-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_15962572-16157929

-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_19095-T1
Valid prediction for Augustus_model.g12917.t1
Valid prediction for Augustus_model.g12919.t1
Valid prediction for GlimmerHMM_glimmerT_19090-T1
Valid prediction for snap_scaffold_7-snap.3046-T1
Valid prediction for GlimmerHMM_glimmerT_19112-T1
Valid prediction for snap_scaffold_7-snap.3044-T1
Valid prediction for GeneMark_model.32149_t
Valid prediction for GeneMark_model.32180_t
Valid prediction for snap_scaffold_7-snap.3065-T1
Valid prediction for GeneMark_model.32154_t
Valid prediction for snap_scaffold_7-snap.3033-T1
Valid prediction for GeneMark_model.32145_t
Valid prediction for snap_scaffold_7-snap.3071-T1
Valid prediction for snap_scaffold_7-snap.3070-T1
Valid prediction for Augustus_model.g12926.t1
Valid prediction for GeneMark_model.32177_t
Valid prediction for GlimmerHMM_glimmerT_19109-T1
Valid prediction for GeneMark_model.32183_t
Valid prediction for HiQ_model.g12928.t1
Valid prediction for snap_scaffold_7-snap.3038-T1
Valid prediction for GlimmerHMM_glimmerT_19097-T1
Valid prediction for GeneMark_model.32170_t
Valid prediction for GeneMark_model.32164_t
Valid prediction for GeneMark_model.32162_t
Valid prediction for GeneMark_model.32143_t
Valid prediction for snap_scaffold_7-snap.3035-T1
Valid prediction for GeneMark_model.32147_t
Valid prediction for GlimmerHMM_glimmerT_19110-T1
Valid prediction for GeneMark_model.32173_t
Valid prediction for snap_scaffold_7-snap.3049-T1
Valid prediction for snap_scaffold_7-snap.3057-T1
Valid prediction for snap_scaffold_7-snap.3037-T1
Valid prediction for snap_scaffold_7-snap.3047-T1
Valid prediction for GlimmerHMM_glimmerT_19104-T1
Valid prediction for GlimmerHMM_glimmerT_19094-T1
Valid prediction for GeneMark_model.32168_t
Valid prediction for snap_scaffold_7-snap.3069-T1
Valid prediction for GeneMark_model.32160_t
Valid prediction for snap_scaffold_7-snap.3054-T1
Valid prediction for snap_scaffold_7-snap.3064-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3039-T1
Valid prediction for Augustus_model.g12922.t1
Valid prediction for GeneMark_model.32158_t
Couldn't classify 177860, 177937
Sorry, prediction pasa_asmbl_51345.p1 fails validation.
(TCC)	 TT	177860-177937	GT	ACG
(GAG)	 AG	178827-178917	GT	AGG
(AGA)	 AG	179106-179142	GT	AGG
(CTT)	 AG	179469-179535	GT	AAG
(AAT)	 AG	179632-179822	GT	AGG
(CAG)	 AG	180250-180372	GT	GGG
(AGC)	 AG	180930-181014	GT	AGG
(GCT)	 AG	181168-181285	GT	AAG
(GAG)	 AG	181685-182253	AG	AGA
add_exon() Sorry, pasa_asmbl_51345.p1 178827-178917-terminal-3 is invalid.
-recovered pasa_asmbl_51345.p1, terminal, 178827, 178917
add_exon() Sorry, pasa_asmbl_51345.p1 179106-179142-terminal-3 is invalid.
-recovered pasa_asmbl_51345.p1, terminal, 179106, 179142
-recovered pasa_asmbl_51345.p1, terminal, 181685, 182253
-recovered pasa_asmbl_51345.p1, internal, 178827, 178917
-recovered pasa_asmbl_51345.p1, internal, 179106, 179142
-recovered pasa_asmbl_51345.p1, internal, 179469, 179535
-recovered pasa_asmbl_51345.p1, internal, 179632, 179822
-recovered pasa_asmbl_51345.p1, internal, 180250, 180372
-recovered pasa_asmbl_51345.p1, internal, 180930, 181014
-recovered pasa_asmbl_51345.p1, internal, 181168, 181285
Valid prediction for GlimmerHMM_glimmerT_19098-T1
Valid prediction for GeneMark_model.32151_t
Valid prediction for GlimmerHMM_glimmerT_19091-T1
Valid prediction for GeneMark_model.32163_t
Valid prediction for GlimmerHMM_glimmerT_19105-T1
Valid prediction for snap_scaffold_7-snap.3062-T1
Valid prediction for GeneMark_model.32181_t
Valid prediction for snap_scaffold_7-snap.3060-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_19093-T1
Valid prediction for Augustus_model.g12918.t1
Valid prediction for Augustus_model.g12925.t1
Valid prediction for snap_scaffold_7-snap.3058-T1
Valid prediction for snap_scaffold_7-snap.3034-T1
Valid prediction for snap_scaffold_7-snap.3050-T1
Valid prediction for snap_scaffold_7-snap.3051-T1
Valid prediction for GeneMark_model.32144_t

