-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_16442544-16585150

-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.g3635.t1
Valid prediction for snap_scaffold_2-snap.3211-T1
Valid prediction for snap_scaffold_2-snap.3191-T1
Valid prediction for snap_scaffold_2-snap.3195-T1
Valid prediction for GeneMark_model.8578_t
Valid prediction for Augustus_model.g3637.t1
Valid prediction for Augustus_model.g3644.t1
Valid prediction for snap_scaffold_2-snap.3220-T1
Valid prediction for GeneMark_model.8599_t
Valid prediction for GlimmerHMM_glimmerT_5366-T1
Valid prediction for GeneMark_model.8580_t
Valid prediction for snap_scaffold_2-snap.3206-T1
Valid prediction for GeneMark_model.8561_t
Valid prediction for GeneMark_model.8571_t
Valid prediction for GeneMark_model.8557_t
Valid prediction for snap_scaffold_2-snap.3218-T1
Valid prediction for Augustus_model.g3642.t1
Valid prediction for GeneMark_model.8584_t
Valid prediction for GeneMark_model.8582_t
Valid prediction for GeneMark_model.8569_t
Valid prediction for GlimmerHMM_glimmerT_5358-T1
Valid prediction for snap_scaffold_2-snap.3192-T1
Valid prediction for Augustus_model.g3634.t1
Valid prediction for GlimmerHMM_glimmerT_5379-T1
Valid prediction for snap_scaffold_2-snap.3193-T1
Valid prediction for GlimmerHMM_glimmerT_5365-T1
Valid prediction for GlimmerHMM_glimmerT_5361-T1
Valid prediction for GeneMark_model.8567_t
Valid prediction for snap_scaffold_2-snap.3209-T1
Valid prediction for GeneMark_model.8577_t
Valid prediction for GeneMark_model.8593_t
Valid prediction for GeneMark_model.8600_t
Valid prediction for snap_scaffold_2-snap.3204-T1
Valid prediction for GeneMark_model.8574_t
Valid prediction for snap_scaffold_2-snap.3188-T1
Valid prediction for GeneMark_model.8559_t
Valid prediction for Augustus_model.g3641.t1
Valid prediction for GlimmerHMM_glimmerT_5378-T1
Valid prediction for GeneMark_model.8563_t
Valid prediction for GlimmerHMM_glimmerT_5368-T1
Valid prediction for GlimmerHMM_glimmerT_5370-T1
Valid prediction for GlimmerHMM_glimmerT_5360-T1
Valid prediction for GeneMark_model.8565_t
Valid prediction for GeneMark_model.8575_t
Valid prediction for GeneMark_model.8597_t
Valid prediction for GeneMark_model.8588_t
Valid prediction for GeneMark_model.8590_t
Valid prediction for GeneMark_model.8586_t
Valid prediction for snap_scaffold_2-snap.3196-T1
Valid prediction for Augustus_model.g3647.t1
Valid prediction for GeneMark_model.8595_t
Valid prediction for snap_scaffold_2-snap.3186-T1
Valid prediction for snap_scaffold_2-snap.3187-T1
Valid prediction for GlimmerHMM_glimmerT_5377-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.8576_t
Valid prediction for Augustus_model.g3648.t1
Valid prediction for GeneMark_model.8560_t
Valid prediction for GeneMark_model.8598_t
Valid prediction for GlimmerHMM_glimmerT_5375-T1
Valid prediction for Augustus_model.g3633.t1
Valid prediction for Augustus_model.g3640.t1
Valid prediction for GlimmerHMM_glimmerT_5369-T1
Valid prediction for GeneMark_model.8570_t
Valid prediction for GeneMark_model.8594_t
Couldn't classify 54156, 54281
Sorry, prediction pasa_asmbl_23714.p1 fails validation.
(GAG)	 CA	54156-54281	GT	TGG
(TAC)	 AG	55099-55173	GT	TGG
(CTG)	 AG	56715-56813	GT	CTG
(ATG)	 AG	57352-57525	GT	CGG
(GGC)	 AG	58235-58318	GT	AGG
(CTT)	 AG	58813-58890	GA	GAG
-recovered pasa_asmbl_23714.p1, initial, 57352, 57525
-recovered pasa_asmbl_23714.p1, terminal, 58813, 58890
-recovered pasa_asmbl_23714.p1, internal, 55099, 55173
-recovered pasa_asmbl_23714.p1, internal, 56715, 56813
-recovered pasa_asmbl_23714.p1, internal, 57352, 57525
-recovered pasa_asmbl_23714.p1, internal, 58235, 58318
Couldn't classify 108595, 108648
Sorry, prediction pasa_asmbl_23709.p1 fails validation.
(GAC)	 GC	108595-108648	GT	TTG
(TTG)	 AG	110404-110598	GT	TTG
(TTT)	 AG	111180-111254	GT	ACG
(CTG)	 AG	111381-111479	GT	CGG
(TTT)	 AG	111964-112140	GT	AGG
(GGT)	 AG	112926-113009	GT	AGG
(CTT)	 AG	113264-113311	AT	AGA
-recovered pasa_asmbl_23709.p1, terminal, 113264, 113311
-recovered pasa_asmbl_23709.p1, internal, 110404, 110598
-recovered pasa_asmbl_23709.p1, internal, 111180, 111254
-recovered pasa_asmbl_23709.p1, internal, 111381, 111479
-recovered pasa_asmbl_23709.p1, internal, 111964, 112140
-recovered pasa_asmbl_23709.p1, internal, 112926, 113009
Valid prediction for Augustus_model.g3639.t1
Valid prediction for GlimmerHMM_glimmerT_5364-T1
Valid prediction for GeneMark_model.8562_t
Valid prediction for snap_scaffold_2-snap.3203-T1
Valid prediction for snap_scaffold_2-snap.3213-T1
Valid prediction for GlimmerHMM_glimmerT_5380-T1
Valid prediction for GeneMark_model.8566_t
Valid prediction for snap_scaffold_2-snap.3198-T1
Valid prediction for snap_scaffold_2-snap.3219-T1
Valid prediction for GeneMark_model.8596_t
Valid prediction for GeneMark_model.8592_t
Valid prediction for snap_scaffold_2-snap.3189-T1
Valid prediction for GeneMark_model.8585_t
Valid prediction for snap_scaffold_2-snap.3216-T1
Valid prediction for snap_scaffold_2-snap.3207-T1
Valid prediction for snap_scaffold_2-snap.3214-T1
Valid prediction for GlimmerHMM_glimmerT_5372-T1
Valid prediction for GlimmerHMM_glimmerT_5367-T1
Valid prediction for snap_scaffold_2-snap.3200-T1
Valid prediction for snap_scaffold_2-snap.3215-T1
Valid prediction for GeneMark_model.8589_t
Valid prediction for snap_scaffold_2-snap.3201-T1
Valid prediction for Augustus_model.g3643.t1
