-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_15749097-15955572

-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.g7080.t1
Valid prediction for snap_scaffold_4-snap.3173-T1
Valid prediction for GlimmerHMM_glimmerT_10772-T1
Valid prediction for snap_scaffold_4-snap.3180-T1
Valid prediction for GlimmerHMM_glimmerT_10779-T1
Valid prediction for snap_scaffold_4-snap.3192-T1
Valid prediction for snap_scaffold_4-snap.3201-T1
Valid prediction for snap_scaffold_4-snap.3182-T1
Valid prediction for GlimmerHMM_glimmerT_10788-T1
Valid prediction for snap_scaffold_4-snap.3213-T1
Valid prediction for snap_scaffold_4-snap.3214-T1
Valid prediction for Augustus_model.g7074.t1
Valid prediction for snap_scaffold_4-snap.3175-T1
Valid prediction for snap_scaffold_4-snap.3174-T1
Valid prediction for Augustus_model.g7073.t1
Valid prediction for snap_scaffold_4-snap.3208-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3184-T1
Valid prediction for snap_scaffold_4-snap.3215-T1
Valid prediction for snap_scaffold_4-snap.3199-T1
Valid prediction for snap_scaffold_4-snap.3212-T1
Valid prediction for GlimmerHMM_glimmerT_10767-T1
Valid prediction for snap_scaffold_4-snap.3185-T1
Valid prediction for GlimmerHMM_glimmerT_10778-T1
Valid prediction for snap_scaffold_4-snap.3194-T1
Valid prediction for snap_scaffold_4-snap.3179-T1
Valid prediction for snap_scaffold_4-snap.3193-T1
Valid prediction for snap_scaffold_4-snap.3178-T1
Valid prediction for snap_scaffold_4-snap.3205-T1
Couldn't classify 172235, 172436
Couldn't classify 173136, 173177
Sorry, prediction pasa_asmbl_41955.p1 fails validation.
(GAA)	 TG	172235-172436	GT	TGG
(AGC)	 AG	172629-172792	GT	CTG
(GAG)	 AG	173136-173177	AA	GGA
-recovered pasa_asmbl_41955.p1, internal, 172629, 172792
Valid prediction for snap_scaffold_4-snap.3203-T1
Valid prediction for GlimmerHMM_glimmerT_10780-T1
Valid prediction for snap_scaffold_4-snap.3187-T1
Valid prediction for GlimmerHMM_glimmerT_10781-T1
Valid prediction for GlimmerHMM_glimmerT_10773-T1
Valid prediction for GlimmerHMM_glimmerT_10771-T1
Valid prediction for snap_scaffold_4-snap.3176-T1
Valid prediction for snap_scaffold_4-snap.3210-T1
Valid prediction for GlimmerHMM_glimmerT_10774-T1
Valid prediction for snap_scaffold_4-snap.3190-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: -)Couldn't classify 43155, 43192
Couldn't classify 44066, 44092
Sorry, prediction pasa_asmbl_43572.p1 fails validation.
(CCT)	 AC	43155-43192	GT	AGG
(TGC)	 AG	43479-43683	GT	AGG
(GTT)	 AG	43836-43931	GT	AGG
(GTG)	 AG	44066-44092	GC	AGG
-recovered pasa_asmbl_43572.p1, internal, 43479, 43683
-recovered pasa_asmbl_43572.p1, internal, 43836, 43931
-recovered pasa_asmbl_43572.p1, internal, 44066, 44092
Valid prediction for snap_scaffold_4-snap.3181-T1
Valid prediction for snap_scaffold_4-snap.3177-T1
Couldn't classify 57679, 57747
Couldn't classify 58427, 58519
Sorry, prediction pasa_asmbl_43125.p2 fails validation.
(TTC)	 CC	57679-57747	GT	AGG
(GTG)	 AG	57927-58112	GT	CGG
(AGA)	 AG	58427-58519	AG	ACA
-recovered pasa_asmbl_43125.p2, internal, 57927, 58112
Valid prediction for GlimmerHMM_glimmerT_10770-T1
Valid prediction for Augustus_model.g7076.t1
Valid prediction for Augustus_model.g7077.t1
Valid prediction for snap_scaffold_4-snap.3195-T1
Valid prediction for snap_scaffold_4-snap.3207-T1
Valid prediction for snap_scaffold_4-snap.3197-T1
Valid prediction for snap_scaffold_4-snap.3209-T1
Valid prediction for GlimmerHMM_glimmerT_10785-T1
Valid prediction for GlimmerHMM_glimmerT_10769-T1
Valid prediction for GlimmerHMM_glimmerT_10783-T1
Valid prediction for snap_scaffold_4-snap.3183-T1
Valid prediction for snap_scaffold_4-snap.3204-T1
Valid prediction for GlimmerHMM_glimmerT_10786-T1
Valid prediction for snap_scaffold_4-snap.3198-T1
Valid prediction for Augustus_model.g7079.t1
Couldn't classify 21338, 21578
Sorry, prediction pasa_asmbl_43128.p1 fails validation.
(CAC)	 CC	21338-21578	GT	TGG
(GGC)	 AG	21690-21961	GT	AGG
(GTG)	 AG	22088-22245	GT	AAG
(AGT)	 AG	22527-22678	GT	AGG
(ATC)	 AG	23092-23226	GT	AGG
(CGC)	 AG	23351-23509	GT	AGG
(CCC)	 AG	25626-25912	GG	GAG
-recovered pasa_asmbl_43128.p1, terminal, 25626, 25912
-recovered pasa_asmbl_43128.p1, internal, 21690, 21961
-recovered pasa_asmbl_43128.p1, internal, 22088, 22245
-recovered pasa_asmbl_43128.p1, internal, 22527, 22678
-recovered pasa_asmbl_43128.p1, internal, 23092, 23226
-recovered pasa_asmbl_43128.p1, internal, 23351, 23509
Valid prediction for snap_scaffold_4-snap.3196-T1
Couldn't classify 18402, 19170
Couldn't classify 20744, 20765
Sorry, prediction pasa_asmbl_43129.p1 fails validation.
(GGC)	 CG	18402-19170	GT	AGG
(TGC)	 AG	19543-19682	GT	AGG
(CTC)	 AG	19773-19930	GT	AGG
(GAT)	 AG	20744-20765	CC	CGC
-recovered pasa_asmbl_43129.p1, internal, 19543, 19682
-recovered pasa_asmbl_43129.p1, internal, 19773, 19930
Valid prediction for Augustus_model.g7081.t1
Valid prediction for snap_scaffold_4-snap.3188-T1
Valid prediction for Augustus_model.g7072.t1
Valid prediction for snap_scaffold_4-snap.3171-T1
Valid prediction for Augustus_model.g7070.t1
Valid prediction for snap_scaffold_4-snap.3211-T1
Valid prediction for Augustus_model.g7069.t1
