-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_15328440-15582910

-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.g19344.t1
Valid prediction for snap_scaffold_11-snap.3146-T1
Valid prediction for GeneMark_model.50002_t
Valid prediction for GeneMark_model.49987_t
Valid prediction for GeneMark_model.49998_t
Valid prediction for GeneMark_model.49978_t
Valid prediction for GlimmerHMM_glimmerT_28974-T1
Couldn't classify 249118, 249341
Couldn't classify 250950, 251028
Sorry, prediction pasa_asmbl_6224.p1 fails validation.
(CCG)	 AG	249118-249341	GT	AGG
(GAA)	 AG	249882-249953	GT	TGG
(CAG)	 AG	250950-251028	GG	CAG
-recovered pasa_asmbl_6224.p1, internal, 249118, 249341
-recovered pasa_asmbl_6224.p1, internal, 249882, 249953
Valid prediction for GeneMark_model.49989_t
Valid prediction for snap_scaffold_11-snap.3170-T1
Valid prediction for Augustus_model.g19343.t1
Valid prediction for GlimmerHMM_glimmerT_28971-T1
Valid prediction for GlimmerHMM_glimmerT_28970-T1
Valid prediction for snap_scaffold_11-snap.3165-T1
Valid prediction for GeneMark_model.49980_t
Valid prediction for GeneMark_model.50000_t
Valid prediction for GlimmerHMM_glimmerT_28960-T1
Valid prediction for GeneMark_model.49976_t
Valid prediction for Augustus_model.g19335.t1
Valid prediction for GlimmerHMM_glimmerT_28961-T1
Valid prediction for GlimmerHMM_glimmerT_28962-T1
Valid prediction for GlimmerHMM_glimmerT_28959-T1
Valid prediction for GeneMark_model.49975_t
Valid prediction for snap_scaffold_11-snap.3157-T1
Valid prediction for snap_scaffold_11-snap.3147-T1
Valid prediction for GlimmerHMM_glimmerT_28958-T1
Valid prediction for GlimmerHMM_glimmerT_28954-T1
Valid prediction for GlimmerHMM_glimmerT_28972-T1
Valid prediction for GeneMark_model.49994_t
Valid prediction for snap_scaffold_11-snap.3152-T1
Valid prediction for snap_scaffold_11-snap.3153-T1
Valid prediction for Augustus_model.g19337.t1
Valid prediction for snap_scaffold_11-snap.3156-T1
Valid prediction for GlimmerHMM_glimmerT_28955-T1
Valid prediction for GlimmerHMM_glimmerT_28973-T1
Valid prediction for GeneMark_model.49996_t
Valid prediction for snap_scaffold_11-snap.3167-T1
Valid prediction for Augustus_model.g19341.t1
Valid prediction for snap_scaffold_11-snap.3160-T1
Valid prediction for GlimmerHMM_glimmerT_28965-T1
Valid prediction for Augustus_model.g19345.t1
Valid prediction for GeneMark_model.49973_t
Valid prediction for GeneMark_model.50004_t
Valid prediction for GlimmerHMM_glimmerT_28969-T1
Valid prediction for Augustus_model.g19336.t1
Valid prediction for GlimmerHMM_glimmerT_28964-T1
Valid prediction for GlimmerHMM_glimmerT_28952-T1
Valid prediction for GeneMark_model.49982_t
Valid prediction for snap_scaffold_11-snap.3154-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_28956-T1
Valid prediction for GeneMark_model.49995_t
Valid prediction for Augustus_model.g19334.t1
Valid prediction for GlimmerHMM_glimmerT_28957-T1
Valid prediction for snap_scaffold_11-snap.3148-T1
Valid prediction for GlimmerHMM_glimmerT_28968-T1
Valid prediction for snap_scaffold_11-snap.3145-T1
Valid prediction for GlimmerHMM_glimmerT_28953-T1
Valid prediction for snap_scaffold_11-snap.3163-T1
Valid prediction for GeneMark_model.49981_t
Valid prediction for snap_scaffold_11-snap.3168-T1
Valid prediction for Augustus_model.g19340.t1
Valid prediction for GeneMark_model.50003_t
Valid prediction for GeneMark_model.49983_t
Valid prediction for Augustus_model.g19342.t1
Valid prediction for snap_scaffold_11-snap.3149-T1
Valid prediction for GeneMark_model.49993_t
Valid prediction for GeneMark_model.49984_t
Valid prediction for snap_scaffold_11-snap.3155-T1
Valid prediction for GeneMark_model.50005_t
Valid prediction for GlimmerHMM_glimmerT_28963-T1
Valid prediction for GeneMark_model.49979_t
Valid prediction for GeneMark_model.49977_t
Valid prediction for snap_scaffold_11-snap.3166-T1
Valid prediction for GeneMark_model.50001_t
Valid prediction for GeneMark_model.49985_t
Valid prediction for GeneMark_model.49997_t
Valid prediction for GeneMark_model.49992_t
Valid prediction for GeneMark_model.49990_t
Valid prediction for GeneMark_model.49988_t
Valid prediction for GlimmerHMM_glimmerT_28951-T1
Valid prediction for GeneMark_model.49999_t
Valid prediction for GlimmerHMM_glimmerT_28967-T1
Valid prediction for snap_scaffold_11-snap.3158-T1
Valid prediction for snap_scaffold_11-snap.3164-T1
Valid prediction for GeneMark_model.49986_t
Valid prediction for snap_scaffold_11-snap.3161-T1
Valid prediction for snap_scaffold_11-snap.3169-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g19338.t1
Valid prediction for snap_scaffold_11-snap.3150-T1
Valid prediction for GeneMark_model.49991_t
Valid prediction for snap_scaffold_11-snap.3159-T1
Valid prediction for Augustus_model.g19339.t1
Valid prediction for GlimmerHMM_glimmerT_28966-T1
Valid prediction for snap_scaffold_11-snap.3151-T1
Valid prediction for snap_scaffold_11-snap.3162-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 172312, rend_intergenic: 170309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180974, rend_intergenic: 180063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220251, rend_intergenic: 206528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224541, rend_intergenic: 220583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227144, rend_intergenic: 225336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244311, rend_intergenic: 232311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247201, rend_intergenic: 245126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254471
-exon list size: 404


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 172312, rend_intergenic: 170309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180974, rend_intergenic: 180063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220251, rend_intergenic: 206528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224541, rend_intergenic: 220583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227144, rend_intergenic: 225336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244311, rend_intergenic: 232311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247201, rend_intergenic: 245126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 38922
-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
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 1 - 38861
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 1 - 38298
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 1 - 21470
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 15336

-building DP trellis

-building trellis in range 21507 - 38298
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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