-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_14862731-15124212

-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_14-snap.3104-T1
Valid prediction for snap_scaffold_14-snap.3105-T1
Valid prediction for snap_scaffold_14-snap.3102-T1
Valid prediction for snap_scaffold_14-snap.3082-T1
Valid prediction for GlimmerHMM_glimmerT_35221-T1
Valid prediction for GlimmerHMM_glimmerT_35203-T1
Valid prediction for Augustus_model.g23533.t1
Valid prediction for GlimmerHMM_glimmerT_35192-T1
Valid prediction for snap_scaffold_14-snap.3073-T1
Valid prediction for GlimmerHMM_glimmerT_35190-T1
Valid prediction for GlimmerHMM_glimmerT_35207-T1
Valid prediction for snap_scaffold_14-snap.3084-T1
Valid prediction for snap_scaffold_14-snap.3095-T1
Valid prediction for snap_scaffold_14-snap.3116-T1
Valid prediction for snap_scaffold_14-snap.3088-T1
Valid prediction for Augustus_model.g23530.t1
Valid prediction for snap_scaffold_14-snap.3074-T1
Valid prediction for snap_scaffold_14-snap.3110-T1
Valid prediction for snap_scaffold_14-snap.3077-T1
Valid prediction for Augustus_model.g23535.t1
Valid prediction for GlimmerHMM_glimmerT_35224-T1
Valid prediction for GlimmerHMM_glimmerT_35206-T1
Valid prediction for snap_scaffold_14-snap.3092-T1
Valid prediction for Augustus_model.g23542.t1
Valid prediction for GlimmerHMM_glimmerT_35212-T1
Couldn't classify 257124, 257131
Sorry, prediction pasa_asmbl_12562.p1 fails validation.
(ATG)	 CC	252810-252819	GT	ATG
(ATT)	 AG	253529-253675	GT	AGG
(GGT)	 AG	255417-255502	GT	AGG
(ATC)	 AG	255691-255796	GT	AGG
(ATC)	 AG	256041-256105	GT	GGG
(CCA)	 AG	256963-257023	GT	AGG
(ACT)	 AG	257124-257131	GT	AGG
-recovered pasa_asmbl_12562.p1, initial, 252810, 252819
add_exon() Sorry, pasa_asmbl_12562.p1 253529-253675-terminal-1 is invalid.
-recovered pasa_asmbl_12562.p1, terminal, 253529, 253675
-recovered pasa_asmbl_12562.p1, internal, 253529, 253675
-recovered pasa_asmbl_12562.p1, internal, 255417, 255502
-recovered pasa_asmbl_12562.p1, internal, 255691, 255796
-recovered pasa_asmbl_12562.p1, internal, 256041, 256105
-recovered pasa_asmbl_12562.p1, internal, 256963, 257023
-recovered pasa_asmbl_12562.p1, internal, 257124, 257131
Valid prediction for snap_scaffold_14-snap.3099-T1
Valid prediction for snap_scaffold_14-snap.3086-T1
Valid prediction for snap_scaffold_14-snap.3080-T1
Valid prediction for snap_scaffold_14-snap.3081-T1
Valid prediction for snap_scaffold_14-snap.3090-T1
Valid prediction for snap_scaffold_14-snap.3078-T1
Valid prediction for snap_scaffold_14-snap.3106-T1
Valid prediction for snap_scaffold_14-snap.3071-T1
Valid prediction for GlimmerHMM_glimmerT_35191-T1
Valid prediction for snap_scaffold_14-snap.3114-T1
Couldn't classify 258308, 258396
Sorry, prediction CodingQuarry_transcript_15941-T1 fails validation.
