-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_17087638-17260035

-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_3-snap.3314-T1
Valid prediction for Augustus_model.g5372.t1
Valid prediction for GlimmerHMM_glimmerT_8127-T1
Valid prediction for GlimmerHMM_glimmerT_8153-T1
Valid prediction for snap_scaffold_3-snap.3340-T1
Valid prediction for Augustus_model.g5380.t1
Couldn't classify 51954, 52373
Sorry, prediction pasa_asmbl_40649.p2 fails validation.
(ATG)	 CC	51954-52373	CG	TGC
Valid prediction for pasa_asmbl_40648.p1
Valid prediction for Augustus_model.g5369.t1
Valid prediction for snap_scaffold_3-snap.3306-T1
Valid prediction for snap_scaffold_3-snap.3323-T1
Valid prediction for Augustus_model.g5364.t1
Valid prediction for snap_scaffold_3-snap.3304-T1
Valid prediction for GlimmerHMM_glimmerT_8129-T1
Valid prediction for GlimmerHMM_glimmerT_8143-T1
Valid prediction for GlimmerHMM_glimmerT_8137-T1
Valid prediction for snap_scaffold_3-snap.3318-T1
Valid prediction for GlimmerHMM_glimmerT_8149-T1
Valid prediction for GlimmerHMM_glimmerT_8161-T1
Valid prediction for snap_scaffold_3-snap.3312-T1
Valid prediction for snap_scaffold_3-snap.3327-T1
Valid prediction for GlimmerHMM_glimmerT_8162-T1
Valid prediction for snap_scaffold_3-snap.3303-T1
Valid prediction for GlimmerHMM_glimmerT_8144-T1
Valid prediction for snap_scaffold_3-snap.3311-T1
Couldn't classify 154098, 154172
Couldn't classify 155467, 155619
Sorry, prediction pasa_asmbl_40660.p1 fails validation.
(CCG)	 GA	154098-154172	GT	AGG
(AAT)	 AG	154596-154703	GT	AGG
(GAT)	 AG	155467-155619	TA	GGT
-recovered pasa_asmbl_40660.p1, internal, 154596, 154703
Valid prediction for snap_scaffold_3-snap.3322-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3320-T1
Valid prediction for CodingQuarry_transcript_46431-T1
Valid prediction for GlimmerHMM_glimmerT_8138-T1
Valid prediction for GlimmerHMM_glimmerT_8156-T1
Valid prediction for snap_scaffold_3-snap.3343-T1
Valid prediction for Augustus_model.g5375.t1
Valid prediction for GlimmerHMM_glimmerT_8158-T1
Valid prediction for GlimmerHMM_glimmerT_8133-T1
Valid prediction for GlimmerHMM_glimmerT_8140-T1
Valid prediction for snap_scaffold_3-snap.3336-T1
Valid prediction for HiQ_model.g5365.t1
Valid prediction for pasa_asmbl_40640.p1
Valid prediction for GlimmerHMM_glimmerT_8131-T1
Valid prediction for GlimmerHMM_glimmerT_8132-T1
Valid prediction for Augustus_model.g5382.t1
Valid prediction for pasa_asmbl_40656.p1
Valid prediction for snap_scaffold_3-snap.3309-T1
Valid prediction for snap_scaffold_3-snap.3331-T1
Valid prediction for snap_scaffold_3-snap.3326-T1
Valid prediction for snap_scaffold_3-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_8130-T1
Valid prediction for GlimmerHMM_glimmerT_8151-T1
Valid prediction for snap_scaffold_3-snap.3325-T1
Valid prediction for Augustus_model.g5370.t1
Couldn't classify 54133, 54195
Couldn't classify 55397, 55558
Sorry, prediction pasa_asmbl_40651.p1 fails validation.
