-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_12814136-13032279

-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_11-snap.2743-T1
Valid prediction for GlimmerHMM_glimmerT_28114-T1
Valid prediction for GlimmerHMM_glimmerT_28111-T1
Valid prediction for snap_scaffold_11-snap.2756-T1
Valid prediction for CodingQuarry_transcript_8274-T1
Valid prediction for GlimmerHMM_glimmerT_28094-T1
Valid prediction for GlimmerHMM_glimmerT_28103-T1
Valid prediction for snap_scaffold_11-snap.2739-T1
Valid prediction for snap_scaffold_11-snap.2746-T1
Valid prediction for GlimmerHMM_glimmerT_28116-T1
Valid prediction for Augustus_model.g18619.t1
Valid prediction for snap_scaffold_11-snap.2742-T1
Valid prediction for snap_scaffold_11-snap.2759-T1
Valid prediction for snap_scaffold_11-snap.2731-T1
Valid prediction for snap_scaffold_11-snap.2760-T1
Valid prediction for GlimmerHMM_glimmerT_28109-T1
Valid prediction for Augustus_model.g18605.t1
Valid prediction for GlimmerHMM_glimmerT_28099-T1
Valid prediction for Augustus_model.g18608.t1
Valid prediction for snap_scaffold_11-snap.2737-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g18607.t1
Valid prediction for GlimmerHMM_glimmerT_28108-T1
Valid prediction for GlimmerHMM_glimmerT_28102-T1
Valid prediction for Augustus_model.g18611.t1
Couldn't classify 80220, 80324
Sorry, prediction pasa_asmbl_6026.p1 fails validation.
(ATG)	 CA	77681-77718	GT	GGG
(CTA)	 AG	77951-78099	GT	AGG
(AGG)	 AG	78184-78312	GT	ATG
(TGT)	 AG	78405-78598	GT	AGG
(ATA)	 AG	78853-78933	GT	GGG
(GAG)	 AG	79280-79396	GC	AGG
(GAG)	 AG	79725-79892	GT	AGG
(ATC)	 AG	80220-80324	TG	GCT
-recovered pasa_asmbl_6026.p1, initial, 77681, 77718
-recovered pasa_asmbl_6026.p1, internal, 77951, 78099
-recovered pasa_asmbl_6026.p1, internal, 78184, 78312
-recovered pasa_asmbl_6026.p1, internal, 78405, 78598
-recovered pasa_asmbl_6026.p1, internal, 78853, 78933
-recovered pasa_asmbl_6026.p1, internal, 79280, 79396
-recovered pasa_asmbl_6026.p1, internal, 79725, 79892
Valid prediction for snap_scaffold_11-snap.2752-T1
Couldn't classify 214958, 215296
Sorry, prediction pasa_asmbl_6261.p1 fails validation.
(GCA)	 TG	214958-215296	GT	GTG
(GCT)	 AG	215549-215601	GT	TCG
(CAT)	 AG	215984-216086	TT	AGT
-recovered pasa_asmbl_6261.p1, terminal, 215984, 216086
-recovered pasa_asmbl_6261.p1, internal, 215549, 215601
Valid prediction for GlimmerHMM_glimmerT_28100-T1
Valid prediction for snap_scaffold_11-snap.2726-T1
Valid prediction for snap_scaffold_11-snap.2734-T1
Valid prediction for Augustus_model.g18612.t1
Valid prediction for snap_scaffold_11-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_28098-T1
Valid prediction for snap_scaffold_11-snap.2733-T1
Valid prediction for snap_scaffold_11-snap.2736-T1
Valid prediction for snap_scaffold_11-snap.2757-T1
Valid prediction for snap_scaffold_11-snap.2750-T1
Valid prediction for GlimmerHMM_glimmerT_28122-T1
Valid prediction for Augustus_model.g18603.t1
Valid prediction for Augustus_model.g18606.t1
Valid prediction for snap_scaffold_11-snap.2758-T1
Valid prediction for snap_scaffold_11-snap.2744-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_11-snap.2753-T1
Valid prediction for snap_scaffold_11-snap.2741-T1
Valid prediction for GlimmerHMM_glimmerT_28110-T1
Valid prediction for GlimmerHMM_glimmerT_28097-T1
Valid prediction for snap_scaffold_11-snap.2747-T1
Valid prediction for snap_scaffold_11-snap.2745-T1
Valid prediction for GlimmerHMM_glimmerT_28106-T1
Couldn't classify 81035, 81096
Couldn't classify 82047, 82449
Sorry, prediction pasa_asmbl_7111.p1 fails validation.
