-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_15910259-16080447

-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_5-snap.2926-T1
Couldn't classify 163606, 163633
Sorry, prediction pasa_asmbl_46042.p1 fails validation.
(CTG)	 TT	163606-163633	GT	GAG
(TAG)	 AG	164051-164227	GT	AGG
(CTC)	 AG	164496-164609	GT	CAG
(GTG)	 AG	164775-164924	GT	AGG
(GAG)	 AG	165717-165848	GT	AGG
(TCA)	 AG	166111-166183	GT	AGG
(CGA)	 AG	166705-166981	AC	AAA
-recovered pasa_asmbl_46042.p1, terminal, 166705, 166981
-recovered pasa_asmbl_46042.p1, internal, 164051, 164227
-recovered pasa_asmbl_46042.p1, internal, 164496, 164609
-recovered pasa_asmbl_46042.p1, internal, 164775, 164924
-recovered pasa_asmbl_46042.p1, internal, 165717, 165848
-recovered pasa_asmbl_46042.p1, internal, 166111, 166183
Valid prediction for GlimmerHMM_glimmerT_13308-T1
Valid prediction for GlimmerHMM_glimmerT_13305-T1
Valid prediction for Augustus_model.g8846.t1
Valid prediction for Augustus_model.g8844.t1
Valid prediction for Augustus_model.g8842.t1
Valid prediction for GlimmerHMM_glimmerT_13295-T1
Valid prediction for GlimmerHMM_glimmerT_13299-T1
Couldn't classify 26387, 26492
Sorry, prediction pasa_asmbl_46035.p3 fails validation.
(ATG)	 AG	24496-24686	GT	AAG
(ACC)	 AG	26387-26492	GT	TGG
-recovered pasa_asmbl_46035.p3, initial, 24496, 24686
-recovered pasa_asmbl_46035.p3, internal, 24496, 24686
-recovered pasa_asmbl_46035.p3, internal, 26387, 26492
Valid prediction for snap_scaffold_5-snap.2949-T1
Valid prediction for snap_scaffold_5-snap.2941-T1
Valid prediction for GlimmerHMM_glimmerT_13298-T1
Valid prediction for snap_scaffold_5-snap.2937-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 161189, 161240
Couldn't classify 162284, 162399
Sorry, prediction pasa_asmbl_46041.p1 fails validation.
(GGG)	 TC	161189-161240	GT	AGG
(CGC)	 AG	161371-161441	GT	AGG
(GAA)	 AG	161771-161996	GT	TGG
(TTC)	 AG	162284-162399	GT	AGG
-recovered pasa_asmbl_46041.p1, internal, 161371, 161441
-recovered pasa_asmbl_46041.p1, internal, 161771, 161996
-recovered pasa_asmbl_46041.p1, internal, 162284, 162399
Valid prediction for snap_scaffold_5-snap.2924-T1
Valid prediction for snap_scaffold_5-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_13309-T1
Valid prediction for snap_scaffold_5-snap.2938-T1
Valid prediction for GlimmerHMM_glimmerT_13297-T1
Valid prediction for GlimmerHMM_glimmerT_13310-T1
Valid prediction for Augustus_model.g8845.t1
Valid prediction for snap_scaffold_5-snap.2951-T1
Valid prediction for GlimmerHMM_glimmerT_13296-T1
Valid prediction for snap_scaffold_5-snap.2960-T1
Valid prediction for Augustus_model.g8840.t1
Valid prediction for pasa_asmbl_46033.p1
Valid prediction for Augustus_model.g8850.t1
Valid prediction for snap_scaffold_5-snap.2929-T1
Valid prediction for GlimmerHMM_glimmerT_13293-T1
Valid prediction for GlimmerHMM_glimmerT_13294-T1
Valid prediction for snap_scaffold_5-snap.2931-T1
Valid prediction for snap_scaffold_5-snap.2934-T1
Couldn't classify 112658, 113651
Couldn't classify 113712, 113995
Sorry, prediction CodingQuarry_transcript_52406-T1 fails validation.
(ATG)	 CC	110092-110161	GT	AGG
(CAC)	 AG	112658-113651	CT	GCC
(CCC)	 AC	113712-113995	GT	GGG
(GAT)	 AG	114772-114857	GT	AGG
(CTT)	 AG	114953-115030	GC	AGG
(GCC)	 AG	115143-115289	GT	AGG
(ATT)	 AG	115441-115569	GT	AGG
(GTG)	 AG	115734-115856	GT	TGG
(GAG)	 AG	115962-115976	AC	AGA
-recovered CodingQuarry_transcript_52406-T1, initial, 110092, 110161
-recovered CodingQuarry_transcript_52406-T1, terminal, 115962, 115976
-recovered CodingQuarry_transcript_52406-T1, internal, 114772, 114857
-recovered CodingQuarry_transcript_52406-T1, internal, 114953, 115030
-recovered CodingQuarry_transcript_52406-T1, internal, 115143, 115289
-recovered CodingQuarry_transcript_52406-T1, internal, 115441, 115569
-recovered CodingQuarry_transcript_52406-T1, internal, 115734, 115856
Valid prediction for Augustus_model.g8847.t1
Valid prediction for CodingQuarry_transcript_52405-T1
Valid prediction for snap_scaffold_5-snap.2957-T1
Valid prediction for GlimmerHMM_glimmerT_13292-T1
Valid prediction for HiQ_model.g8839.t1
Valid prediction for Augustus_model.g8852.t1
Valid prediction for snap_scaffold_5-snap.2942-T1
Couldn't classify 157084, 157102
Couldn't classify 158928, 159055
Sorry, prediction pasa_asmbl_46040.p1 fails validation.
(ACA)	 TC	157084-157102	GT	CTG
(CTA)	 AG	157967-158081	GT	CTG
(CCC)	 AG	158223-158407	GT	AGG
(CGG)	 AG	158623-158754	GT	AAG
(GCA)	 AG	158928-159055	AA	CCA
-recovered pasa_asmbl_46040.p1, internal, 157967, 158081
-recovered pasa_asmbl_46040.p1, internal, 158223, 158407
-recovered pasa_asmbl_46040.p1, internal, 158623, 158754
Valid prediction for pasa_asmbl_46036.p1
Valid prediction for snap_scaffold_5-snap.2955-T1
Valid prediction for snap_scaffold_5-snap.2943-T1
Valid prediction for GlimmerHMM_glimmerT_13301-T1
Valid prediction for Augustus_model.g8843.t1
Valid prediction for snap_scaffold_5-snap.2946-T1
Valid prediction for pasa_asmbl_46038.p1
Valid prediction for snap_scaffold_5-snap.2954-T1
Valid prediction for GlimmerHMM_glimmerT_13300-T1
Valid prediction for snap_scaffold_5-snap.2944-T1
Valid prediction for HiQ_model.g8841.t1
Valid prediction for GlimmerHMM_glimmerT_13304-T1
Valid prediction for GlimmerHMM_glimmerT_13291-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_5-snap.2945-T1
Valid prediction for GlimmerHMM_glimmerT_13307-T1
Valid prediction for GlimmerHMM_glimmerT_13288-T1
