1
Valid prediction for snap_scaffold_5-snap.2664-T1
Couldn't classify 156539, 156580
Sorry, prediction pasa_asmbl_45974.p1 fails validation.
(GGG)	 TC	156539-156580	GT	TGG
(GGA)	 AG	156976-157083	GC	AGG
(AAA)	 AG	157307-157447	GT	AGG
(GAA)	 AG	157543-157674	AC	AAA
-recovered pasa_asmbl_45974.p1, terminal, 157543, 157674
-recovered pasa_asmbl_45974.p1, internal, 156976, 157083
-recovered pasa_asmbl_45974.p1, internal, 157307, 157447
Valid prediction for pasa_asmbl_45972.p1
Valid prediction for snap_scaffold_5-snap.2634-T1
Valid prediction for snap_scaffold_5-snap.2649-T1
Valid prediction for GeneMark_model.22425_t
Valid prediction for snap_scaffold_5-snap.2633-T1
Valid prediction for GeneMark_model.22435_t
Valid prediction for snap_scaffold_5-snap.2660-T1
Valid prediction for GlimmerHMM_glimmerT_13355-T1
Valid prediction for GeneMark_model.22452_t
Valid prediction for GlimmerHMM_glimmerT_13348-T1
Valid prediction for GeneMark_model.22428_t
Valid prediction for GeneMark_model.22445_t
Valid prediction for GeneMark_model.22449_t
Valid prediction for snap_scaffold_5-snap.2656-T1
Valid prediction for GeneMark_model.22451_t
Valid prediction for snap_scaffold_5-snap.2655-T1
Valid prediction for GeneMark_model.22426_t
Valid prediction for GlimmerHMM_glimmerT_13358-T1
Valid prediction for Augustus_model.g8933.t1
Valid prediction for GlimmerHMM_glimmerT_13342-T1
Valid prediction for GlimmerHMM_glimmerT_13359-T1
Valid prediction for GlimmerHMM_glimmerT_13350-T1
Valid prediction for snap_scaffold_5-snap.2639-T1
Valid prediction for GlimmerHMM_glimmerT_13352-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13662, rend_intergenic: 5789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22191, rend_intergenic: 16189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41745, rend_intergenic: 35077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272484
-exon list size: 465


building trellis

0.2    
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0.6    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
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2.6    
2.8    
3.0    
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3.6    
3.9    
4.1    
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5.8    
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8.8    
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9.2    
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11.6    
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12.0    
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12.6    
12.8    
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13.5    
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13.9    
14.1    
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14.6    
14.8    
15.0    
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17.3    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.1    
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20.1    
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20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
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25.7    
25.9    
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26.3    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
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49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13662, rend_intergenic: 5789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22191, rend_intergenic: 16189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41745, rend_intergenic: 35077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support