-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_8679877-8892511

-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_36639-T1
Valid prediction for Augustus_model.g24381.t1
Valid prediction for GlimmerHMM_glimmerT_36636-T1
Valid prediction for snap_scaffold_15-snap.1839-T1
Valid prediction for snap_scaffold_15-snap.1830-T1
Valid prediction for pasa_asmbl_15357.p1
Valid prediction for GlimmerHMM_glimmerT_36632-T1
Valid prediction for GlimmerHMM_glimmerT_36637-T1
Valid prediction for snap_scaffold_15-snap.1808-T1
Valid prediction for snap_scaffold_15-snap.1812-T1
Couldn't classify 209474, 209542
Couldn't classify 210198, 210418
Sorry, prediction pasa_asmbl_15360.p1 fails validation.
(CGG)	 GG	209474-209542	GT	AGG
(GGC)	 AG	209689-209770	GT	AGG
(GCT)	 AG	210198-210418	CC	ACC
-recovered pasa_asmbl_15360.p1, internal, 209689, 209770
Valid prediction for snap_scaffold_15-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_36609-T1
Valid prediction for snap_scaffold_15-snap.1822-T1
Couldn't classify 108615, 108649
Sorry, prediction pasa_asmbl_15351.p1 fails validation.
(CGT)	 CC	108615-108649	GT	AGG
(GGC)	 AG	109002-109344	GT	GGG
(CAG)	 AG	109579-109766	GT	AGG
(ACC)	 AG	109997-110097	GT	AGG
(TCC)	 AG	110299-110454	GT	TGG
(TTC)	 AG	110590-110667	GT	AGG
(TGG)	 AG	110800-110962	GT	AGG
(TAA)	 AG	111480-111700	GT	CGG
(AGG)	 AG	111820-111952	GT	AAG
(GAC)	 AG	112148-112284	GT	AGG
(TCT)	 AG	112448-112539	GT	AGG
(CCT)	 AG	112818-112924	GT	AGG
(TTG)	 AG	113122-113125	GA	GAG
-recovered pasa_asmbl_15351.p1, terminal, 110590, 110667
-recovered pasa_asmbl_15351.p1, terminal, 113122, 113125
-recovered pasa_asmbl_15351.p1, internal, 109002, 109344
-recovered pasa_asmbl_15351.p1, internal, 109579, 109766
-recovered pasa_asmbl_15351.p1, internal, 109997, 110097
-recovered pasa_asmbl_15351.p1, internal, 110299, 110454
-recovered pasa_asmbl_15351.p1, internal, 110590, 110667
-recovered pasa_asmbl_15351.p1, internal, 110800, 110962
-recovered pasa_asmbl_15351.p1, internal, 111480, 111700
-recovered pasa_asmbl_15351.p1, internal, 111820, 111952
-recovered pasa_asmbl_15351.p1, internal, 112148, 112284
-recovered pasa_asmbl_15351.p1, internal, 112448, 112539
-recovered pasa_asmbl_15351.p1, internal, 112818, 112924
Valid prediction for GlimmerHMM_glimmerT_36630-T1
Valid prediction for GlimmerHMM_glimmerT_36635-T1
Valid prediction for CodingQuarry_transcript_18083-T1
Valid prediction for Augustus_model.g24385.t1
Valid prediction for snap_scaffold_15-snap.1813-T1
Valid prediction for snap_scaffold_15-snap.1821-T1
Valid prediction for snap_scaffold_15-snap.1833-T1
Valid prediction for snap_scaffold_15-snap.1807-T1
Valid prediction for snap_scaffold_15-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_36621-T1
Valid prediction for GlimmerHMM_glimmerT_36619-T1
Valid prediction for snap_scaffold_15-snap.1834-T1
Valid prediction for GlimmerHMM_glimmerT_36610-T1
Valid prediction for snap_scaffold_15-snap.1801-T1
Valid prediction for Augustus_model.g24377.t1
Valid prediction for GlimmerHMM_glimmerT_36615-T1
Valid prediction for snap_scaffold_15-snap.1810-T1
Valid prediction for GlimmerHMM_glimmerT_36620-T1
Valid prediction for GlimmerHMM_glimmerT_36617-T1
Valid prediction for GlimmerHMM_glimmerT_36634-T1
Valid prediction for Augustus_model.g24391.t1
Valid prediction for Augustus_model.g24379.t1