-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.32167_t
Valid prediction for GlimmerHMM_glimmerT_19089-T1
Valid prediction for GlimmerHMM_glimmerT_19107-T1
Valid prediction for GeneMark_model.32169_t
Valid prediction for GeneMark_model.32155_t
Valid prediction for snap_scaffold_7-snap.3066-T1
Valid prediction for snap_scaffold_7-snap.3041-T1
Valid prediction for snap_scaffold_7-snap.3045-T1
Valid prediction for GeneMark_model.32182_t
Valid prediction for snap_scaffold_7-snap.3048-T1
Valid prediction for GlimmerHMM_glimmerT_19092-T1
Valid prediction for snap_scaffold_7-snap.3055-T1
Valid prediction for snap_scaffold_7-snap.3068-T1
Valid prediction for GeneMark_model.32161_t
Valid prediction for Augustus_model.g12923.t1
Valid prediction for GeneMark_model.32156_t
Valid prediction for GlimmerHMM_glimmerT_19108-T1
Valid prediction for GeneMark_model.32146_t
Valid prediction for GlimmerHMM_glimmerT_19088-T1
Valid prediction for Augustus_model.g12921.t1
Valid prediction for GlimmerHMM_glimmerT_19099-T1
Couldn't classify 39976, 40005
Sorry, prediction pasa_asmbl_50215.p2 fails validation.
(TGG)	 AG	39976-40005	GT	AGG
(AAA)	 AG	40259-40612	AC	GAA
-recovered pasa_asmbl_50215.p2, terminal, 40259, 40612
-recovered pasa_asmbl_50215.p2, internal, 39976, 40005
Valid prediction for GeneMark_model.32172_t
Valid prediction for GeneMark_model.32165_t
Valid prediction for snap_scaffold_7-snap.3059-T1
Valid prediction for snap_scaffold_7-snap.3036-T1
Valid prediction for snap_scaffold_7-snap.3040-T1
Valid prediction for snap_scaffold_7-snap.3067-T1
Valid prediction for GlimmerHMM_glimmerT_19096-T1
Valid prediction for snap_scaffold_7-snap.3063-T1
Valid prediction for GeneMark_model.32175_t
Valid prediction for GeneMark_model.32184_t
Valid prediction for pasa_asmbl_50220.p1
Valid prediction for GeneMark_model.32157_t
Valid prediction for CodingQuarry_transcript_57587-T1
Valid prediction for GlimmerHMM_glimmerT_19100-T1
Valid prediction for snap_scaffold_7-snap.3053-T1
Valid prediction for GlimmerHMM_glimmerT_19111-T1
Valid prediction for GeneMark_model.32153_t
Valid prediction for HiQ_model.g12927.t1
Valid prediction for snap_scaffold_7-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_19101-T1
Valid prediction for snap_scaffold_7-snap.3042-T1
Valid prediction for snap_scaffold_7-snap.3061-T1
Valid prediction for GeneMark_model.32150_t
Valid prediction for GeneMark_model.32166_t
Valid prediction for GeneMark_model.32142_t
Valid prediction for GeneMark_model.32179_t
Valid prediction for Augustus_model.g12924.t1
Valid prediction for GeneMark_model.32159_t
Valid prediction for GeneMark_model.32148_t
Valid prediction for GeneMark_model.32174_t
Valid prediction for snap_scaffold_7-snap.3052-T1
Valid prediction for GlimmerHMM_glimmerT_19102-T1
Valid prediction for GeneMark_model.32152_t
Valid prediction for GeneMark_model.32185_t
Valid prediction for GlimmerHMM_glimmerT_19103-T1
Valid prediction for snap_scaffold_7-snap.3043-T1
Valid prediction for GeneMark_model.32178_t
Valid prediction for GlimmerHMM_glimmerT_19106-T1
Couldn't classify 33243, 34069
Sorry, prediction pasa_asmbl_50217.p1 fails validation.
(ATG)	 CC	31182-31262	GT	TGG
(CAC)	 AG	32640-32694	GT	GGG
(AAC)	 AG	33243-34069	GT	AGG
-recovered pasa_asmbl_50217.p1, initial, 31182, 31262
-recovered pasa_asmbl_50217.p1, internal, 32640, 32694
-recovered pasa_asmbl_50217.p1, internal, 33243, 34069
Valid prediction for Augustus_model.g12920.t1
Valid prediction for GeneMark_model.32171_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 67180, rend_intergenic: 64890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90900, rend_intergenic: 89097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118032, rend_intergenic: 116762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143297, rend_intergenic: 136944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153407, rend_intergenic: 143912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159217, rend_intergenic: 154747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162865, rend_intergenic: 159328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195358
-exon list size: 544


