-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_10639460-10957028

-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_27844-T1
Valid prediction for GlimmerHMM_glimmerT_27854-T1
Valid prediction for GlimmerHMM_glimmerT_27859-T1
Valid prediction for snap_scaffold_11-snap.2376-T1
Valid prediction for snap_scaffold_11-snap.2363-T1
Valid prediction for snap_scaffold_11-snap.2396-T1
Valid prediction for snap_scaffold_11-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_27846-T1
Valid prediction for snap_scaffold_11-snap.2403-T1
Valid prediction for snap_scaffold_11-snap.2406-T1
Valid prediction for snap_scaffold_11-snap.2372-T1
Valid prediction for snap_scaffold_11-snap.2370-T1
Valid prediction for snap_scaffold_11-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_27856-T1
Valid prediction for snap_scaffold_11-snap.2404-T1
Valid prediction for Augustus_model.g18440.t1
Valid prediction for GlimmerHMM_glimmerT_27842-T1
Valid prediction for snap_scaffold_11-snap.2400-T1
Valid prediction for GlimmerHMM_glimmerT_27857-T1
Valid prediction for GlimmerHMM_glimmerT_27838-T1
Valid prediction for snap_scaffold_11-snap.2378-T1
Valid prediction for snap_scaffold_11-snap.2379-T1
Valid prediction for Augustus_model.g18444.t1
Valid prediction for Augustus_model.g18438.t1
Valid prediction for Augustus_model.g18447.t1
Valid prediction for snap_scaffold_11-snap.2394-T1
Valid prediction for Augustus_model.g18445.t1
Valid prediction for snap_scaffold_11-snap.2364-T1
Valid prediction for snap_scaffold_11-snap.2401-T1
Couldn't classify 181810, 182706
Sorry, prediction pasa_asmbl_5950.p1 fails validation.
(ACC)	 TG	181810-182706	GT	AGG
(GTA)	 AG	182799-182999	AC	AAA
-recovered pasa_asmbl_5950.p1, terminal, 182799, 182999
Valid prediction for snap_scaffold_11-snap.2385-T1
Valid prediction for Augustus_model.g18443.t1
Valid prediction for GlimmerHMM_glimmerT_27849-T1
Valid prediction for Augustus_model.g18441.t1
Valid prediction for snap_scaffold_11-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_27863-T1
Valid prediction for snap_scaffold_11-snap.2366-T1
Valid prediction for snap_scaffold_11-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_27837-T1
Valid prediction for snap_scaffold_11-snap.2405-T1
Valid prediction for snap_scaffold_11-snap.2383-T1
Valid prediction for GlimmerHMM_glimmerT_27843-T1
Valid prediction for Augustus_model.g18442.t1
Valid prediction for Augustus_model.g18439.t1
Valid prediction for snap_scaffold_11-snap.2382-T1
Valid prediction for GlimmerHMM_glimmerT_27841-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.g18453.t1
Valid prediction for snap_scaffold_11-snap.2387-T1
Valid prediction for Augustus_model.g18446.t1
Valid prediction for snap_scaffold_11-snap.2373-T1
Valid prediction for snap_scaffold_11-snap.2397-T1
Valid prediction for snap_scaffold_11-snap.2390-T1
Valid prediction for snap_scaffold_11-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_27847-T1
Valid prediction for Augustus_model.g18448.t1
Valid prediction for snap_scaffold_11-snap.2386-T1
Valid prediction for snap_scaffold_11-snap.2389-T1
Valid prediction for Augustus_model.g18452.t1
Valid prediction for GlimmerHMM_glimmerT_27855-T1
Valid prediction for snap_scaffold_11-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_27840-T1
Valid prediction for snap_scaffold_11-snap.2402-T1
Valid prediction for snap_scaffold_11-snap.2374-T1
Valid prediction for snap_scaffold_11-snap.2381-T1
Valid prediction for snap_scaffold_11-snap.2391-T1
Valid prediction for GlimmerHMM_glimmerT_27862-T1
Valid prediction for GlimmerHMM_glimmerT_27861-T1
Valid prediction for CodingQuarry_transcript_8238-T1
Valid prediction for Augustus_model.g18451.t1
Valid prediction for snap_scaffold_11-snap.2393-T1
Valid prediction for snap_scaffold_11-snap.2365-T1
Valid prediction for GlimmerHMM_glimmerT_27864-T1
Valid prediction for snap_scaffold_11-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_27853-T1
Couldn't classify 101770, 101894
Sorry, prediction pasa_asmbl_7000.p1 fails validation.
