-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_16593831-16793159

-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_5253-T1
Valid prediction for snap_scaffold_2-snap.3193-T1
Valid prediction for snap_scaffold_2-snap.3205-T1
Valid prediction for Augustus_model.g3557.t1
Valid prediction for Augustus_model.g3570.t1
Valid prediction for snap_scaffold_2-snap.3209-T1
Valid prediction for snap_scaffold_2-snap.3217-T1
Valid prediction for snap_scaffold_2-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_5282-T1
Valid prediction for GlimmerHMM_glimmerT_5256-T1
Valid prediction for snap_scaffold_2-snap.3216-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3190-T1
Valid prediction for GlimmerHMM_glimmerT_5280-T1
Valid prediction for Augustus_model.g3562.t1
Valid prediction for GlimmerHMM_glimmerT_5250-T1
Valid prediction for GlimmerHMM_glimmerT_5284-T1
Valid prediction for snap_scaffold_2-snap.3207-T1
Valid prediction for GlimmerHMM_glimmerT_5265-T1
Valid prediction for GlimmerHMM_glimmerT_5258-T1
Valid prediction for Augustus_model.g3565.t1
Valid prediction for snap_scaffold_2-snap.3195-T1
Valid prediction for Augustus_model.g3559.t1
Valid prediction for Augustus_model.g3567.t1
Valid prediction for Augustus_model.g3566.t1
Valid prediction for GlimmerHMM_glimmerT_5270-T1
Valid prediction for GlimmerHMM_glimmerT_5263-T1
Valid prediction for snap_scaffold_2-snap.3211-T1
Valid prediction for GlimmerHMM_glimmerT_5272-T1
Valid prediction for CodingQuarry_transcript_28802-T1
Valid prediction for GlimmerHMM_glimmerT_5260-T1
Valid prediction for GlimmerHMM_glimmerT_5254-T1
Valid prediction for snap_scaffold_2-snap.3199-T1
Valid prediction for Augustus_model.g3560.t1
Valid prediction for snap_scaffold_2-snap.3203-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5278-T1
Valid prediction for GlimmerHMM_glimmerT_5279-T1
Valid prediction for GlimmerHMM_glimmerT_5275-T1
Valid prediction for GlimmerHMM_glimmerT_5276-T1
Couldn't classify 133653, 133725
Couldn't classify 135656, 135810
Sorry, prediction pasa_asmbl_25429.p1 fails validation.
(GAC)	 AA	133653-133725	GT	AGG
(GCG)	 AG	133847-134089	GT	CGG
(AGG)	 AG	134223-134398	GT	AGG
(ATT)	 AG	134554-134627	GT	AGG
(GTC)	 AG	134752-134913	GT	GGG
(AGC)	 AG	135354-135511	GT	AGG
(GGG)	 AG	135656-135810	CT	CGC
-recovered pasa_asmbl_25429.p1, internal, 133847, 134089
-recovered pasa_asmbl_25429.p1, internal, 134223, 134398
-recovered pasa_asmbl_25429.p1, internal, 134554, 134627
-recovered pasa_asmbl_25429.p1, internal, 134752, 134913
-recovered pasa_asmbl_25429.p1, internal, 135354, 135511
Valid prediction for snap_scaffold_2-snap.3222-T1
Valid prediction for snap_scaffold_2-snap.3210-T1
Valid prediction for snap_scaffold_2-snap.3220-T1
Valid prediction for GlimmerHMM_glimmerT_5259-T1
Valid prediction for Augustus_model.g3564.t1
Valid prediction for GlimmerHMM_glimmerT_5257-T1
Valid prediction for GlimmerHMM_glimmerT_5262-T1
Valid prediction for snap_scaffold_2-snap.3196-T1
Valid prediction for GlimmerHMM_glimmerT_5264-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_5281-T1
Valid prediction for snap_scaffold_2-snap.3215-T1
Valid prediction for Augustus_model.g3568.t1
Valid prediction for snap_scaffold_2-snap.3206-T1
Valid prediction for snap_scaffold_2-snap.3194-T1
Valid prediction for HiQ_model.g3569.t1
Valid prediction for GlimmerHMM_glimmerT_5277-T1
Valid prediction for snap_scaffold_2-snap.3189-T1
Valid prediction for Augustus_model.g3571.t1
Valid prediction for Augustus_model.g3572.t1
Valid prediction for snap_scaffold_2-snap.3218-T1
Valid prediction for snap_scaffold_2-snap.3201-T1
Valid prediction for snap_scaffold_2-snap.3204-T1
Valid prediction for snap_scaffold_2-snap.3208-T1
Couldn't classify 54483, 54517
Sorry, prediction pasa_asmbl_24018.p1 fails validation.
(ATT)	 TG	54483-54517	GT	AGG
(TGT)	 AG	54744-55170	AT	AGA
-recovered pasa_asmbl_24018.p1, terminal, 54744, 55170
Valid prediction for snap_scaffold_2-snap.3224-T1
Valid prediction for snap_scaffold_2-snap.3225-T1
Valid prediction for GlimmerHMM_glimmerT_5274-T1
Valid prediction for Augustus_model.g3556.t1
Valid prediction for snap_scaffold_2-snap.3213-T1
Valid prediction for snap_scaffold_2-snap.3221-T1
Valid prediction for GlimmerHMM_glimmerT_5266-T1
Valid prediction for GlimmerHMM_glimmerT_5252-T1
Valid prediction for snap_scaffold_2-snap.3192-T1
