-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_15675152-15853180

-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_5112-T1
Valid prediction for Augustus_model.g3453.t1
Valid prediction for GlimmerHMM_glimmerT_5122-T1
Valid prediction for snap_scaffold_2-snap.3023-T1
Valid prediction for GlimmerHMM_glimmerT_5120-T1
Valid prediction for snap_scaffold_2-snap.3006-T1
Valid prediction for snap_scaffold_2-snap.3000-T1
Valid prediction for pasa_asmbl_25073.p1
Valid prediction for snap_scaffold_2-snap.3027-T1
Valid prediction for Augustus_model.g3458.t1
Valid prediction for GlimmerHMM_glimmerT_5119-T1
Valid prediction for Augustus_model.g3454.t1
Valid prediction for snap_scaffold_2-snap.3004-T1
Valid prediction for snap_scaffold_2-snap.3002-T1
Valid prediction for GlimmerHMM_glimmerT_5116-T1
Valid prediction for Augustus_model.g3466.t1
Valid prediction for Augustus_model.g3469.t1
Valid prediction for HiQ_model.g3448.t1
Valid prediction for GlimmerHMM_glimmerT_5118-T1
Valid prediction for Augustus_model.g3463.t1
Valid prediction for Augustus_model.g3449.t1
Valid prediction for Augustus_model.g3470.t1
Valid prediction for Augustus_model.g3461.t1
Valid prediction for snap_scaffold_2-snap.3009-T1
Valid prediction for Augustus_model.g3468.t1
Valid prediction for snap_scaffold_2-snap.3024-T1
Valid prediction for CodingQuarry_transcript_28779-T1
Valid prediction for snap_scaffold_2-snap.3017-T1
Valid prediction for GlimmerHMM_glimmerT_5134-T1
Couldn't classify 161473, 162009
Sorry, prediction pasa_asmbl_25076.p1 fails validation.
(AGT)	 CC	161473-162009	CA	AAC
Valid prediction for snap_scaffold_2-snap.2995-T1
Valid prediction for snap_scaffold_2-snap.3003-T1
Valid prediction for Augustus_model.g3457.t1
Valid prediction for HiQ_model.g3451.t1
Valid prediction for snap_scaffold_2-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_5129-T1
Valid prediction for pasa_asmbl_25067.p1
Valid prediction for GlimmerHMM_glimmerT_5125-T1
Valid prediction for CodingQuarry_transcript_28780-T1
Valid prediction for GlimmerHMM_glimmerT_5107-T1
Valid prediction for GlimmerHMM_glimmerT_5111-T1
Valid prediction for snap_scaffold_2-snap.3011-T1
Couldn't classify 145719, 145795
Sorry, prediction pasa_asmbl_25075.p1 fails validation.
(ATG)	 GT	141309-142107	GT	AGG
(AGT)	 AG	144883-144939	GT	GGG
(ATC)	 AG	145719-145795	GG	CAG
-recovered pasa_asmbl_25075.p1, initial, 141309, 142107
-recovered pasa_asmbl_25075.p1, internal, 144883, 144939
Valid prediction for GlimmerHMM_glimmerT_5130-T1
Valid prediction for snap_scaffold_2-snap.3020-T1
Valid prediction for snap_scaffold_2-snap.2994-T1
Valid prediction for Augustus_model.g3465.t1
Valid prediction for GlimmerHMM_glimmerT_5108-T1
Valid prediction for snap_scaffold_2-snap.3029-T1
Valid prediction for snap_scaffold_2-snap.3007-T1
Valid prediction for Augustus_model.g3456.t1
Valid prediction for CodingQuarry_transcript_28778-T1
Valid prediction for Augustus_model.g3455.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.2996-T1
Valid prediction for GlimmerHMM_glimmerT_5109-T1
Valid prediction for snap_scaffold_2-snap.3012-T1
Valid prediction for GlimmerHMM_glimmerT_5132-T1
Valid prediction for snap_scaffold_2-snap.3022-T1
Valid prediction for GlimmerHMM_glimmerT_5135-T1
Valid prediction for snap_scaffold_2-snap.3019-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2998-T1
Valid prediction for snap_scaffold_2-snap.3026-T1
Valid prediction for snap_scaffold_2-snap.2997-T1
Valid prediction for Augustus_model.g3464.t1
Valid prediction for snap_scaffold_2-snap.3021-T1
Valid prediction for snap_scaffold_2-snap.3008-T1
Valid prediction for snap_scaffold_2-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_5115-T1
Couldn't classify 170716, 171021
Sorry, prediction pasa_asmbl_23653.p1 fails validation.
(ATG)	 AC	170716-171021	CT	ATC
Valid prediction for GlimmerHMM_glimmerT_5123-T1
Valid prediction for snap_scaffold_2-snap.3010-T1
Valid prediction for GlimmerHMM_glimmerT_5136-T1
Valid prediction for GlimmerHMM_glimmerT_5114-T1
Couldn't classify 148828, 149037
Sorry, prediction pasa_asmbl_23654.p1 fails validation.