(GGA)	 AA	81035-81096	GT	AGG
(CCT)	 AG	82047-82449	CA	TCC
Valid prediction for snap_scaffold_11-snap.2730-T1
Valid prediction for snap_scaffold_11-snap.2755-T1
Valid prediction for Augustus_model.g18614.t1
Couldn't classify 82543, 83082
Sorry, prediction pasa_asmbl_7110.p1 fails validation.
(ACA)	 CA	82543-83082	GC	GAG
Valid prediction for CodingQuarry_transcript_8276-T1
Valid prediction for snap_scaffold_11-snap.2724-T1
Valid prediction for Augustus_model.g18617.t1
Valid prediction for HiQ_model.g18609.t1
Valid prediction for GlimmerHMM_glimmerT_28121-T1
Valid prediction for Augustus_model.g18618.t1
Valid prediction for snap_scaffold_11-snap.2735-T1
Valid prediction for HiQ_model.g18610.t1
Valid prediction for GlimmerHMM_glimmerT_28119-T1
Valid prediction for snap_scaffold_11-snap.2749-T1
Valid prediction for snap_scaffold_11-snap.2748-T1
Valid prediction for Augustus_model.g18604.t1
Valid prediction for snap_scaffold_11-snap.2751-T1
Valid prediction for GlimmerHMM_glimmerT_28101-T1
Valid prediction for GlimmerHMM_glimmerT_28118-T1
Valid prediction for GlimmerHMM_glimmerT_28095-T1
Valid prediction for snap_scaffold_11-snap.2738-T1
Valid prediction for snap_scaffold_11-snap.2740-T1
Valid prediction for GlimmerHMM_glimmerT_28115-T1
Valid prediction for GlimmerHMM_glimmerT_28104-T1
Valid prediction for GlimmerHMM_glimmerT_28117-T1
Valid prediction for pasa_asmbl_7104.p1
Valid prediction for GlimmerHMM_glimmerT_28107-T1
Valid prediction for Augustus_model.g18616.t1
Valid prediction for Augustus_model.g18615.t1
Valid prediction for GlimmerHMM_glimmerT_28113-T1
Valid prediction for GlimmerHMM_glimmerT_28105-T1
Valid prediction for pasa_asmbl_7101.p1
Valid prediction for CodingQuarry_transcript_8275-T1
Valid prediction for snap_scaffold_11-snap.2727-T1
Valid prediction for GlimmerHMM_glimmerT_28112-T1
Valid prediction for snap_scaffold_11-snap.2754-T1
Valid prediction for Augustus_model.g18613.t1
Valid prediction for snap_scaffold_11-snap.2732-T1
Valid prediction for GlimmerHMM_glimmerT_28120-T1
Valid prediction for snap_scaffold_11-snap.2725-T1
Valid prediction for snap_scaffold_11-snap.2729-T1
Couldn't classify 118088, 118513
Sorry, prediction pasa_asmbl_7107.p1 fails validation.
(ATG)	 GA	117259-117293	GT	GAG
(GGA)	 AG	117475-117552	GT	AGG
(GGT)	 AG	117752-117809	GT	AGG
(GAT)	 AG	118088-118513	GG	ATG
-recovered pasa_asmbl_7107.p1, initial, 117259, 117293
-recovered pasa_asmbl_7107.p1, internal, 117475, 117552
-recovered pasa_asmbl_7107.p1, internal, 117752, 117809
Valid prediction for GlimmerHMM_glimmerT_28096-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19331, rend_intergenic: 14462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49258, rend_intergenic: 39924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64064, rend_intergenic: 57877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73204, rend_intergenic: 64372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96956, rend_intergenic: 87612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182993, rend_intergenic: 180414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218144
-exon list size: 294


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.0    
3.4    
3.7    
4.1    
4.4    
4.7    
5.1    
5.4    
5.7    
6.1    
6.4    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.8    
9.1    
9.5    
9.8    
10.1    
10.5    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.9    
16.2    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.6    
18.9    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.0    
27.4    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.1    
31.4    
31.8    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.1    
35.5    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.3    
44.6    
44.9    
45.3    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.7    
55.1    
55.4    
55.7    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.5    
64.9    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.2    
68.6    
68.9    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.6    
73.0    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.1    
81.4    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.8    
84.1    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.5    
89.9    
90.2    
90.5    
90.9    
91.2    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.6    
93.9    
94.3    
94.6    
94.9    
95.3    
95.6    
95.9    
96.3    
96.6    
97.0    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 19331, rend_intergenic: 14462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49258, rend_intergenic: 39924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64064, rend_intergenic: 57877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73204, rend_intergenic: 64372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96956, rend_intergenic: 87612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182993, rend_intergenic: 180414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 36682
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20245
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14036
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 2251 - 14036