-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_3432751-3657061

-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_6281-T1
Valid prediction for snap_scaffold_3-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_6278-T1
Valid prediction for Augustus_model.g4082.t1
Valid prediction for snap_scaffold_3-snap.756-T1
Valid prediction for snap_scaffold_3-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_6286-T1
Valid prediction for snap_scaffold_3-snap.755-T1
Valid prediction for snap_scaffold_3-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_6294-T1
Valid prediction for snap_scaffold_3-snap.762-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.758-T1
Valid prediction for snap_scaffold_3-snap.768-T1
Valid prediction for snap_scaffold_3-snap.773-T1
Valid prediction for snap_scaffold_3-snap.759-T1
Valid prediction for Augustus_model.g4087.t1
Valid prediction for snap_scaffold_3-snap.764-T1
Valid prediction for GlimmerHMM_glimmerT_6284-T1
Valid prediction for snap_scaffold_3-snap.752-T1
Valid prediction for snap_scaffold_3-snap.780-T1
Valid prediction for CodingQuarry_transcript_46117-T1
Valid prediction for pasa_asmbl_38780.p1
Valid prediction for snap_scaffold_3-snap.777-T1
Valid prediction for snap_scaffold_3-snap.778-T1
Valid prediction for Augustus_model.g4081.t1
Couldn't classify 120324, 120329
Couldn't classify 122921, 122953
Sorry, prediction pasa_asmbl_39953.p1 fails validation.
(CAG)	 AC	120324-120329	GT	GGG
(GGC)	 AG	120460-120580	GT	GGG
(TCC)	 AG	120677-120976	GT	AGG
(GAG)	 AG	121381-121461	GT	GGG
(GTG)	 AG	122538-122728	GT	TGG
(CTG)	 AG	122921-122953	CA	ACC
add_exon() Sorry, pasa_asmbl_39953.p1 120677-120976-terminal-1 is invalid.
-recovered pasa_asmbl_39953.p1, terminal, 120677, 120976
-recovered pasa_asmbl_39953.p1, internal, 120460, 120580
-recovered pasa_asmbl_39953.p1, internal, 120677, 120976
-recovered pasa_asmbl_39953.p1, internal, 121381, 121461
-recovered pasa_asmbl_39953.p1, internal, 122538, 122728
Valid prediction for snap_scaffold_3-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_6295-T1
Valid prediction for GlimmerHMM_glimmerT_6291-T1
Valid prediction for GlimmerHMM_glimmerT_6297-T1
Valid prediction for GlimmerHMM_glimmerT_6288-T1
Valid prediction for snap_scaffold_3-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_6289-T1
Valid prediction for GlimmerHMM_glimmerT_6298-T1
Valid prediction for snap_scaffold_3-snap.760-T1
Valid prediction for snap_scaffold_3-snap.749-T1
Couldn't classify 115499, 116083
Couldn't classify 116389, 116490
Sorry, prediction pasa_asmbl_39952.p1 fails validation.
(GAC)	 AT	115499-116083	GT	AGG
(TGT)	 AG	116389-116490	AT	AGA
Valid prediction for snap_scaffold_3-snap.771-T1
Valid prediction for GlimmerHMM_glimmerT_6280-T1
Valid prediction for snap_scaffold_3-snap.783-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_6299-T1
Valid prediction for Augustus_model.g4088.t1
Valid prediction for GlimmerHMM_glimmerT_6296-T1
Valid prediction for GlimmerHMM_glimmerT_6293-T1
Valid prediction for snap_scaffold_3-snap.754-T1
Valid prediction for Augustus_model.g4083.t1
Valid prediction for snap_scaffold_3-snap.776-T1
Valid prediction for snap_scaffold_3-snap.785-T1
Valid prediction for snap_scaffold_3-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_6290-T1
Valid prediction for GlimmerHMM_glimmerT_6282-T1
Valid prediction for snap_scaffold_3-snap.784-T1
Valid prediction for snap_scaffold_3-snap.782-T1
Valid prediction for Augustus_model.g4084.t1
Valid prediction for snap_scaffold_3-snap.775-T1
Valid prediction for GlimmerHMM_glimmerT_6279-T1
Valid prediction for GlimmerHMM_glimmerT_6292-T1
Valid prediction for snap_scaffold_3-snap.781-T1
Valid prediction for snap_scaffold_3-snap.763-T1
Valid prediction for Augustus_model.g4085.t1
Valid prediction for GlimmerHMM_glimmerT_6285-T1
Valid prediction for snap_scaffold_3-snap.779-T1
Valid prediction for Augustus_model.g4089.t1
Valid prediction for snap_scaffold_3-snap.772-T1
Valid prediction for snap_scaffold_3-snap.787-T1
Valid prediction for Augustus_model.g4086.t1
Valid prediction for snap_scaffold_3-snap.774-T1
Valid prediction for GlimmerHMM_glimmerT_6283-T1
Valid prediction for snap_scaffold_3-snap.786-T1
Valid prediction for snap_scaffold_3-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_6287-T1
Valid prediction for pasa_asmbl_39771.p1
Valid prediction for GlimmerHMM_glimmerT_6277-T1
Valid prediction for snap_scaffold_3-snap.769-T1
Valid prediction for snap_scaffold_3-snap.750-T1
Valid prediction for snap_scaffold_3-snap.751-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5758, rend_intergenic: 3006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11302, rend_intergenic: 8774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98092, rend_intergenic: 92163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120852, rend_intergenic: 114201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131536, rend_intergenic: 128347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152796, rend_intergenic: 137148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173981, rend_intergenic: 163218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181610, rend_intergenic: 176587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 218823, rend_intergenic: 218820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224311
-exon list size: 330


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 5758, rend_intergenic: 3006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11302, rend_intergenic: 8774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98092, rend_intergenic: 92163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120852, rend_intergenic: 114201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131536, rend_intergenic: 128347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152796, rend_intergenic: 137148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173981, rend_intergenic: 163218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181610, rend_intergenic: 176587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 218823, rend_intergenic: 218820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support