(ACA)	 GG	148828-149037	GT	AGG
(CTG)	 AG	149384-149530	GT	TGG
(GAC)	 AG	149667-149744	GT	CTG
(GTC)	 AG	149857-149908	GT	AGG
(ATG)	 AG	150239-150363	GT	CTG
(CCA)	 AG	150537-150744	GT	CTG
(CGT)	 AG	150913-150977	GT	AGG
(CCT)	 AG	151116-151174	GT	TGG
(TTT)	 AG	151325-151370	GT	TGG
(GTG)	 AG	151485-151598	CA	GAC
add_exon() Sorry, pasa_asmbl_23654.p1 150239-150363-initial-1 is invalid.
-recovered pasa_asmbl_23654.p1, initial, 150239, 150363
-recovered pasa_asmbl_23654.p1, terminal, 151485, 151598
-recovered pasa_asmbl_23654.p1, internal, 149384, 149530
-recovered pasa_asmbl_23654.p1, internal, 149667, 149744
-recovered pasa_asmbl_23654.p1, internal, 149857, 149908
-recovered pasa_asmbl_23654.p1, internal, 150239, 150363
-recovered pasa_asmbl_23654.p1, internal, 150537, 150744
-recovered pasa_asmbl_23654.p1, internal, 150913, 150977
-recovered pasa_asmbl_23654.p1, internal, 151116, 151174
-recovered pasa_asmbl_23654.p1, internal, 151325, 151370
Valid prediction for GlimmerHMM_glimmerT_5110-T1
Valid prediction for Augustus_model.g3459.t1
Couldn't classify 83180, 83259
Sorry, prediction pasa_asmbl_23658.p1 fails validation.
(ATG)	 GG	81796-81835	GT	AGG
(TGG)	 AG	82581-82776	GT	GCG
(GTA)	 AG	82886-83079	GT	AGG
(AGA)	 AG	83180-83259	GG	CTG
-recovered pasa_asmbl_23658.p1, initial, 81796, 81835
-recovered pasa_asmbl_23658.p1, internal, 82581, 82776
-recovered pasa_asmbl_23658.p1, internal, 82886, 83079
Valid prediction for snap_scaffold_2-snap.3015-T1
Valid prediction for snap_scaffold_2-snap.3014-T1
Valid prediction for Augustus_model.g3462.t1
Valid prediction for snap_scaffold_2-snap.3028-T1
Valid prediction for GlimmerHMM_glimmerT_5117-T1
Valid prediction for Augustus_model.g3467.t1
Valid prediction for GlimmerHMM_glimmerT_5121-T1
Valid prediction for GlimmerHMM_glimmerT_5124-T1
Valid prediction for GlimmerHMM_glimmerT_5106-T1
Valid prediction for snap_scaffold_2-snap.2999-T1
Valid prediction for snap_scaffold_2-snap.3005-T1
Valid prediction for snap_scaffold_2-snap.3013-T1
Valid prediction for Augustus_model.g3450.t1
Valid prediction for snap_scaffold_2-snap.3030-T1
Valid prediction for GlimmerHMM_glimmerT_5128-T1
Valid prediction for GlimmerHMM_glimmerT_5133-T1
Couldn't classify 171263, 171490
Couldn't classify 173737, 173790
Sorry, prediction pasa_asmbl_23652.p1 fails validation.
(GAG)	 AG	171263-171490	GT	TGG
(TGG)	 AG	171590-171659	GT	AGG
(GTC)	 AG	171753-171922	GT	AGG
(GTC)	 AG	172703-172941	GT	AAG
(GCA)	 AG	173048-173114	GT	AGG
(CTG)	 AG	173285-173343	GT	AGG
(TGG)	 AG	173467-173611	GT	CGG
(ATG)	 AG	173737-173790	CT	CCC
-recovered pasa_asmbl_23652.p1, internal, 171263, 171490
-recovered pasa_asmbl_23652.p1, internal, 171590, 171659
-recovered pasa_asmbl_23652.p1, internal, 171753, 171922
-recovered pasa_asmbl_23652.p1, internal, 172703, 172941
-recovered pasa_asmbl_23652.p1, internal, 173048, 173114
-recovered pasa_asmbl_23652.p1, internal, 173285, 173343
-recovered pasa_asmbl_23652.p1, internal, 173467, 173611
Valid prediction for GlimmerHMM_glimmerT_5127-T1
Valid prediction for snap_scaffold_2-snap.3001-T1
Valid prediction for GlimmerHMM_glimmerT_5113-T1
Valid prediction for snap_scaffold_2-snap.3016-T1
Valid prediction for snap_scaffold_2-snap.3018-T1
Valid prediction for Augustus_model.g3460.t1
Valid prediction for Augustus_model.g3452.t1
Valid prediction for GlimmerHMM_glimmerT_5131-T1
Valid prediction for GlimmerHMM_glimmerT_5126-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 79565, rend_intergenic: 77636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86023, rend_intergenic: 82601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89406, rend_intergenic: 86084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120957, rend_intergenic: 119368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129454, rend_intergenic: 125198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134428, rend_intergenic: 132048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158427, rend_intergenic: 153534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170122, rend_intergenic: 167365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178029
-exon list size: 369


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 79565, rend_intergenic: 77636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86023, rend_intergenic: 82601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89406, rend_intergenic: 86084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120957, rend_intergenic: 119368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129454, rend_intergenic: 125198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134428, rend_intergenic: 132048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158427, rend_intergenic: 153534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170122, rend_intergenic: 167365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support