-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_19051400-19262159

-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 pasa_asmbl_25263.p1
Valid prediction for snap_scaffold_2-snap.3753-T1
Valid prediction for GlimmerHMM_glimmerT_5630-T1
Valid prediction for snap_scaffold_2-snap.3747-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3756-T1
Valid prediction for Augustus_model.g3768.t1
Valid prediction for Augustus_model.g3766.t1
Valid prediction for snap_scaffold_2-snap.3742-T1
Valid prediction for snap_scaffold_2-snap.3732-T1
Valid prediction for snap_scaffold_2-snap.3752-T1
Valid prediction for GlimmerHMM_glimmerT_5636-T1
Valid prediction for Augustus_model.g3763.t1
Valid prediction for snap_scaffold_2-snap.3751-T1
Valid prediction for snap_scaffold_2-snap.3736-T1
Valid prediction for snap_scaffold_2-snap.3737-T1
Valid prediction for snap_scaffold_2-snap.3727-T1
Valid prediction for Augustus_model.g3762.t1
Valid prediction for GlimmerHMM_glimmerT_5626-T1
Valid prediction for Augustus_model.g3769.t1
Valid prediction for snap_scaffold_2-snap.3739-T1
Valid prediction for GlimmerHMM_glimmerT_5620-T1
Valid prediction for GlimmerHMM_glimmerT_5621-T1
Valid prediction for snap_scaffold_2-snap.3755-T1
Valid prediction for snap_scaffold_2-snap.3760-T1
Valid prediction for GlimmerHMM_glimmerT_5631-T1
Valid prediction for snap_scaffold_2-snap.3746-T1
Valid prediction for snap_scaffold_2-snap.3734-T1
Valid prediction for pasa_asmbl_25269.p1
Valid prediction for Augustus_model.g3761.t1
Valid prediction for snap_scaffold_2-snap.3743-T1
Valid prediction for GlimmerHMM_glimmerT_5622-T1
Valid prediction for snap_scaffold_2-snap.3758-T1
Valid prediction for snap_scaffold_2-snap.3730-T1
Valid prediction for snap_scaffold_2-snap.3740-T1
Valid prediction for snap_scaffold_2-snap.3724-T1
Valid prediction for Augustus_model.g3765.t1
Valid prediction for GlimmerHMM_glimmerT_5641-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.g3764.t1
Valid prediction for Augustus_model.g3770.t1
Couldn't classify 59510, 59586
Sorry, prediction pasa_asmbl_23856.p1 fails validation.
(AAG)	 CT	59510-59586	GT	AGG
(ATT)	 AG	60197-60300	GT	AGG
(ATG)	 AG	62332-62465	GT	CCG
(GAG)	 AG	62793-62855	GT	CAG
(CAT)	 AG	63220-63357	CC	AAC
add_exon() Sorry, pasa_asmbl_23856.p1 62332-62465-initial-1 is invalid.
-recovered pasa_asmbl_23856.p1, initial, 62332, 62465
add_exon() Sorry, pasa_asmbl_23856.p1 60197-60300-terminal-2 is invalid.
-recovered pasa_asmbl_23856.p1, terminal, 60197, 60300
-recovered pasa_asmbl_23856.p1, terminal, 63220, 63357
-recovered pasa_asmbl_23856.p1, internal, 60197, 60300
-recovered pasa_asmbl_23856.p1, internal, 62332, 62465
-recovered pasa_asmbl_23856.p1, internal, 62793, 62855
Valid prediction for GlimmerHMM_glimmerT_5640-T1
Valid prediction for snap_scaffold_2-snap.3757-T1
Valid prediction for GlimmerHMM_glimmerT_5642-T1
Valid prediction for GlimmerHMM_glimmerT_5635-T1
Valid prediction for Augustus_model.g3772.t1
Valid prediction for snap_scaffold_2-snap.3749-T1
Valid prediction for GlimmerHMM_glimmerT_5634-T1
Valid prediction for snap_scaffold_2-snap.3741-T1
Valid prediction for snap_scaffold_2-snap.3745-T1
Valid prediction for GlimmerHMM_glimmerT_5637-T1
Valid prediction for GlimmerHMM_glimmerT_5627-T1
Valid prediction for GlimmerHMM_glimmerT_5632-T1
Valid prediction for snap_scaffold_2-snap.3728-T1
Valid prediction for snap_scaffold_2-snap.3748-T1
Valid prediction for GlimmerHMM_glimmerT_5643-T1
Valid prediction for snap_scaffold_2-snap.3731-T1
Valid prediction for GlimmerHMM_glimmerT_5633-T1
Valid prediction for GlimmerHMM_glimmerT_5619-T1
Valid prediction for snap_scaffold_2-snap.3725-T1
Valid prediction for GlimmerHMM_glimmerT_5624-T1
Valid prediction for snap_scaffold_2-snap.3726-T1
Valid prediction for snap_scaffold_2-snap.3744-T1
Valid prediction for GlimmerHMM_glimmerT_5639-T1
Valid prediction for snap_scaffold_2-snap.3750-T1
Valid prediction for Augustus_model.g3767.t1
Valid prediction for snap_scaffold_2-snap.3738-T1
Valid prediction for GlimmerHMM_glimmerT_5628-T1
Valid prediction for Augustus_model.g3771.t1
Valid prediction for snap_scaffold_2-snap.3735-T1
Valid prediction for GlimmerHMM_glimmerT_5629-T1
Valid prediction for GlimmerHMM_glimmerT_5623-T1
Valid prediction for snap_scaffold_2-snap.3723-T1
Valid prediction for GlimmerHMM_glimmerT_5638-T1
Valid prediction for GlimmerHMM_glimmerT_5625-T1
Valid prediction for snap_scaffold_2-snap.3754-T1
Valid prediction for snap_scaffold_2-snap.3733-T1
Valid prediction for snap_scaffold_2-snap.3729-T1
Couldn't classify 57140, 57232
Couldn't classify 58231, 58344
Sorry, prediction pasa_asmbl_23997.p1 fails validation.
(CGT)	 CA	57140-57232	GT	TGG
(GAG)	 AG	57533-57646	GT	TGG
(GTG)	 AG	58231-58344	TT	GGT
-recovered pasa_asmbl_23997.p1, internal, 57533, 57646

