-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_3258792-3422765

-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_21-snap.636-T1
Valid prediction for GlimmerHMM_glimmerT_47390-T1
Valid prediction for snap_scaffold_21-snap.618-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g31570.t1
Valid prediction for snap_scaffold_21-snap.612-T1
Couldn't classify 65091, 65456
Sorry, prediction pasa_asmbl_28485.p1 fails validation.
(CCC)	 TA	65091-65456	CC	CGC
Valid prediction for snap_scaffold_21-snap.637-T1
Valid prediction for snap_scaffold_21-snap.633-T1
Valid prediction for GlimmerHMM_glimmerT_47371-T1
Valid prediction for Augustus_model.g31577.t1
Valid prediction for snap_scaffold_21-snap.609-T1
Valid prediction for snap_scaffold_21-snap.607-T1
Valid prediction for snap_scaffold_21-snap.615-T1
Valid prediction for Augustus_model.g31576.t1
Valid prediction for Augustus_model.g31560.t1
Couldn't classify 54787, 54835
Couldn't classify 61785, 61850
Sorry, prediction pasa_asmbl_28484.p1 fails validation.
(ATC)	 AG	54787-54835	GT	AGG
(AGC)	 AG	55702-55851	GT	GGG
(CTG)	 AG	57537-57609	GT	TGG
(GAT)	 AG	58308-58502	GT	TGG
(GTC)	 AG	59302-59383	GT	AGG
(CAC)	 AG	61785-61850	GA	CTG
add_exon() Sorry, pasa_asmbl_28484.p1 54787-54835-terminal-3 is invalid.
-recovered pasa_asmbl_28484.p1, terminal, 54787, 54835
-recovered pasa_asmbl_28484.p1, internal, 54787, 54835
-recovered pasa_asmbl_28484.p1, internal, 55702, 55851
-recovered pasa_asmbl_28484.p1, internal, 57537, 57609
-recovered pasa_asmbl_28484.p1, internal, 58308, 58502
-recovered pasa_asmbl_28484.p1, internal, 59302, 59383
Valid prediction for GlimmerHMM_glimmerT_47374-T1
Valid prediction for GlimmerHMM_glimmerT_47377-T1
Valid prediction for GlimmerHMM_glimmerT_47387-T1
Valid prediction for Augustus_model.g31575.t1
Valid prediction for Augustus_model.g31565.t1
Valid prediction for snap_scaffold_21-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_47385-T1
Valid prediction for Augustus_model.g31569.t1
Valid prediction for snap_scaffold_21-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_47378-T1
Couldn't classify 68999, 69132
Couldn't classify 70916, 71044
Sorry, prediction pasa_asmbl_28486.p1 fails validation.
(CAG)	 TT	68999-69132	GC	AGG
(GCG)	 AG	69727-69850	GT	ACG
(AAT)	 AG	70300-70479	GT	AGG
(GTC)	 AG	70681-70773	GT	AGG
(GAG)	 AG	70916-71044	GG	GAG
-recovered pasa_asmbl_28486.p1, internal, 69727, 69850
-recovered pasa_asmbl_28486.p1, internal, 70300, 70479
-recovered pasa_asmbl_28486.p1, internal, 70681, 70773
Valid prediction for GlimmerHMM_glimmerT_47369-T1
Valid prediction for snap_scaffold_21-snap.639-T1
Valid prediction for GlimmerHMM_glimmerT_47384-T1
Valid prediction for snap_scaffold_21-snap.632-T1
Valid prediction for snap_scaffold_21-snap.631-T1
Valid prediction for snap_scaffold_21-snap.641-T1
Valid prediction for snap_scaffold_21-snap.605-T1
Valid prediction for Augustus_model.g31568.t1
Valid prediction for Augustus_model.g31579.t1
Valid prediction for snap_scaffold_21-snap.627-T1
Valid prediction for snap_scaffold_21-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_47383-T1
Valid prediction for snap_scaffold_21-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_47392-T1
Valid prediction for GlimmerHMM_glimmerT_47388-T1
Valid prediction for GlimmerHMM_glimmerT_47391-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 Augustus_model.g31563.t1
Valid prediction for Augustus_model.g31564.t1
Valid prediction for Augustus_model.g31566.t1
Valid prediction for Augustus_model.g31578.t1
Valid prediction for snap_scaffold_21-snap.644-T1
Valid prediction for snap_scaffold_21-snap.608-T1
Valid prediction for snap_scaffold_21-snap.625-T1
Valid prediction for snap_scaffold_21-snap.629-T1
Valid prediction for snap_scaffold_21-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_47380-T1
Valid prediction for snap_scaffold_21-snap.611-T1
Valid prediction for snap_scaffold_21-snap.630-T1
Valid prediction for snap_scaffold_21-snap.623-T1
Valid prediction for GlimmerHMM_glimmerT_47379-T1
Couldn't classify 82961, 83066
Couldn't classify 85556, 85602
Sorry, prediction pasa_asmbl_28233.p1 fails validation.