Valid prediction for snap_scaffold_5-snap.2928-T1
Valid prediction for snap_scaffold_5-snap.2950-T1
Valid prediction for snap_scaffold_5-snap.2953-T1
Valid prediction for snap_scaffold_5-snap.2940-T1
Valid prediction for snap_scaffold_5-snap.2927-T1
Valid prediction for snap_scaffold_5-snap.2948-T1
Valid prediction for Augustus_model.g8851.t1
Valid prediction for snap_scaffold_5-snap.2935-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13312-T1
Valid prediction for Augustus_model.g8849.t1
Valid prediction for GlimmerHMM_glimmerT_13306-T1
Valid prediction for snap_scaffold_5-snap.2952-T1
Valid prediction for snap_scaffold_5-snap.2925-T1
Couldn't classify 63687, 64049
Couldn't classify 64202, 64315
Sorry, prediction pasa_asmbl_44737.p1 fails validation.
(GAC)	 AG	63687-64049	GT	CGG
(CCG)	 AG	64202-64315	CG	AGC
-recovered pasa_asmbl_44737.p1, internal, 63687, 64049
Valid prediction for snap_scaffold_5-snap.2939-T1
Valid prediction for snap_scaffold_5-snap.2961-T1
Valid prediction for GlimmerHMM_glimmerT_13311-T1
Valid prediction for snap_scaffold_5-snap.2956-T1
Valid prediction for GlimmerHMM_glimmerT_13290-T1
Couldn't classify 61743, 61798
Couldn't classify 63244, 63485
Sorry, prediction pasa_asmbl_44741.p1 fails validation.
(AGC)	 TC	61743-61798	GC	AGG
(GAC)	 AG	62394-62434	GT	AGG
(TTT)	 AG	63244-63485	AG	AGA
-recovered pasa_asmbl_44741.p1, internal, 62394, 62434
Valid prediction for GlimmerHMM_glimmerT_13302-T1
Valid prediction for snap_scaffold_5-snap.2933-T1
Valid prediction for snap_scaffold_5-snap.2930-T1
Valid prediction for snap_scaffold_5-snap.2959-T1
Valid prediction for GlimmerHMM_glimmerT_13303-T1
Valid prediction for Augustus_model.g8848.t1
Valid prediction for GlimmerHMM_glimmerT_13289-T1
Valid prediction for snap_scaffold_5-snap.2936-T1
Valid prediction for snap_scaffold_5-snap.2958-T1
Valid prediction for snap_scaffold_5-snap.2947-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16501, rend_intergenic: 9008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17286, rend_intergenic: 16514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18196, rend_intergenic: 17520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28606, rend_intergenic: 28478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31756, rend_intergenic: 29066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45633, rend_intergenic: 41734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53477, rend_intergenic: 50071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69273, rend_intergenic: 59768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95276, rend_intergenic: 91819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102277, rend_intergenic: 96149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124608, rend_intergenic: 120464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131719, rend_intergenic: 129100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144325, rend_intergenic: 133775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146610, rend_intergenic: 144840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150269, rend_intergenic: 146753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152693, rend_intergenic: 150658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166981, rend_intergenic: 155766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170189
-exon list size: 388


building trellis

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1.0    
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3.8    
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10.0    
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11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
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13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
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    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
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    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 16501, rend_intergenic: 9008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17286, rend_intergenic: 16514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18196, rend_intergenic: 17520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28606, rend_intergenic: 28478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31756, rend_intergenic: 29066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45633, rend_intergenic: 41734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53477, rend_intergenic: 50071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69273, rend_intergenic: 59768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95276, rend_intergenic: 91819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102277, rend_intergenic: 96149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124608, rend_intergenic: 120464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131719, rend_intergenic: 129100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144325, rend_intergenic: 133775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146610, rend_intergenic: 144840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150269, rend_intergenic: 146753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152693, rend_intergenic: 150658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166981, rend_intergenic: 155766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support