-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_4290561-4546762

-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_3756-T1
Valid prediction for GeneMark_model.6131_t
Valid prediction for Augustus_model.g2502.t1
Valid prediction for snap_scaffold_2-snap.1028-T1
Valid prediction for snap_scaffold_2-snap.1002-T1
Valid prediction for GeneMark_model.6129_t
Valid prediction for GeneMark_model.6132_t
Valid prediction for snap_scaffold_2-snap.1018-T1
Valid prediction for snap_scaffold_2-snap.1024-T1
Valid prediction for GeneMark_model.6143_t
Valid prediction for GlimmerHMM_glimmerT_3752-T1
Valid prediction for snap_scaffold_2-snap.999-T1
Valid prediction for snap_scaffold_2-snap.1029-T1
Valid prediction for snap_scaffold_2-snap.1004-T1
Valid prediction for GeneMark_model.6128_t
Valid prediction for snap_scaffold_2-snap.1016-T1
Valid prediction for GeneMark_model.6124_t
Valid prediction for GlimmerHMM_glimmerT_3766-T1
Valid prediction for snap_scaffold_2-snap.1000-T1
Valid prediction for snap_scaffold_2-snap.1011-T1
Valid prediction for GlimmerHMM_glimmerT_3761-T1
Valid prediction for GeneMark_model.6148_t
Valid prediction for snap_scaffold_2-snap.1015-T1
Valid prediction for GeneMark_model.6135_t
Valid prediction for GeneMark_model.6141_t
Valid prediction for snap_scaffold_2-snap.1025-T1
Valid prediction for GeneMark_model.6127_t
Couldn't classify 190514, 190981
Sorry, prediction pasa_asmbl_24371.p1 fails validation.
(GTG)	 GC	190514-190981	CC	AAC
Valid prediction for GeneMark_model.6144_t
Valid prediction for snap_scaffold_2-snap.1014-T1
Valid prediction for snap_scaffold_2-snap.995-T1
Valid prediction for Augustus_model.g2499.t1
Valid prediction for snap_scaffold_2-snap.1010-T1
Valid prediction for Augustus_model.g2506.t1
Valid prediction for HiQ_model.g2503.t1
Valid prediction for GeneMark_model.6149_t
Valid prediction for snap_scaffold_2-snap.1027-T1
Couldn't classify 75174, 75335
Sorry, prediction pasa_asmbl_24366.p1 fails validation.
(AGC)	 AC	75174-75335	GT	TGG
(CAC)	 AG	76044-76128	GT	CTG
(ATC)	 AG	76319-76506	AG	AAA
-recovered pasa_asmbl_24366.p1, terminal, 76319, 76506
-recovered pasa_asmbl_24366.p1, internal, 76044, 76128
Couldn't classify 184382, 184530
Couldn't classify 186698, 186801
Sorry, prediction pasa_asmbl_24369.p1 fails validation.
(GCT)	 AG	184382-184530	GT	GGG
(TTA)	 AG	184776-184896	GT	GAG
(GTC)	 AG	185139-185250	GT	AGG
(ATG)	 AG	186698-186801	GT	AAG
add_exon() Sorry, pasa_asmbl_24369.p1 186698-186801-initial-1 is invalid.
-recovered pasa_asmbl_24369.p1, initial, 186698, 186801
-recovered pasa_asmbl_24369.p1, internal, 184382, 184530
-recovered pasa_asmbl_24369.p1, internal, 184776, 184896
-recovered pasa_asmbl_24369.p1, internal, 185139, 185250
-recovered pasa_asmbl_24369.p1, internal, 186698, 186801
Valid prediction for GlimmerHMM_glimmerT_3765-T1
Valid prediction for GlimmerHMM_glimmerT_3757-T1
Valid prediction for GeneMark_model.6133_t
Valid prediction for CodingQuarry_transcript_28474-T1
Valid prediction for snap_scaffold_2-snap.1026-T1
Valid prediction for snap_scaffold_2-snap.993-T1
Valid prediction for GeneMark_model.6136_t
Valid prediction for GeneMark_model.6122_t
Valid prediction for snap_scaffold_2-snap.1007-T1
Valid prediction for snap_scaffold_2-snap.1006-T1
Valid prediction for GlimmerHMM_glimmerT_3754-T1
Valid prediction for CodingQuarry_transcript_28473-T1
Valid prediction for GlimmerHMM_glimmerT_3748-T1
Valid prediction for GlimmerHMM_glimmerT_3753-T1
Valid prediction for Augustus_model.g2498.t1
Valid prediction for Augustus_model.g2501.t1
Valid prediction for GlimmerHMM_glimmerT_3759-T1
Valid prediction for snap_scaffold_2-snap.1008-T1
Valid prediction for GeneMark_model.6139_t
Valid prediction for snap_scaffold_2-snap.1023-T1
Valid prediction for GeneMark_model.6121_t
Couldn't classify 187720, 187889
Couldn't classify 190113, 190435
Sorry, prediction pasa_asmbl_24370.p1 fails validation.
(ATC)	 AG	187720-187889	GC	AGG
(AGG)	 AG	188914-189140	GT	TGG
(GTG)	 AG	190113-190435	AC	ACA
-recovered pasa_asmbl_24370.p1, internal, 187720, 187889
-recovered pasa_asmbl_24370.p1, internal, 188914, 189140
Valid prediction for snap_scaffold_2-snap.1012-T1
Valid prediction for Augustus_model.g2495.t1
Valid prediction for snap_scaffold_2-snap.1019-T1
Valid prediction for pasa_asmbl_24367.p1