building trellis

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29.9    
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30.2    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
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31.9    
32.1    
32.2    
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32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.1    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 67180, rend_intergenic: 64890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90900, rend_intergenic: 89097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118032, rend_intergenic: 116762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143297, rend_intergenic: 136944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153407, rend_intergenic: 143912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159217, rend_intergenic: 154747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162865, rend_intergenic: 159328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 59682
-exon list size: 128


building trellis

0.8    
1.5    
2.3    
3.1    
3.8    
4.6    
5.4    
6.2    
6.9    
7.7    
8.5    
9.2    
10.0    
10.8    
11.5    
12.3    
13.1    
13.8    
14.6    
15.4    
16.2    
16.9    
17.7    
18.5    
19.2    
20.0    
20.8    
21.5    
22.3    
23.1    
23.8    
24.6    
25.4    
26.2    
26.9    
27.7    
28.5    
29.2    
30.0    
30.8    
31.5    
32.3    
33.1    
33.8    
34.6    
35.4    
36.2    
36.9    
37.7    
38.5    
39.2    
40.0    
40.8    
41.5    
42.3    
43.1    
43.8    
44.6    
45.4    
46.2    
46.9    
47.7    
48.5    
49.2    
50.0    
50.8    
51.5    
52.3    
53.1    
53.8    
54.6    
55.4    
56.2    
56.9    
57.7    
58.5    
59.2    
60.0    
60.8    
61.5    
62.3    
63.1    
63.8    
64.6    
65.4    
66.2    
66.9    
67.7    
68.5    
69.2    
70.0    
70.8    
71.5    
72.3    
73.1    
73.8    
74.6    
75.4    
76.2    
76.9    
77.7    
78.5    
79.2    
80.0    
80.8    
81.5    
82.3    
83.1    
83.8    
84.6    
85.4    
86.2    
86.9    
87.7    
88.5    
89.2    
90.0    
90.8    
91.5    
92.3    
93.1    
93.8    
94.6    
95.4    
96.2    
96.9    
97.7    
98.5    
99.2    
-found 6 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 14597
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 4182 - 14597
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 37966 - 59682
-exon list size: 54


building trellis

1.8    
3.6    
5.4    
7.1    
8.9    
10.7    
12.5    
14.3    
16.1    
17.9    
19.6    
21.4    
23.2    
25.0    
26.8    
28.6    
30.4    
32.1    
33.9    
35.7    
37.5    
39.3    
41.1    
42.9    
44.6    
46.4    
48.2    
50.0    
51.8    
53.6    
55.4    
57.1    
58.9    
60.7    
62.5    
64.3    
66.1    
67.9    
69.6    
71.4    
73.2    
75.0    
76.8    
78.6    
80.4    
82.1    
83.9    
85.7    
87.5    
89.3    
91.1    
92.9    
94.6    
96.4    
98.2    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support