Valid prediction for GeneMark_model.8581_t
Valid prediction for GlimmerHMM_glimmerT_5376-T1
Valid prediction for snap_scaffold_2-snap.3210-T1
Valid prediction for snap_scaffold_2-snap.3217-T1
Valid prediction for GeneMark_model.8587_t
Valid prediction for snap_scaffold_2-snap.3197-T1
Valid prediction for snap_scaffold_2-snap.3194-T1
Valid prediction for snap_scaffold_2-snap.3185-T1
Valid prediction for snap_scaffold_2-snap.3199-T1
Valid prediction for GeneMark_model.8564_t
Valid prediction for GeneMark_model.8572_t
Valid prediction for GlimmerHMM_glimmerT_5362-T1
Valid prediction for snap_scaffold_2-snap.3208-T1
Valid prediction for Augustus_model.g3638.t1
Valid prediction for GlimmerHMM_glimmerT_5373-T1
Valid prediction for Augustus_model.g3646.t1
Valid prediction for GlimmerHMM_glimmerT_5363-T1
Valid prediction for GeneMark_model.8601_t
Valid prediction for GeneMark_model.8558_t
Valid prediction for snap_scaffold_2-snap.3190-T1
Valid prediction for snap_scaffold_2-snap.3202-T1
Valid prediction for Augustus_model.g3645.t1
Valid prediction for GeneMark_model.8583_t
Valid prediction for GeneMark_model.8568_t
Valid prediction for snap_scaffold_2-snap.3212-T1
Valid prediction for GeneMark_model.8579_t
Valid prediction for snap_scaffold_2-snap.3205-T1
Valid prediction for Augustus_model.g3636.t1
Valid prediction for GlimmerHMM_glimmerT_5374-T1
Valid prediction for GlimmerHMM_glimmerT_5359-T1
Valid prediction for GlimmerHMM_glimmerT_5371-T1
Valid prediction for GeneMark_model.8573_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14758, rend_intergenic: 10027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35695, rend_intergenic: 29862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42467, rend_intergenic: 38517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68550, rend_intergenic: 66082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71873, rend_intergenic: 68604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78691, rend_intergenic: 72736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81373, rend_intergenic: 78982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90404, rend_intergenic: 85099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96776, rend_intergenic: 94272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137198, rend_intergenic: 134036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138571, rend_intergenic: 137587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141405, rend_intergenic: 139174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142607
-exon list size: 584


building trellis

0.2    
0.3    
0.5    
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0.9    
1.0    
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1.7    
1.9    
2.0    
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2.4    
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2.9    
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3.2    
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3.6    
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3.9    
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6.7    
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8.0    
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14.5    
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16.9    
17.1    
17.2    
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17.6    
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17.9    
18.1    
18.3    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.5    
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20.0    
20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
21.2    
21.3    
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21.7    
21.8    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.5    
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23.9    
24.1    
24.2    
24.4    
24.6    
24.7    
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25.1    
25.3    
25.4    
25.6    
25.8    
25.9    
26.1    
26.3    
26.5    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.3    
32.4    
32.6    
32.8    
32.9    
33.1    
33.3    
33.4    
33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.8    
39.9    
40.1    
40.3    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.6    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.4    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 14758, rend_intergenic: 10027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35695, rend_intergenic: 29862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42467, rend_intergenic: 38517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68550, rend_intergenic: 66082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71873, rend_intergenic: 68604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78691, rend_intergenic: 72736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81373, rend_intergenic: 78982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90404, rend_intergenic: 85099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96776, rend_intergenic: 94272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137198, rend_intergenic: 134036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138571, rend_intergenic: 137587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141405, rend_intergenic: 139174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support