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14912, rend_intergenic: 6697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22476, rend_intergenic: 16407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37611, rend_intergenic: 30320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45833, rend_intergenic: 37671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56992, rend_intergenic: 46016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75092, rend_intergenic: 57597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86188, rend_intergenic: 80015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97840, rend_intergenic: 91564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104783, rend_intergenic: 98365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124968, rend_intergenic: 107079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135076, rend_intergenic: 130166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145129, rend_intergenic: 141684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171720, rend_intergenic: 151459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184988, rend_intergenic: 172260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193055, rend_intergenic: 185202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197205, rend_intergenic: 193222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199721, rend_intergenic: 198190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210760
-exon list size: 359


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.2    
4.4    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.5    
35.7    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.3    
64.5    
64.8    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.1    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.6    
95.8    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 14912, rend_intergenic: 6697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22476, rend_intergenic: 16407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37611, rend_intergenic: 30320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45833, rend_intergenic: 37671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56992, rend_intergenic: 46016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75092, rend_intergenic: 57597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86188, rend_intergenic: 80015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97840, rend_intergenic: 91564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104783, rend_intergenic: 98365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124968, rend_intergenic: 107079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135076, rend_intergenic: 130166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145129, rend_intergenic: 141684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171720, rend_intergenic: 151459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184988, rend_intergenic: 172260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193055, rend_intergenic: 185202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197205, rend_intergenic: 193222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199721, rend_intergenic: 198190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support