-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_1066869-1230566

-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 Augustus_model.g19036.t1
Valid prediction for GlimmerHMM_glimmerT_28820-T1
Valid prediction for snap_scaffold_12-snap.285-T1
Valid prediction for Augustus_model.g19044.t1
Valid prediction for snap_scaffold_12-snap.272-T1
Valid prediction for snap_scaffold_12-snap.282-T1
Valid prediction for snap_scaffold_12-snap.265-T1
Valid prediction for snap_scaffold_12-snap.257-T1
Valid prediction for snap_scaffold_12-snap.267-T1
Valid prediction for snap_scaffold_12-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_28821-T1
Valid prediction for HiQ_model.g19045.t1
Valid prediction for snap_scaffold_12-snap.269-T1
Valid prediction for GlimmerHMM_glimmerT_28808-T1
Couldn't classify 109925, 109998
Sorry, prediction pasa_asmbl_7460.p1 fails validation.
(GTG)	 AG	109925-109998	GT	AGG
(CTG)	 AG	110293-110351	GT	TGG
(GTA)	 AG	111067-111208	GT	CAG
(GTA)	 AG	111477-111558	GT	TGG
(GAT)	 AG	111852-112044	GT	GGG
(TGG)	 AG	113504-113693	GT	TGG
(GGA)	 AG	114095-114208	GT	TGG
(GGA)	 AG	114904-115060	GT	AGG
(GGT)	 AG	116053-116268	GT	AGG
(CCT)	 AG	118692-118811	GT	AGG
(AAG)	 AG	119414-119552	GT	AGG
(CAG)	 AG	119664-119779	GT	AGG
(AAA)	 AG	120321-120377	AG	GAA
-recovered pasa_asmbl_7460.p1, terminal, 120321, 120377
-recovered pasa_asmbl_7460.p1, internal, 109925, 109998
-recovered pasa_asmbl_7460.p1, internal, 110293, 110351
-recovered pasa_asmbl_7460.p1, internal, 111067, 111208
-recovered pasa_asmbl_7460.p1, internal, 111477, 111558
-recovered pasa_asmbl_7460.p1, internal, 111852, 112044
-recovered pasa_asmbl_7460.p1, internal, 113504, 113693
-recovered pasa_asmbl_7460.p1, internal, 114095, 114208
-recovered pasa_asmbl_7460.p1, internal, 114904, 115060
-recovered pasa_asmbl_7460.p1, internal, 116053, 116268
-recovered pasa_asmbl_7460.p1, internal, 118692, 118811
-recovered pasa_asmbl_7460.p1, internal, 119414, 119552
-recovered pasa_asmbl_7460.p1, internal, 119664, 119779
Valid prediction for snap_scaffold_12-snap.258-T1
Valid prediction for GlimmerHMM_glimmerT_28812-T1
Valid prediction for GlimmerHMM_glimmerT_28819-T1
Valid prediction for GlimmerHMM_glimmerT_28806-T1
Valid prediction for HiQ_model.g19037.t1
Valid prediction for GlimmerHMM_glimmerT_28805-T1
Valid prediction for Augustus_model.g19043.t1
Valid prediction for Augustus_model.g19038.t1
Valid prediction for snap_scaffold_12-snap.277-T1
Valid prediction for Augustus_model.g19035.t1
Valid prediction for GlimmerHMM_glimmerT_28811-T1
Valid prediction for snap_scaffold_12-snap.283-T1
Valid prediction for CodingQuarry_transcript_10127-T1
Valid prediction for HiQ_model.g19041.t1
Valid prediction for GlimmerHMM_glimmerT_28818-T1
Valid prediction for Augustus_model.g19040.t1
Valid prediction for snap_scaffold_12-snap.273-T1
Valid prediction for GlimmerHMM_glimmerT_28815-T1
Valid prediction for snap_scaffold_12-snap.279-T1
Couldn't classify 156054, 158885
Couldn't classify 163238, 163382
Sorry, prediction pasa_asmbl_7464.p1 fails validation.