(ATG)	 CC	253540-253675	GT	AGG
(GGT)	 AG	255417-255502	GT	AGG
(ATC)	 AG	255691-255796	GT	AGG
(ATC)	 AG	256041-256105	GT	GGG
(CCA)	 AG	256963-257023	GT	AGG
(CTG)	 CC	258308-258396	GT	AGG
(CGC)	 AG	259126-259239	AC	AAA
-recovered CodingQuarry_transcript_15941-T1, initial, 253540, 253675
-recovered CodingQuarry_transcript_15941-T1, terminal, 259126, 259239
-recovered CodingQuarry_transcript_15941-T1, internal, 255417, 255502
-recovered CodingQuarry_transcript_15941-T1, internal, 255691, 255796
-recovered CodingQuarry_transcript_15941-T1, internal, 256041, 256105
-recovered CodingQuarry_transcript_15941-T1, internal, 256963, 257023
Valid prediction for GlimmerHMM_glimmerT_35193-T1
Valid prediction for GlimmerHMM_glimmerT_35210-T1
Valid prediction for snap_scaffold_14-snap.3101-T1
Valid prediction for Augustus_model.g23537.t1
Valid prediction for GlimmerHMM_glimmerT_35208-T1
Valid prediction for Augustus_model.g23540.t1
Valid prediction for GlimmerHMM_glimmerT_35218-T1
Valid prediction for Augustus_model.g23532.t1
Valid prediction for Augustus_model.g23547.t1
Valid prediction for snap_scaffold_14-snap.3115-T1
Valid prediction for snap_scaffold_14-snap.3096-T1
Valid prediction for snap_scaffold_14-snap.3117-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35201-T1
Valid prediction for snap_scaffold_14-snap.3118-T1
Valid prediction for snap_scaffold_14-snap.3085-T1
Valid prediction for GlimmerHMM_glimmerT_35222-T1
Valid prediction for GlimmerHMM_glimmerT_35196-T1
Valid prediction for Augustus_model.g23549.t1
Valid prediction for Augustus_model.g23551.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_35205-T1
Valid prediction for Augustus_model.g23550.t1
Valid prediction for GlimmerHMM_glimmerT_35209-T1
Valid prediction for GlimmerHMM_glimmerT_35198-T1
Valid prediction for GlimmerHMM_glimmerT_35194-T1
Valid prediction for Augustus_model.g23538.t1
Valid prediction for GlimmerHMM_glimmerT_35216-T1
Valid prediction for GlimmerHMM_glimmerT_35200-T1
Valid prediction for snap_scaffold_14-snap.3093-T1
Valid prediction for GlimmerHMM_glimmerT_35213-T1
Valid prediction for GlimmerHMM_glimmerT_35197-T1
Valid prediction for snap_scaffold_14-snap.3112-T1
Valid prediction for Augustus_model.g23541.t1
Valid prediction for GlimmerHMM_glimmerT_35211-T1
Valid prediction for GlimmerHMM_glimmerT_35199-T1
Valid prediction for snap_scaffold_14-snap.3091-T1
Valid prediction for Augustus_model.g23531.t1
Valid prediction for Augustus_model.g23534.t1
Valid prediction for snap_scaffold_14-snap.3109-T1
Valid prediction for snap_scaffold_14-snap.3087-T1
Valid prediction for snap_scaffold_14-snap.3072-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35215-T1
Valid prediction for snap_scaffold_14-snap.3089-T1
Valid prediction for GlimmerHMM_glimmerT_35202-T1
Valid prediction for snap_scaffold_14-snap.3103-T1
Valid prediction for snap_scaffold_14-snap.3098-T1
Valid prediction for snap_scaffold_14-snap.3111-T1
Couldn't classify 129098, 129403
Sorry, prediction pasa_asmbl_13702.p1 fails validation.
(ATG)	 GG	129098-129403	CG	CCC
Valid prediction for snap_scaffold_14-snap.3097-T1
Valid prediction for Augustus_model.g23543.t1
Valid prediction for GlimmerHMM_glimmerT_35204-T1
Valid prediction for snap_scaffold_14-snap.3107-T1
Valid prediction for snap_scaffold_14-snap.3100-T1
Valid prediction for snap_scaffold_14-snap.3075-T1
Valid prediction for snap_scaffold_14-snap.3083-T1
Couldn't classify 77685, 77770
Couldn't classify 79248, 79284
Sorry, prediction pasa_asmbl_13704.p1 fails validation.