Valid prediction for Augustus_model.g3561.t1
Valid prediction for GlimmerHMM_glimmerT_5251-T1
Valid prediction for Augustus_model.g3563.t1
Valid prediction for snap_scaffold_2-snap.3197-T1
Valid prediction for snap_scaffold_2-snap.3212-T1
Valid prediction for GlimmerHMM_glimmerT_5255-T1
Valid prediction for snap_scaffold_2-snap.3198-T1
Valid prediction for Augustus_model.g3558.t1
Valid prediction for GlimmerHMM_glimmerT_5269-T1
Valid prediction for GlimmerHMM_glimmerT_5283-T1
Valid prediction for GlimmerHMM_glimmerT_5268-T1
Valid prediction for GlimmerHMM_glimmerT_5271-T1
Valid prediction for GlimmerHMM_glimmerT_5267-T1
Valid prediction for snap_scaffold_2-snap.3219-T1
Valid prediction for GlimmerHMM_glimmerT_5261-T1
Valid prediction for snap_scaffold_2-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_5273-T1
Valid prediction for snap_scaffold_2-snap.3191-T1
Valid prediction for snap_scaffold_2-snap.3200-T1
Valid prediction for snap_scaffold_2-snap.3214-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9872, rend_intergenic: 5199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17091, rend_intergenic: 15056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20469, rend_intergenic: 17185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24935, rend_intergenic: 20624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40191, rend_intergenic: 26969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41987, rend_intergenic: 41274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45618, rend_intergenic: 42121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67610, rend_intergenic: 49596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72761, rend_intergenic: 70765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79580, rend_intergenic: 73032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79644, rend_intergenic: 79601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96148, rend_intergenic: 79829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116167, rend_intergenic: 96183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140627, rend_intergenic: 116939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143862, rend_intergenic: 141008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160325, rend_intergenic: 146593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164385, rend_intergenic: 162369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172664, rend_intergenic: 164697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199329
-exon list size: 508


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 9872, rend_intergenic: 5199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17091, rend_intergenic: 15056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20469, rend_intergenic: 17185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24935, rend_intergenic: 20624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40191, rend_intergenic: 26969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41987, rend_intergenic: 41274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45618, rend_intergenic: 42121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67610, rend_intergenic: 49596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72761, rend_intergenic: 70765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79580, rend_intergenic: 73032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79644, rend_intergenic: 79601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96148, rend_intergenic: 79829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116167, rend_intergenic: 96183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140627, rend_intergenic: 116939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143862, rend_intergenic: 141008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160325, rend_intergenic: 146593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164385, rend_intergenic: 162369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172664, rend_intergenic: 164697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 186998 - 199329
-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

-building DP trellis

-building trellis in range 186998 - 198826
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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