Valid prediction for GlimmerHMM_glimmerT_36607-T1
Valid prediction for GlimmerHMM_glimmerT_36624-T1
Valid prediction for snap_scaffold_15-snap.1809-T1
Valid prediction for snap_scaffold_15-snap.1802-T1
Valid prediction for snap_scaffold_15-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_36627-T1
Valid prediction for GlimmerHMM_glimmerT_36608-T1
Valid prediction for snap_scaffold_15-snap.1837-T1
Valid prediction for GlimmerHMM_glimmerT_36618-T1
Valid prediction for GlimmerHMM_glimmerT_36638-T1
Valid prediction for snap_scaffold_15-snap.1817-T1
Valid prediction for Augustus_model.g24380.t1
Valid prediction for Augustus_model.g24376.t1
Valid prediction for snap_scaffold_15-snap.1838-T1
Valid prediction for Augustus_model.g24386.t1
Couldn't classify 16773, 17494
Sorry, prediction pasa_asmbl_15347.p1 fails validation.
(CCC)	 AA	16773-17494	GT	AAG
(AAT)	 AG	18278-18419	GG	AAG
-recovered pasa_asmbl_15347.p1, terminal, 18278, 18419
Valid prediction for snap_scaffold_15-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_36623-T1
Valid prediction for GlimmerHMM_glimmerT_36616-T1
Valid prediction for snap_scaffold_15-snap.1799-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 GlimmerHMM_glimmerT_36606-T1
Valid prediction for CodingQuarry_transcript_18084-T1
Valid prediction for pasa_asmbl_14356.p1
Valid prediction for snap_scaffold_15-snap.1819-T1
Valid prediction for Augustus_model.g24388.t1
Valid prediction for snap_scaffold_15-snap.1829-T1
Valid prediction for snap_scaffold_15-snap.1836-T1
Valid prediction for snap_scaffold_15-snap.1824-T1
Couldn't classify 181565, 181613
Sorry, prediction pasa_asmbl_14349.p1 fails validation.
(ATG)	 TT	179523-179544	GT	TGG
(TTG)	 AG	179660-179757	GC	AGG
(AAC)	 AG	180097-180178	GT	AGG
(TGA)	 AG	180292-180392	GT	AGG
(CTG)	 AG	180533-180648	GT	AGG
(AGA)	 AG	180790-180890	GT	AGG
(CTT)	 AG	181010-181099	GT	TGG
(CGG)	 AG	181207-181411	GT	AGG
(TGA)	 AG	181565-181613	AG	ACA
-recovered pasa_asmbl_14349.p1, initial, 179523, 179544
-recovered pasa_asmbl_14349.p1, internal, 179660, 179757
-recovered pasa_asmbl_14349.p1, internal, 180097, 180178
-recovered pasa_asmbl_14349.p1, internal, 180292, 180392
-recovered pasa_asmbl_14349.p1, internal, 180533, 180648
-recovered pasa_asmbl_14349.p1, internal, 180790, 180890
-recovered pasa_asmbl_14349.p1, internal, 181010, 181099
-recovered pasa_asmbl_14349.p1, internal, 181207, 181411
Valid prediction for GlimmerHMM_glimmerT_36613-T1
Valid prediction for GlimmerHMM_glimmerT_36612-T1
Valid prediction for pasa_asmbl_14353.p1
Valid prediction for GlimmerHMM_glimmerT_36629-T1
Valid prediction for GlimmerHMM_glimmerT_36633-T1
Valid prediction for GlimmerHMM_glimmerT_36625-T1
Valid prediction for GlimmerHMM_glimmerT_36622-T1
Valid prediction for snap_scaffold_15-snap.1820-T1
Valid prediction for HiQ_model.g24383.t1
Valid prediction for snap_scaffold_15-snap.1806-T1
Valid prediction for pasa_asmbl_14907.p1
Valid prediction for snap_scaffold_15-snap.1814-T1
Valid prediction for HiQ_model.g24378.t1
Valid prediction for snap_scaffold_15-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_36626-T1
Valid prediction for GlimmerHMM_glimmerT_36611-T1
Valid prediction for HiQ_model.g24382.t1
Couldn't classify 175269, 175469
Couldn't classify 178551, 178589
Sorry, prediction pasa_asmbl_14350.p1 fails validation.