-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_2-snap.1003-T1
Couldn't classify 219123, 219269
Sorry, prediction pasa_asmbl_23091.p1 fails validation.
(GCC)	 AA	219123-219269	GT	AGG
(GAA)	 AG	220032-220199	GT	AGG
(GTG)	 AG	222956-223297	TG	AGT
-recovered pasa_asmbl_23091.p1, terminal, 222956, 223297
-recovered pasa_asmbl_23091.p1, internal, 220032, 220199
Valid prediction for Augustus_model.g2500.t1
Valid prediction for GlimmerHMM_glimmerT_3747-T1
Valid prediction for snap_scaffold_2-snap.1017-T1
Valid prediction for snap_scaffold_2-snap.1031-T1
Valid prediction for GeneMark_model.6130_t
Valid prediction for GeneMark_model.6142_t
Valid prediction for snap_scaffold_2-snap.1001-T1
Valid prediction for GlimmerHMM_glimmerT_3763-T1
Valid prediction for GeneMark_model.6145_t
Valid prediction for snap_scaffold_2-snap.1022-T1
Valid prediction for GeneMark_model.6119_t
Valid prediction for snap_scaffold_2-snap.1005-T1
Valid prediction for snap_scaffold_2-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_3767-T1
Valid prediction for GlimmerHMM_glimmerT_3751-T1
Valid prediction for Augustus_model.g2507.t1
Valid prediction for snap_scaffold_2-snap.1009-T1
Valid prediction for HiQ_model.g2494.t1
Valid prediction for CodingQuarry_transcript_28472-T1
Couldn't classify 40467, 40574
Sorry, prediction pasa_asmbl_23105.p1 fails validation.
(ATT)	 AG	40467-40574	GT	TAG
(AAA)	 AG	42191-42247	GT	AGG
(AGT)	 AG	42366-42518	GT	TGG
(GAG)	 AG	42643-42847	GT	AGG
(TCA)	 AG	43474-43530	GT	ATG
(GGA)	 AG	44050-44153	GT	AGG
(GTC)	 AG	44390-44499	GT	AGG
(AAA)	 AG	44776-44806	CT	AAC
-recovered pasa_asmbl_23105.p1, terminal, 44776, 44806
-recovered pasa_asmbl_23105.p1, internal, 40467, 40574
-recovered pasa_asmbl_23105.p1, internal, 42191, 42247
-recovered pasa_asmbl_23105.p1, internal, 42366, 42518
-recovered pasa_asmbl_23105.p1, internal, 42643, 42847
-recovered pasa_asmbl_23105.p1, internal, 43474, 43530
-recovered pasa_asmbl_23105.p1, internal, 44050, 44153
-recovered pasa_asmbl_23105.p1, internal, 44390, 44499
Valid prediction for GlimmerHMM_glimmerT_3762-T1
Valid prediction for Augustus_model.g2492.t1
Valid prediction for GlimmerHMM_glimmerT_3760-T1
Valid prediction for CodingQuarry_transcript_28475-T1
Valid prediction for snap_scaffold_2-snap.998-T1
Valid prediction for GeneMark_model.6123_t
Valid prediction for snap_scaffold_2-snap.996-T1
Valid prediction for GlimmerHMM_glimmerT_3755-T1
Valid prediction for Augustus_model.g2504.t1
Couldn't classify 188138, 188242
Couldn't classify 188961, 189464
Sorry, prediction pasa_asmbl_23099.p1 fails validation.
(CCG)	 TG	188138-188242	GT	TGG
(GCG)	 AG	188961-189464	GG	GGG
Valid prediction for snap_scaffold_2-snap.1020-T1
Valid prediction for GlimmerHMM_glimmerT_3745-T1
Couldn't classify 189902, 189982
Sorry, prediction pasa_asmbl_23098.p1 fails validation.
(GGC)	 TG	189902-189982	GT	TTG
(TCC)	 AG	190974-191189	GT	AGG
(CTC)	 AG	191322-191480	GT	TGG
(AAG)	 AG	191595-191786	GC	AAG
-recovered pasa_asmbl_23098.p1, terminal, 191595, 191786
-recovered pasa_asmbl_23098.p1, internal, 190974, 191189
-recovered pasa_asmbl_23098.p1, internal, 191322, 191480
-recovered pasa_asmbl_23098.p1, internal, 191595, 191786
Valid prediction for GlimmerHMM_glimmerT_3746-T1
Valid prediction for GlimmerHMM_glimmerT_3764-T1