(AGG)	 AC	77685-77770	GT	TAG
(TCC)	 AG	78493-78606	GT	AGG
(TGG)	 AG	78839-78967	GT	TCG
(GAT)	 AG	79248-79284	AA	GGA
-recovered pasa_asmbl_13704.p1, internal, 78493, 78606
-recovered pasa_asmbl_13704.p1, internal, 78839, 78967
Valid prediction for Augustus_model.g23545.t1
Valid prediction for Augustus_model.g23539.t1
Valid prediction for snap_scaffold_14-snap.3113-T1
Valid prediction for snap_scaffold_14-snap.3108-T1
Valid prediction for Augustus_model.g23536.t1
Valid prediction for snap_scaffold_14-snap.3079-T1
Valid prediction for GlimmerHMM_glimmerT_35214-T1
Valid prediction for Augustus_model.g23546.t1
Couldn't classify 47592, 47694
Couldn't classify 54056, 54147
Sorry, prediction pasa_asmbl_13706.p1 fails validation.
(TGC)	 AG	47592-47694	GT	GGG
(CCC)	 AG	50314-50544	GT	TGG
(CGT)	 AG	51032-51169	GT	AGG
(CCT)	 AG	54056-54147	CT	AGC
-recovered pasa_asmbl_13706.p1, internal, 47592, 47694
-recovered pasa_asmbl_13706.p1, internal, 50314, 50544
-recovered pasa_asmbl_13706.p1, internal, 51032, 51169
Valid prediction for GlimmerHMM_glimmerT_35219-T1
Valid prediction for GlimmerHMM_glimmerT_35220-T1
Valid prediction for Augustus_model.g23548.t1
Valid prediction for snap_scaffold_14-snap.3076-T1
Valid prediction for Augustus_model.g23544.t1
Valid prediction for GlimmerHMM_glimmerT_35195-T1
Valid prediction for pasa_asmbl_13705.p1
Valid prediction for GlimmerHMM_glimmerT_35217-T1
Valid prediction for GlimmerHMM_glimmerT_35223-T1
Valid prediction for snap_scaffold_14-snap.3094-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5502, rend_intergenic: 4889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14174, rend_intergenic: 6278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17881, rend_intergenic: 15140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26111, rend_intergenic: 21255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43382, rend_intergenic: 32763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62537, rend_intergenic: 43455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63662, rend_intergenic: 63401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81275, rend_intergenic: 64849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102621, rend_intergenic: 96730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126044, rend_intergenic: 110371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127330, rend_intergenic: 126184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139349, rend_intergenic: 131894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152798, rend_intergenic: 144655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159073, rend_intergenic: 152895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172777, rend_intergenic: 171337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184024, rend_intergenic: 173193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209787, rend_intergenic: 202077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225924, rend_intergenic: 210121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245209, rend_intergenic: 226321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261482
-exon list size: 451


building trellis

0.2    
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1.1    
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1.8    
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2.6    
2.9    
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3.8    
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4.6    
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17.9    
18.1    
18.3    
18.5    
18.8    
19.0    
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19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.6    
21.9    
22.1    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.6    
23.8    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.6    
53.9    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.5    
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70.0    
70.2    
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70.6    
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71.1    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
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75.9    
76.2    
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77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.4    
78.6    
78.8    
79.0    
79.2    
79.5    
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79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 5502, rend_intergenic: 4889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14174, rend_intergenic: 6278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17881, rend_intergenic: 15140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26111, rend_intergenic: 21255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43382, rend_intergenic: 32763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62537, rend_intergenic: 43455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63662, rend_intergenic: 63401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81275, rend_intergenic: 64849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102621, rend_intergenic: 96730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126044, rend_intergenic: 110371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127330, rend_intergenic: 126184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139349, rend_intergenic: 131894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152798, rend_intergenic: 144655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159073, rend_intergenic: 152895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172777, rend_intergenic: 171337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184024, rend_intergenic: 173193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209787, rend_intergenic: 202077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225924, rend_intergenic: 210121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245209, rend_intergenic: 226321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13410
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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