-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_2958640-3342574

-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_400-T1
Valid prediction for Augustus_model.g310.t1
Valid prediction for snap_scaffold_1-snap.500-T1
Valid prediction for snap_scaffold_1-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_387-T1
Valid prediction for snap_scaffold_1-snap.487-T1
Valid prediction for pasa_asmbl_1576.p1
Valid prediction for GeneMark_model.460_t
Valid prediction for snap_scaffold_1-snap.492-T1
Couldn't classify 59859, 59909
Couldn't classify 62369, 62433
Sorry, prediction pasa_asmbl_1561.p1 fails validation.
(TCC)	 AC	59859-59909	GT	TGG
(ACC)	 AG	60448-60607	GT	GGG
(AGT)	 AG	60868-60971	GC	AGG
(GTG)	 AG	61204-61300	GT	TGG
(AGA)	 AG	62369-62433	GA	CAG
-recovered pasa_asmbl_1561.p1, internal, 60448, 60607
-recovered pasa_asmbl_1561.p1, internal, 60868, 60971
-recovered pasa_asmbl_1561.p1, internal, 61204, 61300
Couldn't classify 317793, 317878
Sorry, prediction pasa_asmbl_1581.p1 fails validation.
(ATG)	 CC	315438-315559	GT	TGG
(GGG)	 AG	315742-315856	GT	AGG
(AGA)	 AG	316195-316302	GT	AGG
(AAC)	 AG	316425-316508	GT	ATG
(CCT)	 AG	316680-317040	GT	AGG
(ATA)	 AG	317228-317275	GT	GGG
(GTA)	 AG	317793-317878	GT	AGG
-recovered pasa_asmbl_1581.p1, initial, 315438, 315559
-recovered pasa_asmbl_1581.p1, internal, 315742, 315856
-recovered pasa_asmbl_1581.p1, internal, 316195, 316302
-recovered pasa_asmbl_1581.p1, internal, 316425, 316508
-recovered pasa_asmbl_1581.p1, internal, 316680, 317040
-recovered pasa_asmbl_1581.p1, internal, 317228, 317275
-recovered pasa_asmbl_1581.p1, internal, 317793, 317878
Valid prediction for snap_scaffold_1-snap.506-T1
Valid prediction for GeneMark_model.453_t
Valid prediction for Augustus_model.g327.t1
Valid prediction for GeneMark_model.461_t
Couldn't classify 207520, 207809
Couldn't classify 211458, 211634
Sorry, prediction pasa_asmbl_1569.p1 fails validation.
(GTC)	 AG	207520-207809	GT	AGG
(GAT)	 AG	208000-208189	GT	AAG
(AGA)	 AG	208281-208424	GT	TGG
(GTC)	 AG	208623-208850	GT	TGG
(GGT)	 AG	209057-209286	GT	AGG
(ATT)	 AG	211197-211284	GT	AGG
(GAT)	 AG	211458-211634	TA	CGT
add_exon() Sorry, pasa_asmbl_1569.p1 207520-207809-terminal-2 is invalid.
-recovered pasa_asmbl_1569.p1, terminal, 207520, 207809
-recovered pasa_asmbl_1569.p1, internal, 207520, 207809
-recovered pasa_asmbl_1569.p1, internal, 208000, 208189
-recovered pasa_asmbl_1569.p1, internal, 208281, 208424
-recovered pasa_asmbl_1569.p1, internal, 208623, 208850
-recovered pasa_asmbl_1569.p1, internal, 209057, 209286
-recovered pasa_asmbl_1569.p1, internal, 211197, 211284
Valid prediction for HiQ_model.g319.t1
Valid prediction for Augustus_model.g312.t1
Valid prediction for GlimmerHMM_glimmerT_405-T1
Valid prediction for GlimmerHMM_glimmerT_399-T1
Valid prediction for snap_scaffold_1-snap.509-T1
Valid prediction for snap_scaffold_1-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_392-T1
Valid prediction for Augustus_model.g314.t1
Valid prediction for GlimmerHMM_glimmerT_410-T1
Valid prediction for GeneMark_model.443_t
Valid prediction for GlimmerHMM_glimmerT_389-T1
Valid prediction for GlimmerHMM_glimmerT_394-T1
Valid prediction for Augustus_model.g311.t1
Couldn't classify 55524, 55768
Couldn't classify 57532, 57586
Sorry, prediction pasa_asmbl_2764.p1 fails validation.
(GTG)	 AC	55524-55768	GT	AGG
(GAC)	 AG	57532-57586	AA	ACA
Valid prediction for Augustus_model.g307.t1
Couldn't classify 335641, 335940
Sorry, prediction pasa_asmbl_1591.p1 fails validation.
(CGC)	 AT	335641-335940	GT	CAG
(CTA)	 AG	336050-336220	CT	GAC
-recovered pasa_asmbl_1591.p1, terminal, 336050, 336220
Valid prediction for HiQ_model.g321.t1
Valid prediction for snap_scaffold_1-snap.513-T1
Valid prediction for GeneMark_model.439_t
Valid prediction for GlimmerHMM_glimmerT_408-T1
Valid prediction for snap_scaffold_1-snap.496-T1
Valid prediction for Augustus_model.g318.t1