(CCC)	 TC	101770-101894	GT	AGG
(GAC)	 AG	103932-104397	CT	GAC
-recovered pasa_asmbl_7000.p1, terminal, 103932, 104397
Valid prediction for GlimmerHMM_glimmerT_27839-T1
Valid prediction for GlimmerHMM_glimmerT_27850-T1
Valid prediction for snap_scaffold_11-snap.2399-T1
Valid prediction for snap_scaffold_11-snap.2367-T1
Valid prediction for snap_scaffold_11-snap.2375-T1
Valid prediction for snap_scaffold_11-snap.2395-T1
Valid prediction for snap_scaffold_11-snap.2371-T1
Valid prediction for snap_scaffold_11-snap.2384-T1
Valid prediction for GlimmerHMM_glimmerT_27851-T1
Valid prediction for GlimmerHMM_glimmerT_27845-T1
Valid prediction for CodingQuarry_transcript_8241-T1
Valid prediction for pasa_asmbl_7003.p1
Valid prediction for Augustus_model.g18449.t1
Valid prediction for snap_scaffold_11-snap.2368-T1
Valid prediction for snap_scaffold_11-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_27860-T1
Valid prediction for GlimmerHMM_glimmerT_27858-T1
Valid prediction for Augustus_model.g18450.t1
Valid prediction for GlimmerHMM_glimmerT_27848-T1
Valid prediction for CodingQuarry_transcript_8240-T1
Valid prediction for snap_scaffold_11-snap.2369-T1
Valid prediction for GlimmerHMM_glimmerT_27852-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64257, rend_intergenic: 62659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73991, rend_intergenic: 71339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85318, rend_intergenic: 83522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113640, rend_intergenic: 112427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217630, rend_intergenic: 216602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223570, rend_intergenic: 218542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226730, rend_intergenic: 224727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230792, rend_intergenic: 227256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234126, rend_intergenic: 231046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241284, rend_intergenic: 235707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252728, rend_intergenic: 247257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259945, rend_intergenic: 257979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278804, rend_intergenic: 261111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 317569
-exon list size: 288


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.4    
3.8    
4.1    
4.5    
4.8    
5.2    
5.5    
5.9    
6.2    
6.6    
6.9    
7.2    
7.6    
7.9    
8.3    
8.6    
9.0    
9.3    
9.7    
10.0    
10.3    
10.7    
11.0    
11.4    
11.7    
12.1    
12.4    
12.8    
13.1    
13.4    
13.8    
14.1    
14.5    
14.8    
15.2    
15.5    
15.9    
16.2    
16.6    
16.9    
17.2    
17.6    
17.9    
18.3    
18.6    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.4    
21.7    
22.1    
22.4    
22.8    
23.1    
23.4    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.6    
26.9    
27.2    
27.6    
27.9    
28.3    
28.6    
29.0    
29.3    
29.7    
30.0    
30.3    
30.7    
31.0    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.9    
36.2    
36.6    
36.9    
37.2    
37.6    
37.9    
38.3    
38.6    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.4    
41.7    
42.1    
42.4    
42.8    
43.1    
43.4    
43.8    
44.1    
44.5    
44.8    
45.2    
45.5    
45.9    
46.2    
46.6    
46.9    
47.2    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.8    
53.1    
53.4    
53.8    
54.1    
54.5    
54.8    
55.2    
55.5    
55.9    
56.2    
56.6    
56.9    
57.2    
57.6    
57.9    
58.3    
58.6    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.4    
61.7    
62.1    
62.4    
62.8    
63.1    
63.4    
63.8    
64.1    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
69.0    
69.3    
69.7    
70.0    
70.3    
70.7    
71.0    
71.4    
71.7    
72.1    
72.4    
72.8    
73.1    
73.4    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.6    
76.9    
77.2    
77.6    
77.9    
78.3    
78.6    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.4    
81.7    
82.1    
82.4    
82.8    
83.1    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.5    
85.9    
86.2    
86.6    
86.9    
87.2    
87.6    
87.9    
88.3    
88.6    
89.0    
89.3    
89.7    
90.0    
90.3    
90.7    
91.0    
91.4    
91.7    
92.1    
92.4    
92.8    
93.1    
93.4    
93.8    
94.1    
94.5    
94.8    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 64257, rend_intergenic: 62659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73991, rend_intergenic: 71339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85318, rend_intergenic: 83522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113640, rend_intergenic: 112427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217630, rend_intergenic: 216602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223570, rend_intergenic: 218542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226730, rend_intergenic: 224727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230792, rend_intergenic: 227256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234126, rend_intergenic: 231046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241284, rend_intergenic: 235707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252728, rend_intergenic: 247257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259945, rend_intergenic: 257979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278804, rend_intergenic: 261111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support