-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_931980-1092450

-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 GeneMark_model.62452_t
Valid prediction for Augustus_model.g24409.t1
Valid prediction for snap_scaffold_15-snap.234-T1
Valid prediction for GeneMark_model.62455_t
Valid prediction for snap_scaffold_15-snap.236-T1
Couldn't classify 32391, 32569
Sorry, prediction pasa_asmbl_13932.p1 fails validation.
(TCC)	 AT	32391-32569	GT	TGG
(GTA)	 AG	33122-34868	TC	GAT
-recovered pasa_asmbl_13932.p1, terminal, 33122, 34868
Valid prediction for Augustus_model.g24414.t1
Valid prediction for snap_scaffold_15-snap.225-T1
Valid prediction for GeneMark_model.62439_t
Valid prediction for GeneMark_model.62436_t
Valid prediction for GeneMark_model.62447_t
Valid prediction for snap_scaffold_15-snap.233-T1
Couldn't classify 14737, 14790
Sorry, prediction pasa_asmbl_13928.p1 fails validation.
(TGG)	 AC	14737-14790	GT	CGG
(GTG)	 AG	17737-17910	GT	AGG
(GAC)	 AG	20239-20407	GT	AGG
(ACC)	 AG	20748-20860	GA	AAG
-recovered pasa_asmbl_13928.p1, terminal, 20748, 20860
-recovered pasa_asmbl_13928.p1, internal, 17737, 17910
-recovered pasa_asmbl_13928.p1, internal, 20239, 20407
Valid prediction for snap_scaffold_15-snap.223-T1
Valid prediction for GlimmerHMM_glimmerT_36306-T1
Valid prediction for GeneMark_model.62445_t
Valid prediction for GeneMark_model.62441_t
Valid prediction for snap_scaffold_15-snap.238-T1
Valid prediction for GeneMark_model.62468_t
Valid prediction for snap_scaffold_15-snap.241-T1
Valid prediction for snap_scaffold_15-snap.239-T1
Valid prediction for snap_scaffold_15-snap.231-T1
Valid prediction for snap_scaffold_15-snap.237-T1
Valid prediction for GeneMark_model.62443_t
Valid prediction for GeneMark_model.62461_t
Valid prediction for GeneMark_model.62460_t
Valid prediction for GlimmerHMM_glimmerT_36304-T1
Valid prediction for snap_scaffold_15-snap.218-T1
Valid prediction for GeneMark_model.62444_t
Valid prediction for snap_scaffold_15-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_36316-T1
Valid prediction for Augustus_model.g24417.t1
Valid prediction for GeneMark_model.62450_t
Valid prediction for snap_scaffold_15-snap.221-T1
Valid prediction for GlimmerHMM_glimmerT_36313-T1
Valid prediction for GlimmerHMM_glimmerT_36312-T1
Valid prediction for Augustus_model.g24416.t1
Valid prediction for snap_scaffold_15-snap.224-T1
Couldn't classify 24274, 24551
Couldn't classify 27095, 27347
Sorry, prediction pasa_asmbl_13931.p1 fails validation.
(TAC)	 TG	24274-24551	GT	TGG
(GTT)	 AG	27095-27347	GG	AGG
Valid prediction for GeneMark_model.62438_t
Valid prediction for snap_scaffold_15-snap.229-T1
Valid prediction for Augustus_model.g24408.t1
Valid prediction for Augustus_model.g24411.t1
Valid prediction for GeneMark_model.62465_t
Valid prediction for GlimmerHMM_glimmerT_36303-T1
Valid prediction for snap_scaffold_15-snap.216-T1
Valid prediction for Augustus_model.g24412.t1
Valid prediction for Augustus_model.g24410.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_15-snap.228-T1
Valid prediction for snap_scaffold_15-snap.219-T1
Valid prediction for GlimmerHMM_glimmerT_36318-T1
Valid prediction for snap_scaffold_15-snap.222-T1
Valid prediction for GlimmerHMM_glimmerT_36308-T1
Valid prediction for GlimmerHMM_glimmerT_36305-T1
Valid prediction for GeneMark_model.62459_t
Valid prediction for pasa_asmbl_14959.p1
Valid prediction for GeneMark_model.62442_t
Valid prediction for GlimmerHMM_glimmerT_36311-T1
Valid prediction for snap_scaffold_15-snap.232-T1
Valid prediction for GeneMark_model.62456_t
Valid prediction for HiQ_model.g24413.t1
Valid prediction for snap_scaffold_15-snap.226-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_36317-T1
Valid prediction for GeneMark_model.62469_t
Valid prediction for snap_scaffold_15-snap.240-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.62462_t
Valid prediction for GeneMark_model.62437_t
Valid prediction for GlimmerHMM_glimmerT_36310-T1
Valid prediction for GeneMark_model.62451_t
Valid prediction for GeneMark_model.62467_t
Valid prediction for GlimmerHMM_glimmerT_36314-T1
Valid prediction for GeneMark_model.62457_t
Valid prediction for GeneMark_model.62446_t
Valid prediction for CodingQuarry_transcript_17857-T1
Valid prediction for GlimmerHMM_glimmerT_36315-T1
Valid prediction for GlimmerHMM_glimmerT_36309-T1
Valid prediction for GeneMark_model.62466_t
Valid prediction for GeneMark_model.62464_t
Valid prediction for GeneMark_model.62440_t
Valid prediction for GeneMark_model.62453_t
Valid prediction for snap_scaffold_15-snap.217-T1
Valid prediction for snap_scaffold_15-snap.230-T1
Valid prediction for GeneMark_model.62454_t
Valid prediction for Augustus_model.g24415.t1
Valid prediction for GeneMark_model.62449_t
Valid prediction for snap_scaffold_15-snap.227-T1
Valid prediction for GeneMark_model.62458_t
Valid prediction for GlimmerHMM_glimmerT_36307-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13386, rend_intergenic: 6772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25947, rend_intergenic: 24133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34468, rend_intergenic: 29781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48567, rend_intergenic: 46732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144747, rend_intergenic: 142733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160471
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 13 predictions from path traversal
Error with prediction: snap lend_intergenic: 13386, rend_intergenic: 6772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25947, rend_intergenic: 24133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34468, rend_intergenic: 29781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48567, rend_intergenic: 46732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144747, rend_intergenic: 142733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 150380 - 160471
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 150445 - 160471
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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