(CTG)	 TG	82961-83066	GT	AGG
(GAT)	 AG	83211-83312	GT	AGG
(AGG)	 AG	84722-84839	GT	AGG
(GTA)	 AG	85030-85241	GT	CAG
(AAG)	 AG	85556-85602	GT	TTG
-recovered pasa_asmbl_28233.p1, internal, 83211, 83312
-recovered pasa_asmbl_28233.p1, internal, 84722, 84839
-recovered pasa_asmbl_28233.p1, internal, 85030, 85241
-recovered pasa_asmbl_28233.p1, internal, 85556, 85602
Valid prediction for Augustus_model.g31561.t1
Valid prediction for Augustus_model.g31574.t1
Valid prediction for Augustus_model.g31562.t1
Valid prediction for GlimmerHMM_glimmerT_47375-T1
Valid prediction for snap_scaffold_21-snap.617-T1
Valid prediction for snap_scaffold_21-snap.622-T1
Couldn't classify 87229, 87660
Sorry, prediction pasa_asmbl_27524.p2 fails validation.
(CCC)	 AC	87229-87660	TT	AGT
Valid prediction for GlimmerHMM_glimmerT_47373-T1
Valid prediction for GlimmerHMM_glimmerT_47381-T1
Valid prediction for snap_scaffold_21-snap.638-T1
Valid prediction for Augustus_model.g31571.t1
Valid prediction for snap_scaffold_21-snap.610-T1
Valid prediction for snap_scaffold_21-snap.640-T1
Couldn't classify 86593, 86907
Sorry, prediction pasa_asmbl_27525.p1 fails validation.
(AGC)	 TC	86593-86907	AG	TGA
Valid prediction for snap_scaffold_21-snap.621-T1
Valid prediction for snap_scaffold_21-snap.603-T1
Valid prediction for snap_scaffold_21-snap.642-T1
Valid prediction for snap_scaffold_21-snap.634-T1
Valid prediction for snap_scaffold_21-snap.619-T1
Valid prediction for snap_scaffold_21-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_47372-T1
Valid prediction for GlimmerHMM_glimmerT_47382-T1
Valid prediction for GlimmerHMM_glimmerT_47376-T1
Valid prediction for Augustus_model.g31573.t1
Valid prediction for GlimmerHMM_glimmerT_47389-T1
Valid prediction for snap_scaffold_21-snap.626-T1
Valid prediction for snap_scaffold_21-snap.635-T1
Valid prediction for snap_scaffold_21-snap.620-T1
Valid prediction for snap_scaffold_21-snap.616-T1
Valid prediction for snap_scaffold_21-snap.613-T1
Valid prediction for snap_scaffold_21-snap.628-T1
Valid prediction for Augustus_model.g31567.t1
Valid prediction for Augustus_model.g31572.t1
Valid prediction for GlimmerHMM_glimmerT_47386-T1
Valid prediction for GlimmerHMM_glimmerT_47370-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16816, rend_intergenic: 5494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20539, rend_intergenic: 17102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22943, rend_intergenic: 21329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27320, rend_intergenic: 23584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52422, rend_intergenic: 46961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56331, rend_intergenic: 52826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72543, rend_intergenic: 61637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93015, rend_intergenic: 90927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101256, rend_intergenic: 100693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117616, rend_intergenic: 110595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120352, rend_intergenic: 117994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125070, rend_intergenic: 124318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127668, rend_intergenic: 126140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141949, rend_intergenic: 136472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163974
-exon list size: 357


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 16816, rend_intergenic: 5494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20539, rend_intergenic: 17102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22943, rend_intergenic: 21329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27320, rend_intergenic: 23584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52422, rend_intergenic: 46961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56331, rend_intergenic: 52826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72543, rend_intergenic: 61637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93015, rend_intergenic: 90927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101256, rend_intergenic: 100693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117616, rend_intergenic: 110595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120352, rend_intergenic: 117994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125070, rend_intergenic: 124318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127668, rend_intergenic: 126140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141949, rend_intergenic: 136472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support