-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_2478668-2750332

-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_28982-T1
Valid prediction for GlimmerHMM_glimmerT_28977-T1
Valid prediction for snap_scaffold_12-snap.542-T1
Valid prediction for Augustus_model.g19121.t1
Valid prediction for Augustus_model.g19120.t1
Valid prediction for GlimmerHMM_glimmerT_28978-T1
Valid prediction for Augustus_model.g19130.t1
Valid prediction for GlimmerHMM_glimmerT_28976-T1
Valid prediction for HiQ_model.g19122.t1
Couldn't classify 179427, 179628
Sorry, prediction pasa_asmbl_7505.p1 fails validation.
(GGC)	 AG	179427-179628	GT	AGG
(ATC)	 AG	181001-181131	GT	AGG
(CTG)	 AG	182923-183041	GT	CGG
(AGC)	 AG	183771-184032	TT	AAT
-recovered pasa_asmbl_7505.p1, terminal, 183771, 184032
-recovered pasa_asmbl_7505.p1, internal, 179427, 179628
-recovered pasa_asmbl_7505.p1, internal, 181001, 181131
-recovered pasa_asmbl_7505.p1, internal, 182923, 183041
Valid prediction for snap_scaffold_12-snap.539-T1
Valid prediction for snap_scaffold_12-snap.520-T1
Valid prediction for snap_scaffold_12-snap.547-T1
Valid prediction for snap_scaffold_12-snap.536-T1
Valid prediction for snap_scaffold_12-snap.540-T1
Valid prediction for HiQ_model.g19124.t1
Valid prediction for GlimmerHMM_glimmerT_28970-T1
Valid prediction for GlimmerHMM_glimmerT_28984-T1
Valid prediction for Augustus_model.g19126.t1
Valid prediction for snap_scaffold_12-snap.545-T1
Valid prediction for snap_scaffold_12-snap.538-T1
Valid prediction for snap_scaffold_12-snap.553-T1
Valid prediction for Augustus_model.g19129.t1
Valid prediction for snap_scaffold_12-snap.531-T1
Valid prediction for snap_scaffold_12-snap.557-T1
Valid prediction for snap_scaffold_12-snap.535-T1
Couldn't classify 185261, 185701
Sorry, prediction pasa_asmbl_7510.p1 fails validation.
(TCC)	 CC	185261-185701	TG	GAT
Valid prediction for Augustus_model.g19125.t1
Valid prediction for GlimmerHMM_glimmerT_28983-T1
Valid prediction for pasa_asmbl_7514.p1
Valid prediction for Augustus_model.g19132.t1
Valid prediction for snap_scaffold_12-snap.525-T1
Valid prediction for GlimmerHMM_glimmerT_28973-T1
Valid prediction for snap_scaffold_12-snap.507-T1
Valid prediction for HiQ_model.g19119.t1
Valid prediction for GlimmerHMM_glimmerT_28985-T1
Valid prediction for snap_scaffold_12-snap.533-T1
Valid prediction for snap_scaffold_12-snap.550-T1
Couldn't classify 227868, 227987
Couldn't classify 230990, 231053
Sorry, prediction pasa_asmbl_7515.p1 fails validation.
(GCC)	 GG	227868-227987	GT	CGG
(CAA)	 AG	228207-228270	GT	CAG
(ATG)	 AG	228468-228557	GT	AGG
(CCA)	 AG	229374-229603	GT	GGG
(TTG)	 AG	230052-230126	GT	AGG
(GGC)	 AG	230332-230395	GT	CGG
(GTG)	 AG	230615-230774	GT	AGG
(GTG)	 AG	230990-231053	CT	GGC
add_exon() Sorry, pasa_asmbl_7515.p1 228468-228557-initial-1 is invalid.
-recovered pasa_asmbl_7515.p1, initial, 228468, 228557
-recovered pasa_asmbl_7515.p1, internal, 228207, 228270
-recovered pasa_asmbl_7515.p1, internal, 228468, 228557
-recovered pasa_asmbl_7515.p1, internal, 229374, 229603
-recovered pasa_asmbl_7515.p1, internal, 230052, 230126
-recovered pasa_asmbl_7515.p1, internal, 230332, 230395
-recovered pasa_asmbl_7515.p1, internal, 230615, 230774
Valid prediction for snap_scaffold_12-snap.527-T1
Valid prediction for Augustus_model.g19128.t1
Valid prediction for Augustus_model.g19127.t1
Valid prediction for GlimmerHMM_glimmerT_28987-T1
Valid prediction for snap_scaffold_12-snap.515-T1
Valid prediction for snap_scaffold_12-snap.551-T1
Valid prediction for snap_scaffold_12-snap.505-T1
Valid prediction for snap_scaffold_12-snap.512-T1
Valid prediction for snap_scaffold_12-snap.554-T1
Valid prediction for GlimmerHMM_glimmerT_28980-T1
Valid prediction for snap_scaffold_12-snap.518-T1
Valid prediction for snap_scaffold_12-snap.524-T1
Valid prediction for snap_scaffold_12-snap.543-T1
Couldn't classify 102279, 102388
Sorry, prediction pasa_asmbl_7499.p1 fails validation.