Valid prediction for snap_scaffold_4-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_10784-T1
Valid prediction for snap_scaffold_4-snap.3206-T1
Valid prediction for snap_scaffold_4-snap.3167-T1
Valid prediction for GlimmerHMM_glimmerT_10777-T1
Valid prediction for snap_scaffold_4-snap.3172-T1
Couldn't classify 15932, 16021
Couldn't classify 17876, 17889
Sorry, prediction pasa_asmbl_43130.p1 fails validation.
(GAT)	 CT	15932-16021	GT	AGG
(AGG)	 AG	16533-16715	GT	AGG
(GTG)	 AG	16996-17128	GT	GGG
(AGC)	 AG	17266-17456	GT	AGG
(ATG)	 AG	17627-17765	GT	CGG
(AGG)	 AG	17876-17889	AG	CCA
-recovered pasa_asmbl_43130.p1, initial, 17627, 17765
-recovered pasa_asmbl_43130.p1, internal, 16533, 16715
-recovered pasa_asmbl_43130.p1, internal, 16996, 17128
-recovered pasa_asmbl_43130.p1, internal, 17266, 17456
-recovered pasa_asmbl_43130.p1, internal, 17627, 17765
Valid prediction for snap_scaffold_4-snap.3189-T1
Valid prediction for snap_scaffold_4-snap.3169-T1
Valid prediction for Augustus_model.g7078.t1
Couldn't classify 65241, 65555
Sorry, prediction pasa_asmbl_43124.p2 fails validation.
(TGC)	 AG	65241-65555	GA	GAG
Valid prediction for snap_scaffold_4-snap.3200-T1
Valid prediction for Augustus_model.g7068.t1
Valid prediction for GlimmerHMM_glimmerT_10768-T1
Valid prediction for snap_scaffold_4-snap.3170-T1
Valid prediction for GlimmerHMM_glimmerT_10789-T1
Valid prediction for GlimmerHMM_glimmerT_10775-T1
Valid prediction for Augustus_model.g7071.t1
Valid prediction for GlimmerHMM_glimmerT_10787-T1
Valid prediction for snap_scaffold_4-snap.3186-T1
Valid prediction for snap_scaffold_4-snap.3191-T1
Valid prediction for GlimmerHMM_glimmerT_10782-T1
Valid prediction for snap_scaffold_4-snap.3168-T1
Valid prediction for Augustus_model.g7075.t1
Valid prediction for GlimmerHMM_glimmerT_10776-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 71742, rend_intergenic: 62987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79588, rend_intergenic: 73666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96268, rend_intergenic: 87639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103850, rend_intergenic: 96510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107519, rend_intergenic: 103908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112145, rend_intergenic: 108640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116308, rend_intergenic: 113536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125624, rend_intergenic: 121285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131785, rend_intergenic: 129283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135370, rend_intergenic: 133340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141491, rend_intergenic: 140643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147497, rend_intergenic: 141871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154663, rend_intergenic: 152592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169177, rend_intergenic: 163823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192167, rend_intergenic: 181006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206476
-exon list size: 379


building trellis

0.3    
0.5    
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1.0    
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1.6    
1.8    
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3.7    
3.9    
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4.5    
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5.2    
5.5    
5.8    
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6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
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17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 71742, rend_intergenic: 62987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79588, rend_intergenic: 73666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96268, rend_intergenic: 87639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103850, rend_intergenic: 96510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107519, rend_intergenic: 103908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112145, rend_intergenic: 108640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116308, rend_intergenic: 113536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125624, rend_intergenic: 121285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131785, rend_intergenic: 129283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135370, rend_intergenic: 133340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141491, rend_intergenic: 140643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147497, rend_intergenic: 141871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154663, rend_intergenic: 152592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169177, rend_intergenic: 163823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192167, rend_intergenic: 181006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 192168 - 206476
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 192663 - 206476
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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