-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_1-161273

-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 HiQ_model.g37510.t1
Valid prediction for GeneMark_model.97890_t
Couldn't classify 31654, 31738
Sorry, prediction pasa_asmbl_35195.p1 fails validation.
(ATG)	 CG	29273-29392	GT	AGG
(TGG)	 AG	29729-29842	GT	TGG
(AAT)	 AG	29982-30113	GT	AGG
(GGG)	 AG	30191-30322	GT	ATG
(ATC)	 AG	30405-30479	GT	CTG
(AAG)	 AG	30601-30758	GT	GGG
(CTT)	 AG	30938-31017	GT	TGG
(CTG)	 AG	31094-31277	GT	AGG
(CGT)	 AG	31654-31738	CT	GAC
-recovered pasa_asmbl_35195.p1, initial, 29273, 29392
-recovered pasa_asmbl_35195.p1, internal, 29729, 29842
-recovered pasa_asmbl_35195.p1, internal, 29982, 30113
-recovered pasa_asmbl_35195.p1, internal, 30191, 30322
-recovered pasa_asmbl_35195.p1, internal, 30405, 30479
-recovered pasa_asmbl_35195.p1, internal, 30601, 30758
-recovered pasa_asmbl_35195.p1, internal, 30938, 31017
-recovered pasa_asmbl_35195.p1, internal, 31094, 31277
Valid prediction for GeneMark_model.97881_t
Valid prediction for GlimmerHMM_glimmerT_56266-T1
Valid prediction for Augustus_model.g37514.t1
Valid prediction for GlimmerHMM_glimmerT_56270-T1
Valid prediction for GlimmerHMM_glimmerT_56259-T1
Valid prediction for GeneMark_model.97889_t
Valid prediction for GeneMark_model.97884_t
Valid prediction for GlimmerHMM_glimmerT_56265-T1
Valid prediction for GlimmerHMM_glimmerT_56248-T1
Valid prediction for snap_scaffold_26-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_56261-T1
Valid prediction for GeneMark_model.97906_t
Valid prediction for GlimmerHMM_glimmerT_56255-T1
Valid prediction for snap_scaffold_26-snap.20-T1
Valid prediction for Augustus_model.g37507.t1
Valid prediction for GlimmerHMM_glimmerT_56258-T1
Couldn't classify 31996, 32183
Sorry, prediction pasa_asmbl_35196.p1 fails validation.
(CAG)	 CC	31996-32183	GT	AGG
(CCT)	 AG	32451-32612	GT	TGG
(GAT)	 AG	32749-32889	GT	AAG
(GTT)	 AG	33173-33254	GT	AGG
(GTG)	 AG	33358-33582	GG	AAG
-recovered pasa_asmbl_35196.p1, terminal, 33358, 33582
-recovered pasa_asmbl_35196.p1, internal, 32451, 32612
-recovered pasa_asmbl_35196.p1, internal, 32749, 32889
-recovered pasa_asmbl_35196.p1, internal, 33173, 33254
Valid prediction for Augustus_model.g37517.t1
Valid prediction for GlimmerHMM_glimmerT_56253-T1
Valid prediction for snap_scaffold_26-snap.12-T1
Valid prediction for GeneMark_model.97892_t
Couldn't classify 27137, 27280
Couldn't classify 29238, 29242
Sorry, prediction pasa_asmbl_35194.p1 fails validation.
(GTC)	 AT	27137-27280	GT	AGG
(GTG)	 AG	28263-28397	GT	AGG
(ATT)	 AG	28772-28892	GT	AGG
(ACC)	 AG	29238-29242	GT	TGG
-recovered pasa_asmbl_35194.p1, internal, 28263, 28397
-recovered pasa_asmbl_35194.p1, internal, 28772, 28892
-recovered pasa_asmbl_35194.p1, internal, 29238, 29242
Valid prediction for GlimmerHMM_glimmerT_56250-T1
Valid prediction for HiQ_model.g37516.t1
Valid prediction for snap_scaffold_26-snap.22-T1
Valid prediction for snap_scaffold_26-snap.29-T1
Valid prediction for snap_scaffold_26-snap.36-T1
Valid prediction for GeneMark_model.97886_t
Valid prediction for Augustus_model.g37503.t1
Valid prediction for snap_scaffold_26-snap.10-T1
Valid prediction for snap_scaffold_26-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_56251-T1
Valid prediction for GeneMark_model.97900_t
Valid prediction for GeneMark_model.97905_t
Valid prediction for GlimmerHMM_glimmerT_56246-T1
Valid prediction for Augustus_model.g37511.t1
Valid prediction for snap_scaffold_26-snap.16-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.32-T1
Couldn't classify 118307, 118430
Sorry, prediction pasa_asmbl_35198.p1 fails validation.
