-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_15809169-15994882

-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_13-snap.3118-T1
Valid prediction for snap_scaffold_13-snap.3117-T1
Couldn't classify 173220, 173240
Couldn't classify 173954, 174179
Sorry, prediction CodingQuarry_transcript_13344-T1 fails validation.
(ATG)	 AG	173220-173240	GA	GTG
(GTC)	 AT	173954-174179	GT	GGG
(TTT)	 AG	175483-175526	GT	GAG
-recovered CodingQuarry_transcript_13344-T1, terminal, 175483, 175526
-recovered CodingQuarry_transcript_13344-T1, internal, 175483, 175526
Valid prediction for snap_scaffold_13-snap.3086-T1
Valid prediction for GlimmerHMM_glimmerT_32980-T1
Valid prediction for GlimmerHMM_glimmerT_32987-T1
Valid prediction for snap_scaffold_13-snap.3096-T1
Valid prediction for Augustus_model.g22008.t1
Valid prediction for GlimmerHMM_glimmerT_32966-T1
Valid prediction for snap_scaffold_13-snap.3092-T1
Valid prediction for snap_scaffold_13-snap.3112-T1
Valid prediction for snap_scaffold_13-snap.3115-T1
Valid prediction for snap_scaffold_13-snap.3089-T1
Valid prediction for GlimmerHMM_glimmerT_32983-T1
Valid prediction for snap_scaffold_13-snap.3108-T1
Valid prediction for snap_scaffold_13-snap.3087-T1
Valid prediction for snap_scaffold_13-snap.3103-T1
Valid prediction for snap_scaffold_13-snap.3085-T1
Valid prediction for GlimmerHMM_glimmerT_32968-T1
Valid prediction for snap_scaffold_13-snap.3090-T1
Valid prediction for Augustus_model.g22000.t1
Valid prediction for snap_scaffold_13-snap.3121-T1
Valid prediction for HiQ_model.g22007.t1
Valid prediction for Augustus_model.g22003.t1
Valid prediction for snap_scaffold_13-snap.3083-T1
Couldn't classify 181513, 181763
Sorry, prediction pasa_asmbl_11641.p1 fails validation.
(ATG)	 CC	181121-181397	GT	ACG
(CAA)	 AG	181513-181763	TC	GTT
-recovered pasa_asmbl_11641.p1, initial, 181121, 181397
Valid prediction for GlimmerHMM_glimmerT_32986-T1
Valid prediction for snap_scaffold_13-snap.3088-T1
Valid prediction for GlimmerHMM_glimmerT_32972-T1
Valid prediction for GlimmerHMM_glimmerT_32974-T1
Valid prediction for Augustus_model.g21999.t1
Valid prediction for snap_scaffold_13-snap.3097-T1
Valid prediction for GlimmerHMM_glimmerT_32973-T1
Valid prediction for snap_scaffold_13-snap.3099-T1
Valid prediction for snap_scaffold_13-snap.3104-T1
Valid prediction for snap_scaffold_13-snap.3122-T1
Valid prediction for snap_scaffold_13-snap.3091-T1
Valid prediction for snap_scaffold_13-snap.3107-T1
Valid prediction for GlimmerHMM_glimmerT_32989-T1
Valid prediction for snap_scaffold_13-snap.3094-T1
Valid prediction for snap_scaffold_13-snap.3105-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_13-snap.3114-T1
Valid prediction for GlimmerHMM_glimmerT_32981-T1
Valid prediction for Augustus_model.g21994.t1
Valid prediction for GlimmerHMM_glimmerT_32979-T1
Valid prediction for Augustus_model.g21998.t1
Valid prediction for snap_scaffold_13-snap.3120-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g22004.t1
Valid prediction for snap_scaffold_13-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_32965-T1
Valid prediction for GlimmerHMM_glimmerT_32967-T1
Valid prediction for GlimmerHMM_glimmerT_32978-T1
Couldn't classify 133395, 133438
Couldn't classify 134470, 134508
Sorry, prediction pasa_asmbl_10361.p1 fails validation.
(CTG)	 CT	133395-133438	GT	AGG
(GAA)	 AG	133771-133864	GT	AGG
(GTT)	 AG	134084-134215	GT	AGG
(TTG)	 AG	134470-134508	AC	GCA
-recovered pasa_asmbl_10361.p1, internal, 133771, 133864
-recovered pasa_asmbl_10361.p1, internal, 134084, 134215
Valid prediction for snap_scaffold_13-snap.3084-T1
Valid prediction for Augustus_model.g22006.t1
Valid prediction for snap_scaffold_13-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_32985-T1
Valid prediction for GlimmerHMM_glimmerT_32970-T1
Valid prediction for snap_scaffold_13-snap.3110-T1
Valid prediction for CodingQuarry_transcript_13343-T1
Valid prediction for snap_scaffold_13-snap.3093-T1
Valid prediction for Augustus_model.g22005.t1
Valid prediction for snap_scaffold_13-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_32982-T1
Valid prediction for pasa_asmbl_10254.p1
Valid prediction for Augustus_model.g21997.t1
Valid prediction for GlimmerHMM_glimmerT_32984-T1
Valid prediction for snap_scaffold_13-snap.3095-T1
Valid prediction for snap_scaffold_13-snap.3102-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32971-T1
Valid prediction for Augustus_model.g22001.t1
Valid prediction for GlimmerHMM_glimmerT_32977-T1
Valid prediction for snap_scaffold_13-snap.3111-T1
Valid prediction for GlimmerHMM_glimmerT_32969-T1
Valid prediction for snap_scaffold_13-snap.3106-T1
Valid prediction for snap_scaffold_13-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_32975-T1
Valid prediction for GlimmerHMM_glimmerT_32976-T1
Valid prediction for HiQ_model.g21996.t1
Valid prediction for Augustus_model.g21995.t1
Valid prediction for snap_scaffold_13-snap.3101-T1
Valid prediction for GlimmerHMM_glimmerT_32988-T1
Valid prediction for snap_scaffold_13-snap.3116-T1
Valid prediction for snap_scaffold_13-snap.3098-T1
Valid prediction for snap_scaffold_13-snap.3100-T1
Valid prediction for Augustus_model.g22002.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9296, rend_intergenic: 9003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53038, rend_intergenic: 33868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63618, rend_intergenic: 54141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64083, rend_intergenic: 63775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73528, rend_intergenic: 64114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83147, rend_intergenic: 73916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100878, rend_intergenic: 85412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104141, rend_intergenic: 103221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107007, rend_intergenic: 104555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135084, rend_intergenic: 107889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143510, rend_intergenic: 135124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147730, rend_intergenic: 145798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153342, rend_intergenic: 148748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159476, rend_intergenic: 154005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165830, rend_intergenic: 161670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176063, rend_intergenic: 167307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185114, rend_intergenic: 176347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185714
-exon list size: 384


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.1    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 9296, rend_intergenic: 9003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53038, rend_intergenic: 33868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63618, rend_intergenic: 54141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64083, rend_intergenic: 63775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73528, rend_intergenic: 64114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83147, rend_intergenic: 73916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100878, rend_intergenic: 85412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104141, rend_intergenic: 103221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107007, rend_intergenic: 104555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135084, rend_intergenic: 107889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143510, rend_intergenic: 135124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147730, rend_intergenic: 145798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153342, rend_intergenic: 148748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159476, rend_intergenic: 154005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165830, rend_intergenic: 161670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176063, rend_intergenic: 167307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185114, rend_intergenic: 176347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support