Valid prediction for snap_scaffold_1-snap.498-T1
Valid prediction for snap_scaffold_1-snap.499-T1
Valid prediction for CodingQuarry_transcript_2554-T1
Valid prediction for snap_scaffold_1-snap.515-T1
Valid prediction for Augustus_model.g309.t1
Valid prediction for snap_scaffold_1-snap.491-T1
Valid prediction for Augustus_model.g329.t1
Valid prediction for GlimmerHMM_glimmerT_388-T1
Valid prediction for snap_scaffold_1-snap.519-T1
Valid prediction for pasa_asmbl_1571.p1
Valid prediction for GeneMark_model.444_t
Valid prediction for GeneMark_model.442_t
Valid prediction for GlimmerHMM_glimmerT_397-T1
Valid prediction for GlimmerHMM_glimmerT_402-T1
Valid prediction for GeneMark_model.452_t
Valid prediction for GeneMark_model.445_t
Valid prediction for snap_scaffold_1-snap.508-T1
Valid prediction for GeneMark_model.446_t
Valid prediction for HiQ_model.g324.t1
Valid prediction for snap_scaffold_1-snap.488-T1
Valid prediction for GeneMark_model.448_t
Valid prediction for Augustus_model.g320.t1
Valid prediction for snap_scaffold_1-snap.485-T1
Valid prediction for GeneMark_model.458_t
Valid prediction for snap_scaffold_1-snap.516-T1
Valid prediction for CodingQuarry_transcript_2555-T1
Valid prediction for snap_scaffold_1-snap.494-T1
Valid prediction for HiQ_model.g328.t1
Valid prediction for GeneMark_model.447_t
Valid prediction for GlimmerHMM_glimmerT_409-T1
Valid prediction for GlimmerHMM_glimmerT_391-T1
Valid prediction for GlimmerHMM_glimmerT_395-T1
Valid prediction for snap_scaffold_1-snap.490-T1
Valid prediction for Augustus_model.g305.t1
Couldn't classify 204434, 204600
Sorry, prediction pasa_asmbl_1567.p1 fails validation.
(GAA)	 TG	204434-204600	GT	AGG
(GGG)	 AG	206521-206680	GT	CAG
(CTT)	 AG	206836-207069	TT	GAT
-recovered pasa_asmbl_1567.p1, terminal, 206836, 207069
-recovered pasa_asmbl_1567.p1, internal, 206521, 206680
Valid prediction for Augustus_model.g308.t1
Valid prediction for GlimmerHMM_glimmerT_386-T1
Valid prediction for snap_scaffold_1-snap.505-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_1-snap.501-T1
Valid prediction for GeneMark_model.437_t
Valid prediction for GeneMark_model.455_t
Valid prediction for GlimmerHMM_glimmerT_396-T1
Valid prediction for GlimmerHMM_glimmerT_398-T1
Valid prediction for GlimmerHMM_glimmerT_403-T1
Valid prediction for GlimmerHMM_glimmerT_406-T1
Valid prediction for Augustus_model.g316.t1
Valid prediction for snap_scaffold_1-snap.489-T1
Valid prediction for GeneMark_model.457_t
Valid prediction for Augustus_model.g331.t1
Couldn't classify 190611, 190743
Couldn't classify 192062, 192091
Sorry, prediction pasa_asmbl_138.p1 fails validation.
(CTT)	 CC	190611-190743	GT	AGG
(AGT)	 AG	191706-191854	GT	AGG
(GCA)	 AG	192062-192091	AA	GGA
-recovered pasa_asmbl_138.p1, internal, 191706, 191854
Valid prediction for snap_scaffold_1-snap.512-T1
Valid prediction for snap_scaffold_1-snap.518-T1
Valid prediction for Augustus_model.g317.t1
Couldn't classify 193563, 193673
Couldn't classify 194962, 195148
Sorry, prediction pasa_asmbl_137.p1 fails validation.
(AAG)	 AA	193563-193673	GT	AGG
(CTG)	 AG	193836-193945	GT	AGG
(CCA)	 AG	194962-195148	CC	GGC
-recovered pasa_asmbl_137.p1, internal, 193836, 193945
Valid prediction for Augustus_model.g326.t1
Valid prediction for GeneMark_model.438_t
Valid prediction for GlimmerHMM_glimmerT_412-T1
Valid prediction for CodingQuarry_transcript_2557-T1
Valid prediction for GeneMark_model.454_t
Valid prediction for GeneMark_model.450_t
Valid prediction for snap_scaffold_1-snap.493-T1
Valid prediction for GlimmerHMM_glimmerT_404-T1
Valid prediction for GeneMark_model.462_t
Couldn't classify 210030, 210130
Sorry, prediction pasa_asmbl_134.p1 fails validation.
(GAA)	 CA	210030-210130	GT	AGG
(GGT)	 AG	210345-210477	GT	GGG
(GTG)	 AG	210638-210752	GT	AGG
(TGA)	 AG	210902-210989	GT	ATG
(ATT)	 AG	211107-211182	GT	AGG
-recovered pasa_asmbl_134.p1, terminal, 211107, 211182