(ATG)	 AA	117193-117284	GT	AAG
(TAA)	 AG	117477-117526	GT	AGG
(GCA)	 AG	117852-117957	GT	AAG
(AGA)	 AG	118307-118430	GT	AGG
-recovered pasa_asmbl_35198.p1, initial, 117193, 117284
add_exon() Sorry, pasa_asmbl_35198.p1 117852-117957-terminal-3 is invalid.
-recovered pasa_asmbl_35198.p1, terminal, 117852, 117957
-recovered pasa_asmbl_35198.p1, internal, 117477, 117526
-recovered pasa_asmbl_35198.p1, internal, 117852, 117957
-recovered pasa_asmbl_35198.p1, internal, 118307, 118430
Valid prediction for GeneMark_model.97893_t
Valid prediction for snap_scaffold_26-snap.6-T1
Valid prediction for snap_scaffold_26-snap.15-T1
Valid prediction for snap_scaffold_26-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_56257-T1
Valid prediction for snap_scaffold_26-snap.27-T1
Valid prediction for CodingQuarry_transcript_40143-T1
Valid prediction for snap_scaffold_26-snap.38-T1
Valid prediction for snap_scaffold_26-snap.37-T1
Valid prediction for GeneMark_model.97903_t
Valid prediction for snap_scaffold_26-snap.8-T1
Valid prediction for pasa_asmbl_35200.p1
Valid prediction for GeneMark_model.97878_t

-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 GeneMark_model.97895_t
Couldn't classify 18976, 19046
Sorry, prediction pasa_asmbl_34650.p1 fails validation.
(CCT)	 CT	18976-19046	GT	AGG
(GCT)	 AG	19814-20048	CA	GAC
-recovered pasa_asmbl_34650.p1, terminal, 19814, 20048
Couldn't classify 14739, 14822
Couldn't classify 16414, 16515
Sorry, prediction pasa_asmbl_34651.p1 fails validation.
(GGT)	 AA	14739-14822	GT	AGG
(GGG)	 AG	15029-15175	GT	GCG
(TCC)	 AG	16414-16515	CC	AGC
-recovered pasa_asmbl_34651.p1, internal, 15029, 15175
Valid prediction for snap_scaffold_26-snap.5-T1
Couldn't classify 154926, 155282
Sorry, prediction pasa_asmbl_34638.p1 fails validation.
(CCA)	 CG	154926-155282	GG	GAG
Valid prediction for Augustus_model.g37515.t1
Valid prediction for Augustus_model.g37509.t1
Valid prediction for GlimmerHMM_glimmerT_56267-T1
Valid prediction for snap_scaffold_26-snap.28-T1
Valid prediction for snap_scaffold_26-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_56268-T1
Valid prediction for GeneMark_model.97882_t
Valid prediction for snap_scaffold_26-snap.14-T1
Valid prediction for GeneMark_model.97901_t
Valid prediction for GeneMark_model.97902_t
Valid prediction for snap_scaffold_26-snap.3-T1
Valid prediction for GeneMark_model.97898_t
Valid prediction for Augustus_model.g37513.t1
Valid prediction for GlimmerHMM_glimmerT_56254-T1
Valid prediction for GeneMark_model.97904_t
Couldn't classify 155349, 155507
Sorry, prediction pasa_asmbl_34637.p1 fails validation.
