-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_2590261-2767691

-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_2-snap.614-T1
Valid prediction for pasa_asmbl_25405.p1
Valid prediction for snap_scaffold_2-snap.610-T1
Valid prediction for snap_scaffold_2-snap.623-T1
Valid prediction for snap_scaffold_2-snap.617-T1
Valid prediction for GlimmerHMM_glimmerT_3413-T1
Valid prediction for Augustus_model.g2279.t1
Valid prediction for snap_scaffold_2-snap.611-T1
Valid prediction for snap_scaffold_2-snap.615-T1
Valid prediction for Augustus_model.g2286.t1
Valid prediction for GlimmerHMM_glimmerT_3399-T1
Valid prediction for Augustus_model.g2275.t1
Valid prediction for Augustus_model.g2284.t1
Valid prediction for snap_scaffold_2-snap.616-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g2283.t1
Valid prediction for snap_scaffold_2-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_3406-T1
Valid prediction for snap_scaffold_2-snap.642-T1
Valid prediction for HiQ_model.g2280.t1
Valid prediction for snap_scaffold_2-snap.624-T1
Valid prediction for Augustus_model.g2274.t1
Valid prediction for snap_scaffold_2-snap.626-T1
Valid prediction for snap_scaffold_2-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_3411-T1
Valid prediction for snap_scaffold_2-snap.641-T1
Valid prediction for GlimmerHMM_glimmerT_3402-T1
Valid prediction for snap_scaffold_2-snap.613-T1
Valid prediction for Augustus_model.g2277.t1
Valid prediction for snap_scaffold_2-snap.620-T1
Valid prediction for snap_scaffold_2-snap.634-T1
Valid prediction for snap_scaffold_2-snap.607-T1
Valid prediction for GlimmerHMM_glimmerT_3408-T1
Valid prediction for GlimmerHMM_glimmerT_3410-T1
Valid prediction for snap_scaffold_2-snap.638-T1
Valid prediction for snap_scaffold_2-snap.630-T1
Valid prediction for snap_scaffold_2-snap.628-T1
Valid prediction for GlimmerHMM_glimmerT_3405-T1
Valid prediction for snap_scaffold_2-snap.639-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 snap_scaffold_2-snap.636-T1
Valid prediction for GlimmerHMM_glimmerT_3400-T1
Valid prediction for Augustus_model.g2278.t1
Valid prediction for snap_scaffold_2-snap.633-T1
Valid prediction for snap_scaffold_2-snap.629-T1
Valid prediction for CodingQuarry_transcript_28481-T1
Valid prediction for snap_scaffold_2-snap.640-T1
Valid prediction for GlimmerHMM_glimmerT_3395-T1
Valid prediction for snap_scaffold_2-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_3401-T1
Valid prediction for GlimmerHMM_glimmerT_3407-T1
Valid prediction for snap_scaffold_2-snap.608-T1
Valid prediction for Augustus_model.g2273.t1
Valid prediction for snap_scaffold_2-snap.619-T1
Valid prediction for Augustus_model.g2285.t1
Valid prediction for GlimmerHMM_glimmerT_3403-T1
Valid prediction for snap_scaffold_2-snap.631-T1
Valid prediction for Augustus_model.g2271.t1
Valid prediction for Augustus_model.g2282.t1
Valid prediction for snap_scaffold_2-snap.635-T1
Valid prediction for GlimmerHMM_glimmerT_3412-T1
Valid prediction for GlimmerHMM_glimmerT_3398-T1
Valid prediction for snap_scaffold_2-snap.637-T1
Valid prediction for snap_scaffold_2-snap.622-T1
Valid prediction for Augustus_model.g2281.t1
Valid prediction for snap_scaffold_2-snap.612-T1
Valid prediction for HiQ_model.g2276.t1
Valid prediction for GlimmerHMM_glimmerT_3396-T1
Valid prediction for GlimmerHMM_glimmerT_3397-T1
Valid prediction for Augustus_model.g2272.t1
Valid prediction for snap_scaffold_2-snap.632-T1
Valid prediction for snap_scaffold_2-snap.618-T1
Valid prediction for GlimmerHMM_glimmerT_3404-T1
Valid prediction for Augustus_model.g2269.t1
Valid prediction for snap_scaffold_2-snap.625-T1
Couldn't classify 56956, 57084
Sorry, prediction pasa_asmbl_22913.p1 fails validation.
(CTC)	 AT	56956-57084	GT	AGG
(ATC)	 AG	57172-57501	AA	AGA
-recovered pasa_asmbl_22913.p1, terminal, 57172, 57501
Valid prediction for GlimmerHMM_glimmerT_3409-T1
Valid prediction for Augustus_model.g2270.t1
Valid prediction for snap_scaffold_2-snap.609-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46705, rend_intergenic: 40931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52752, rend_intergenic: 47728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64681, rend_intergenic: 61915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79411, rend_intergenic: 65985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86565, rend_intergenic: 83903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93899, rend_intergenic: 86688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97721, rend_intergenic: 94375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100751, rend_intergenic: 98085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111374, rend_intergenic: 109753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114477, rend_intergenic: 113710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137133, rend_intergenic: 126178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150167, rend_intergenic: 140773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162597, rend_intergenic: 151702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166187, rend_intergenic: 164145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177431
-exon list size: 319


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 46705, rend_intergenic: 40931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52752, rend_intergenic: 47728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64681, rend_intergenic: 61915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79411, rend_intergenic: 65985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86565, rend_intergenic: 83903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93899, rend_intergenic: 86688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97721, rend_intergenic: 94375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100751, rend_intergenic: 98085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111374, rend_intergenic: 109753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114477, rend_intergenic: 113710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137133, rend_intergenic: 126178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150167, rend_intergenic: 140773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162597, rend_intergenic: 151702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166187, rend_intergenic: 164145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support