(TAC)	 TG	175269-175469	GT	GGG
(GCT)	 AG	176248-176426	GT	AGG
(GTA)	 AG	176858-176945	GT	AGG
(GTG)	 AG	177322-177401	GT	AGG
(AAG)	 AG	177587-177649	GT	GAG
(GAA)	 AG	177777-177831	GT	AGG
(CCC)	 AG	177991-178131	GT	TGG
(CAA)	 AG	178271-178345	GT	CAG
(CCT)	 AG	178551-178589	AA	TCA
-recovered pasa_asmbl_14350.p1, internal, 176248, 176426
-recovered pasa_asmbl_14350.p1, internal, 176858, 176945
-recovered pasa_asmbl_14350.p1, internal, 177322, 177401
-recovered pasa_asmbl_14350.p1, internal, 177587, 177649
-recovered pasa_asmbl_14350.p1, internal, 177777, 177831
-recovered pasa_asmbl_14350.p1, internal, 177991, 178131
-recovered pasa_asmbl_14350.p1, internal, 178271, 178345
Valid prediction for Augustus_model.g24389.t1
Valid prediction for snap_scaffold_15-snap.1818-T1
Valid prediction for snap_scaffold_15-snap.1828-T1
Valid prediction for Augustus_model.g24390.t1
Valid prediction for GlimmerHMM_glimmerT_36614-T1
Valid prediction for snap_scaffold_15-snap.1832-T1
Valid prediction for snap_scaffold_15-snap.1827-T1
Valid prediction for snap_scaffold_15-snap.1826-T1
Valid prediction for snap_scaffold_15-snap.1804-T1
Valid prediction for snap_scaffold_15-snap.1800-T1
Valid prediction for snap_scaffold_15-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_36631-T1
Valid prediction for snap_scaffold_15-snap.1816-T1
Valid prediction for Augustus_model.g24387.t1
Valid prediction for pasa_asmbl_14359.p1
Valid prediction for pasa_asmbl_14358.p1
Valid prediction for CodingQuarry_transcript_18082-T1
Valid prediction for CodingQuarry_transcript_18080-T1
Valid prediction for CodingQuarry_transcript_18079-T1
Valid prediction for HiQ_model.g24384.t1
Valid prediction for snap_scaffold_15-snap.1823-T1
Valid prediction for snap_scaffold_15-snap.1835-T1
Valid prediction for GlimmerHMM_glimmerT_36628-T1
Valid prediction for CodingQuarry_transcript_18081-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17200, rend_intergenic: 15640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32363, rend_intergenic: 28622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72332, rend_intergenic: 63101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96806, rend_intergenic: 92766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103746, rend_intergenic: 98260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149986, rend_intergenic: 145997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155455, rend_intergenic: 152410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185498, rend_intergenic: 182148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189415, rend_intergenic: 186184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204597, rend_intergenic: 194772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208147, rend_intergenic: 205571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212635
-exon list size: 332


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
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9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
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    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
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    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
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    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
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    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
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    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
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    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 17200, rend_intergenic: 15640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32363, rend_intergenic: 28622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72332, rend_intergenic: 63101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96806, rend_intergenic: 92766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103746, rend_intergenic: 98260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149986, rend_intergenic: 145997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155455, rend_intergenic: 152410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185498, rend_intergenic: 182148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189415, rend_intergenic: 186184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204597, rend_intergenic: 194772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208147, rend_intergenic: 205571  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

-building DP trellis

-building trellis in range 1 - 15639
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 15585
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 15403
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 14220
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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