(CTG)	 TG	156054-158885	GT	AGG
(CAG)	 AG	161649-161740	GC	TGG
(GTC)	 AG	163238-163382	GG	CCG
-recovered pasa_asmbl_7464.p1, internal, 161649, 161740
Valid prediction for GlimmerHMM_glimmerT_28816-T1
Valid prediction for Augustus_model.g19034.t1
Valid prediction for Augustus_model.g19039.t1
Valid prediction for Augustus_model.g19042.t1
Valid prediction for GlimmerHMM_glimmerT_28817-T1
Valid prediction for GlimmerHMM_glimmerT_28814-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_12-snap.271-T1
Valid prediction for snap_scaffold_12-snap.255-T1
Valid prediction for snap_scaffold_12-snap.286-T1
Valid prediction for snap_scaffold_12-snap.266-T1
Valid prediction for snap_scaffold_12-snap.280-T1
Valid prediction for snap_scaffold_12-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_28810-T1
Valid prediction for snap_scaffold_12-snap.288-T1
Valid prediction for snap_scaffold_12-snap.256-T1
Valid prediction for snap_scaffold_12-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_28809-T1
Valid prediction for snap_scaffold_12-snap.274-T1
Valid prediction for snap_scaffold_12-snap.261-T1
Valid prediction for snap_scaffold_12-snap.270-T1
Valid prediction for snap_scaffold_12-snap.287-T1
Valid prediction for snap_scaffold_12-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_28813-T1
Valid prediction for snap_scaffold_12-snap.281-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28804-T1
Valid prediction for GlimmerHMM_glimmerT_28807-T1
Valid prediction for snap_scaffold_12-snap.264-T1
Valid prediction for snap_scaffold_12-snap.275-T1
Valid prediction for snap_scaffold_12-snap.278-T1
Valid prediction for snap_scaffold_12-snap.290-T1
Valid prediction for snap_scaffold_12-snap.260-T1
Valid prediction for snap_scaffold_12-snap.263-T1
Valid prediction for GlimmerHMM_glimmerT_28822-T1
Valid prediction for snap_scaffold_12-snap.268-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25702, rend_intergenic: 13667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79141, rend_intergenic: 36185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81897, rend_intergenic: 79602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86349, rend_intergenic: 82726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95686, rend_intergenic: 87542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98897, rend_intergenic: 96656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117550, rend_intergenic: 108026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120377, rend_intergenic: 118440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133307, rend_intergenic: 127303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141677, rend_intergenic: 137475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149695, rend_intergenic: 143503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163698
-exon list size: 264


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.6    
3.0    
3.4    
3.8    
4.1    
4.5    
4.9    
5.3    
5.6    
6.0    
6.4    
6.8    
7.1    
7.5    
7.9    
8.3    
8.6    
9.0    
9.4    
9.8    
10.2    
10.5    
10.9    
11.3    
11.7    
12.0    
12.4    
12.8    
13.2    
13.5    
13.9    
14.3    
14.7    
15.0    
15.4    
15.8    
16.2    
16.5    
16.9    
17.3    
17.7    
18.0    
18.4    
18.8    
19.2    
19.5    
19.9    
20.3    
20.7    
21.1    
21.4    
21.8    
22.2    
22.6    
22.9    
23.3    
23.7    
24.1    
24.4    
24.8    
25.2    
25.6    
25.9    
26.3    
26.7    
27.1    
27.4    
27.8    
28.2    
28.6    
28.9    
29.3    
29.7    
30.1    
30.5    
30.8    
31.2    
31.6    
32.0    
32.3    
32.7    
33.1    
33.5    
33.8    
34.2    
34.6    
35.0    
35.3    
35.7    
36.1    
36.5    
36.8    
37.2    
37.6    
38.0    
38.3    
38.7    
39.1    
39.5    
39.8    
40.2    
40.6    
41.0    
41.4    
41.7    
42.1    
42.5    
42.9    
43.2    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.9    
46.2    
46.6    
47.0    
47.4    
47.7    
48.1    
48.5    
48.9    
49.2    
49.6    
50.0    
50.4    
50.8    
51.1    
51.5    
51.9    
52.3    
52.6    
53.0    
53.4    
53.8    
54.1    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.8    
57.1    
57.5    
57.9    
58.3    
58.6    
59.0    
59.4    
59.8    
60.2    
60.5    
60.9    
61.3    
61.7    
62.0    
62.4    
62.8    
63.2    
63.5    
63.9    
64.3    
64.7    
65.0    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.7    
68.0    
68.4    
68.8    
69.2    
69.5    
69.9    
70.3    
70.7    
71.1    
71.4    
71.8    
72.2    
72.6    
72.9    
73.3    
73.7    
74.1    
74.4    
74.8    
75.2    
75.6    
75.9    
76.3    
76.7    
77.1    
77.4    
77.8    
78.2    
78.6    
78.9    
79.3    
79.7    
80.1    
80.5    
80.8    
81.2    
81.6    
82.0    
82.3    
82.7    
83.1    
83.5    
83.8    
84.2    
84.6    
85.0    
85.3    
85.7    
86.1    
86.5    
86.8    
87.2    
87.6    
88.0    
88.3    
88.7    
89.1    
89.5    
89.8    
90.2    
90.6    
91.0    
91.4    
91.7    
92.1    
92.5    
92.9    
93.2    
93.6    
94.0    
94.4    
94.7    
95.1    
95.5    
95.9    
96.2    
96.6    
97.0    
97.4    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 25702, rend_intergenic: 13667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79141, rend_intergenic: 36185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81897, rend_intergenic: 79602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86349, rend_intergenic: 82726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95686, rend_intergenic: 87542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98897, rend_intergenic: 96656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117550, rend_intergenic: 108026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120377, rend_intergenic: 118440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133307, rend_intergenic: 127303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141677, rend_intergenic: 137475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149695, rend_intergenic: 143503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support