(ATG)	 TC	99134-99217	GT	GGG
(TGG)	 AG	99515-99607	GT	AGG
(GTG)	 AG	99963-100059	GT	AGG
(ATT)	 AG	100285-100425	GT	TGG
(GGA)	 AG	102279-102388	TG	CGT
-recovered pasa_asmbl_7499.p1, initial, 99134, 99217
-recovered pasa_asmbl_7499.p1, internal, 99515, 99607
-recovered pasa_asmbl_7499.p1, internal, 99963, 100059
-recovered pasa_asmbl_7499.p1, internal, 100285, 100425
Valid prediction for snap_scaffold_12-snap.528-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_28975-T1
Valid prediction for snap_scaffold_12-snap.555-T1
Valid prediction for snap_scaffold_12-snap.514-T1
Valid prediction for snap_scaffold_12-snap.526-T1
Valid prediction for snap_scaffold_12-snap.546-T1
Valid prediction for Augustus_model.g19113.t1
Valid prediction for Augustus_model.g19116.t1
Valid prediction for Augustus_model.g19114.t1
Valid prediction for snap_scaffold_12-snap.509-T1
Valid prediction for snap_scaffold_12-snap.508-T1
Valid prediction for snap_scaffold_12-snap.549-T1
Valid prediction for snap_scaffold_12-snap.523-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g19117.t1
Valid prediction for snap_scaffold_12-snap.506-T1
Valid prediction for GlimmerHMM_glimmerT_28979-T1
Valid prediction for GlimmerHMM_glimmerT_28986-T1
Valid prediction for snap_scaffold_12-snap.522-T1
Valid prediction for snap_scaffold_12-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_28966-T1
Valid prediction for Augustus_model.g19131.t1
Valid prediction for GlimmerHMM_glimmerT_28969-T1
Valid prediction for snap_scaffold_12-snap.519-T1
Valid prediction for snap_scaffold_12-snap.529-T1
Valid prediction for snap_scaffold_12-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_28965-T1
Valid prediction for snap_scaffold_12-snap.517-T1
Valid prediction for snap_scaffold_12-snap.513-T1
Valid prediction for Augustus_model.g19118.t1
Valid prediction for GlimmerHMM_glimmerT_28974-T1
Valid prediction for snap_scaffold_12-snap.552-T1
Valid prediction for snap_scaffold_12-snap.534-T1
Valid prediction for Augustus_model.g19115.t1
Valid prediction for GlimmerHMM_glimmerT_28968-T1
Valid prediction for Augustus_model.g19111.t1
Valid prediction for snap_scaffold_12-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_28981-T1
Valid prediction for snap_scaffold_12-snap.511-T1
Valid prediction for snap_scaffold_12-snap.521-T1
Valid prediction for snap_scaffold_12-snap.516-T1
Valid prediction for snap_scaffold_12-snap.544-T1
Valid prediction for snap_scaffold_12-snap.541-T1
Valid prediction for Augustus_model.g19123.t1
Valid prediction for snap_scaffold_12-snap.503-T1
Valid prediction for snap_scaffold_12-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_28972-T1
Valid prediction for Augustus_model.g19112.t1
Valid prediction for GlimmerHMM_glimmerT_28967-T1
Valid prediction for snap_scaffold_12-snap.530-T1
Valid prediction for snap_scaffold_12-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_28971-T1
Valid prediction for snap_scaffold_12-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_28964-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8862, rend_intergenic: 7348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15796, rend_intergenic: 13704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26520, rend_intergenic: 23631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37320, rend_intergenic: 34887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55974, rend_intergenic: 51551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58409, rend_intergenic: 56321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118873, rend_intergenic: 114084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139781, rend_intergenic: 132171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146202, rend_intergenic: 140940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148103, rend_intergenic: 147370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152727, rend_intergenic: 149270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155959, rend_intergenic: 152827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176948, rend_intergenic: 171206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183876, rend_intergenic: 182200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197542, rend_intergenic: 191513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209378, rend_intergenic: 207095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219505, rend_intergenic: 217075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222550, rend_intergenic: 220270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 271665
-exon list size: 372


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 8862, rend_intergenic: 7348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15796, rend_intergenic: 13704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26520, rend_intergenic: 23631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37320, rend_intergenic: 34887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55974, rend_intergenic: 51551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58409, rend_intergenic: 56321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118873, rend_intergenic: 114084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139781, rend_intergenic: 132171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146202, rend_intergenic: 140940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148103, rend_intergenic: 147370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152727, rend_intergenic: 149270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155959, rend_intergenic: 152827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176948, rend_intergenic: 171206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183876, rend_intergenic: 182200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197542, rend_intergenic: 191513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209378, rend_intergenic: 207095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219505, rend_intergenic: 217075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222550, rend_intergenic: 220270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support