-recovered pasa_asmbl_134.p1, internal, 210345, 210477
-recovered pasa_asmbl_134.p1, internal, 210638, 210752
-recovered pasa_asmbl_134.p1, internal, 210902, 210989
-recovered pasa_asmbl_134.p1, internal, 211107, 211182
Valid prediction for Augustus_model.g330.t1
Valid prediction for snap_scaffold_1-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_401-T1
Valid prediction for GeneMark_model.456_t
Valid prediction for Augustus_model.g325.t1
Valid prediction for CodingQuarry_transcript_2552-T1
Valid prediction for CodingQuarry_transcript_2553-T1
Valid prediction for GlimmerHMM_glimmerT_390-T1
Valid prediction for Augustus_model.g322.t1
Valid prediction for snap_scaffold_1-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_407-T1
Valid prediction for CodingQuarry_transcript_2556-T1
Valid prediction for snap_scaffold_1-snap.517-T1
Valid prediction for Augustus_model.g306.t1
Valid prediction for Augustus_model.g315.t1
Valid prediction for GeneMark_model.440_t
Valid prediction for GeneMark_model.449_t
Valid prediction for GeneMark_model.441_t
Valid prediction for snap_scaffold_1-snap.514-T1
Valid prediction for snap_scaffold_1-snap.511-T1
Couldn't classify 195450, 195548
Sorry, prediction pasa_asmbl_135.p1 fails validation.
(CTG)	 AA	195450-195548	GT	AGG
(TGT)	 AG	195831-195966	GT	AGG
(TGG)	 AG	196045-196147	GT	AGG
(GGT)	 AG	196439-196550	GT	AAG
(GAT)	 AG	196913-197003	GT	AGG
(GGG)	 AG	197158-197231	AT	GAA
-recovered pasa_asmbl_135.p1, terminal, 197158, 197231
-recovered pasa_asmbl_135.p1, internal, 195831, 195966
-recovered pasa_asmbl_135.p1, internal, 196045, 196147
-recovered pasa_asmbl_135.p1, internal, 196439, 196550
-recovered pasa_asmbl_135.p1, internal, 196913, 197003
Valid prediction for GeneMark_model.451_t
Valid prediction for GlimmerHMM_glimmerT_393-T1
Valid prediction for snap_scaffold_1-snap.503-T1
Valid prediction for pasa_asmbl_141.p1
Valid prediction for snap_scaffold_1-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_411-T1
Valid prediction for Augustus_model.g313.t1
Valid prediction for snap_scaffold_1-snap.502-T1
Valid prediction for Augustus_model.g323.t1
Valid prediction for snap_scaffold_1-snap.486-T1
Valid prediction for GeneMark_model.463_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52342, rend_intergenic: 52067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57345, rend_intergenic: 53269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65505, rend_intergenic: 62242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 383935
-exon list size: 470


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 52342, rend_intergenic: 52067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57345, rend_intergenic: 53269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65505, rend_intergenic: 62242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 29461
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17383
-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

-building DP trellis

-building trellis in range 1 - 16001
-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
	-no exons in range 1 - 15296

-building DP trellis

-building trellis in range 17907 - 29461
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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

-building DP trellis

-building trellis in range 357628 - 383935
-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 357947 - 383935
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 357947 - 369175
-exon list size: 1


building trellis

33.3    
66.7    
-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 357947 - 368688

-building DP trellis

-building trellis in range 369202 - 383935
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 369202 - 381003
-exon list size: 1


building trellis

33.3    
66.7    
-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
	-no exons in range 370022 - 381003