(GGG)	 CA	155349-155507	GT	GGG
(AGT)	 AG	156842-156900	GT	AGG
(TCG)	 AG	156989-157085	GT	AGG
(GAG)	 AG	157355-157513	GT	TGG
(GGA)	 AG	157672-157740	GT	TGG
(ACC)	 AG	158464-158669	GT	CGG
(ATT)	 AG	158761-158914	AG	GAA
-recovered pasa_asmbl_34637.p1, terminal, 158761, 158914
-recovered pasa_asmbl_34637.p1, internal, 156842, 156900
-recovered pasa_asmbl_34637.p1, internal, 156989, 157085
-recovered pasa_asmbl_34637.p1, internal, 157355, 157513
-recovered pasa_asmbl_34637.p1, internal, 157672, 157740
-recovered pasa_asmbl_34637.p1, internal, 158464, 158669
Valid prediction for snap_scaffold_26-snap.18-T1
Valid prediction for snap_scaffold_26-snap.19-T1
Valid prediction for HiQ_model.g37512.t1
Valid prediction for GeneMark_model.97896_t
Valid prediction for GeneMark_model.97887_t
Valid prediction for GlimmerHMM_glimmerT_56245-T1
Valid prediction for GeneMark_model.97885_t
Valid prediction for GlimmerHMM_glimmerT_56247-T1
Valid prediction for snap_scaffold_26-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_56260-T1
Valid prediction for GeneMark_model.97891_t
Valid prediction for GlimmerHMM_glimmerT_56263-T1
Valid prediction for GeneMark_model.97879_t
Valid prediction for snap_scaffold_26-snap.26-T1
Valid prediction for snap_scaffold_26-snap.2-T1
Valid prediction for snap_scaffold_26-snap.23-T1
Couldn't classify 10276, 10377
Couldn't classify 10788, 10907
Sorry, prediction pasa_asmbl_35143.p2 fails validation.
(AGG)	 AG	10276-10377	GT	AGG
(GCT)	 AG	10621-10701	GT	AGG
(GGT)	 AG	10788-10907	CA	CCC
-recovered pasa_asmbl_35143.p2, internal, 10276, 10377
-recovered pasa_asmbl_35143.p2, internal, 10621, 10701
Valid prediction for GeneMark_model.97888_t
Valid prediction for CodingQuarry_transcript_40142-T1
Valid prediction for GlimmerHMM_glimmerT_56252-T1
Valid prediction for snap_scaffold_26-snap.21-T1
Valid prediction for CodingQuarry_transcript_40139-T1
Valid prediction for Augustus_model.g37506.t1
Valid prediction for snap_scaffold_26-snap.33-T1
Valid prediction for Augustus_model.g37505.t1
Valid prediction for GeneMark_model.97894_t
Valid prediction for snap_scaffold_26-snap.7-T1
Valid prediction for snap_scaffold_26-snap.11-T1
Valid prediction for pasa_asmbl_34641.p1
Valid prediction for GeneMark_model.97880_t
Valid prediction for pasa_asmbl_34647.p1
Valid prediction for Augustus_model.g37502.t1
Valid prediction for snap_scaffold_26-snap.34-T1
Valid prediction for snap_scaffold_26-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_56269-T1
Valid prediction for GlimmerHMM_glimmerT_56256-T1
Valid prediction for HiQ_model.g37501.t1
Valid prediction for snap_scaffold_26-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_56264-T1
Valid prediction for snap_scaffold_26-snap.24-T1
Valid prediction for CodingQuarry_transcript_40140-T1
Valid prediction for GlimmerHMM_glimmerT_56249-T1
Valid prediction for snap_scaffold_26-snap.4-T1
Valid prediction for GeneMark_model.97897_t
Valid prediction for snap_scaffold_26-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_56262-T1
Valid prediction for HiQ_model.g37504.t1
Valid prediction for GeneMark_model.97877_t
Valid prediction for Augustus_model.g37508.t1
Valid prediction for snap_scaffold_26-snap.25-T1
Valid prediction for GeneMark_model.97883_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39940, rend_intergenic: 37277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41232, rend_intergenic: 40460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64127, rend_intergenic: 56664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74777, rend_intergenic: 70127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77709, rend_intergenic: 75710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84996, rend_intergenic: 82438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91762, rend_intergenic: 88674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127976, rend_intergenic: 124977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140021, rend_intergenic: 135168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151382, rend_intergenic: 141248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161273
-exon list size: 520


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 39940, rend_intergenic: 37277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41232, rend_intergenic: 40460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64127, rend_intergenic: 56664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74777, rend_intergenic: 70127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77709, rend_intergenic: 75710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84996, rend_intergenic: 82438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91762, rend_intergenic: 88674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127976, rend_intergenic: 124977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140021, rend_intergenic: 135168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151382, rend_intergenic: 141248  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