Valid prediction for GeneMark_model.6140_t
Valid prediction for pasa_asmbl_23096.p1
Valid prediction for snap_scaffold_2-snap.1021-T1
Couldn't classify 99844, 99912
Sorry, prediction pasa_asmbl_23102.p1 fails validation.
(CTT)	 AC	99844-99912	GT	CTG
(ACA)	 AG	101533-101667	GT	AGG
(GAC)	 AG	101827-101913	GT	GGG
(GCG)	 AG	102033-102197	GT	AGG
(GTT)	 AG	102374-102496	GT	GGG
(GAG)	 AG	102837-103006	GT	AGG
(ACT)	 AG	103170-103311	GT	AGG
(GTG)	 AG	103500-103567	GT	AGG
(ATT)	 AG	103661-103764	GT	AGG
(GCT)	 AG	104087-104145	GT	AGG
(GCT)	 AG	104286-104474	CC	GAC
-recovered pasa_asmbl_23102.p1, terminal, 103500, 103567
-recovered pasa_asmbl_23102.p1, terminal, 104286, 104474
-recovered pasa_asmbl_23102.p1, internal, 101533, 101667
-recovered pasa_asmbl_23102.p1, internal, 101827, 101913
-recovered pasa_asmbl_23102.p1, internal, 102033, 102197
-recovered pasa_asmbl_23102.p1, internal, 102374, 102496
-recovered pasa_asmbl_23102.p1, internal, 102837, 103006
-recovered pasa_asmbl_23102.p1, internal, 103170, 103311
-recovered pasa_asmbl_23102.p1, internal, 103500, 103567
-recovered pasa_asmbl_23102.p1, internal, 103661, 103764
-recovered pasa_asmbl_23102.p1, internal, 104087, 104145
Valid prediction for GeneMark_model.6138_t
Valid prediction for HiQ_model.g2493.t1
Valid prediction for GeneMark_model.6120_t
Valid prediction for GeneMark_model.6151_t
Valid prediction for Augustus_model.g2505.t1
Valid prediction for GlimmerHMM_glimmerT_3744-T1
Valid prediction for snap_scaffold_2-snap.997-T1
Valid prediction for GlimmerHMM_glimmerT_3758-T1
Valid prediction for Augustus_model.g2497.t1
Valid prediction for snap_scaffold_2-snap.1030-T1
Valid prediction for Augustus_model.g2496.t1
Valid prediction for GlimmerHMM_glimmerT_3750-T1
Valid prediction for GeneMark_model.6137_t
Valid prediction for GeneMark_model.6126_t
Valid prediction for snap_scaffold_2-snap.994-T1
Valid prediction for GeneMark_model.6147_t
Valid prediction for CodingQuarry_transcript_28476-T1
Valid prediction for Augustus_model.g2508.t1
Valid prediction for GeneMark_model.6125_t
Valid prediction for GeneMark_model.6134_t
Valid prediction for GlimmerHMM_glimmerT_3743-T1
Valid prediction for GeneMark_model.6150_t
Valid prediction for GlimmerHMM_glimmerT_3749-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6648, rend_intergenic: 3931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96197, rend_intergenic: 92764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256202
-exon list size: 478


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 6648, rend_intergenic: 3931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96197, rend_intergenic: 92764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 10405
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 215737 - 256202
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 215737 - 244710
-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 215737 - 242501
-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 215737 - 237174
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 215737 - 232409
-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

-building DP trellis

-building trellis in range 220441 - 232409
-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