(AGA)	 CC	54133-54195	GT	CCG
(GAT)	 AG	54384-54479	GT	AGG
(GAG)	 AG	55397-55558	GT	AGG
-recovered pasa_asmbl_40651.p1, internal, 54384, 54479
-recovered pasa_asmbl_40651.p1, internal, 55397, 55558
Valid prediction for GlimmerHMM_glimmerT_8160-T1
Valid prediction for GlimmerHMM_glimmerT_8148-T1
Valid prediction for GlimmerHMM_glimmerT_8142-T1
Valid prediction for Augustus_model.g5367.t1
Valid prediction for CodingQuarry_transcript_46430-T1
Valid prediction for GlimmerHMM_glimmerT_8163-T1
Valid prediction for GlimmerHMM_glimmerT_8141-T1
Valid prediction for GlimmerHMM_glimmerT_8159-T1
Valid prediction for snap_scaffold_3-snap.3329-T1
Valid prediction for Augustus_model.g5374.t1
Valid prediction for Augustus_model.g5381.t1
Valid prediction for Augustus_model.g5378.t1
Valid prediction for Augustus_model.g5376.t1
Valid prediction for snap_scaffold_3-snap.3308-T1
Valid prediction for snap_scaffold_3-snap.3301-T1
Valid prediction for snap_scaffold_3-snap.3305-T1
Valid prediction for GlimmerHMM_glimmerT_8136-T1
Valid prediction for snap_scaffold_3-snap.3338-T1
Valid prediction for HiQ_model.g5366.t1
Valid prediction for snap_scaffold_3-snap.3317-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_3-snap.3339-T1
Valid prediction for GlimmerHMM_glimmerT_8128-T1
Valid prediction for snap_scaffold_3-snap.3302-T1
Valid prediction for snap_scaffold_3-snap.3299-T1
Valid prediction for snap_scaffold_3-snap.3334-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8147-T1
Valid prediction for snap_scaffold_3-snap.3315-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3316-T1
Valid prediction for Augustus_model.g5379.t1
Valid prediction for snap_scaffold_3-snap.3298-T1
Valid prediction for GlimmerHMM_glimmerT_8155-T1
Valid prediction for snap_scaffold_3-snap.3328-T1
Valid prediction for GlimmerHMM_glimmerT_8146-T1
Valid prediction for Augustus_model.g5368.t1
Valid prediction for GlimmerHMM_glimmerT_8150-T1
Valid prediction for snap_scaffold_3-snap.3310-T1
Valid prediction for GlimmerHMM_glimmerT_8139-T1
Valid prediction for Augustus_model.g5363.t1
Valid prediction for Augustus_model.g5383.t1
Valid prediction for GlimmerHMM_glimmerT_8154-T1
Valid prediction for snap_scaffold_3-snap.3324-T1
Valid prediction for snap_scaffold_3-snap.3341-T1
Valid prediction for snap_scaffold_3-snap.3333-T1
Valid prediction for snap_scaffold_3-snap.3319-T1
Valid prediction for snap_scaffold_3-snap.3300-T1
Couldn't classify 164606, 164810
Sorry, prediction pasa_asmbl_39537.p1 fails validation.
(CAC)	 CC	164606-164810	GT	TGG
(ACG)	 AG	165625-165773	GT	TGG
(GCA)	 AG	165982-166956	AA	GAA
-recovered pasa_asmbl_39537.p1, terminal, 165982, 166956
-recovered pasa_asmbl_39537.p1, internal, 165625, 165773
Valid prediction for Augustus_model.g5371.t1
Valid prediction for GlimmerHMM_glimmerT_8164-T1
Valid prediction for snap_scaffold_3-snap.3321-T1
Valid prediction for Augustus_model.g5373.t1
Valid prediction for snap_scaffold_3-snap.3332-T1
Valid prediction for Augustus_model.g5377.t1
Valid prediction for GlimmerHMM_glimmerT_8145-T1
Valid prediction for GlimmerHMM_glimmerT_8135-T1
Valid prediction for GlimmerHMM_glimmerT_8134-T1
Valid prediction for snap_scaffold_3-snap.3337-T1
Valid prediction for snap_scaffold_3-snap.3335-T1
Valid prediction for GlimmerHMM_glimmerT_8157-T1
Valid prediction for snap_scaffold_3-snap.3307-T1
Valid prediction for GlimmerHMM_glimmerT_8152-T1
Valid prediction for snap_scaffold_3-snap.3313-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13740, rend_intergenic: 11765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15624, rend_intergenic: 14559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34158, rend_intergenic: 25134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39855, rend_intergenic: 34983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46645, rend_intergenic: 41109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59053, rend_intergenic: 46988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63972, rend_intergenic: 59978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79751, rend_intergenic: 77673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83826, rend_intergenic: 80026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88667, rend_intergenic: 85074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97157, rend_intergenic: 92669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103177, rend_intergenic: 100068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117862, rend_intergenic: 113752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139701, rend_intergenic: 128041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149212, rend_intergenic: 146022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154450, rend_intergenic: 149365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163149, rend_intergenic: 159988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172398
-exon list size: 475


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 13740, rend_intergenic: 11765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15624, rend_intergenic: 14559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34158, rend_intergenic: 25134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39855, rend_intergenic: 34983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46645, rend_intergenic: 41109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59053, rend_intergenic: 46988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63972, rend_intergenic: 59978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79751, rend_intergenic: 77673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83826, rend_intergenic: 80026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88667, rend_intergenic: 85074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97157, rend_intergenic: 92669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103177, rend_intergenic: 100068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117862, rend_intergenic: 113752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139701, rend_intergenic: 128041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149212, rend_intergenic: 146022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154450, rend_intergenic: 149365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163149, rend_intergenic: 159988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support