-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_8275062-8523210

-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_10-snap.1665-T1
Valid prediction for snap_scaffold_10-snap.1660-T1
Valid prediction for pasa_asmbl_3322.p1
Valid prediction for pasa_asmbl_3315.p1
Valid prediction for GlimmerHMM_glimmerT_25104-T1
Valid prediction for Augustus_model.g16712.t1
Valid prediction for CodingQuarry_transcript_5481-T1
Couldn't classify 221179, 221326
Sorry, prediction pasa_asmbl_3323.p1 fails validation.
(GAC)	 AA	221179-221326	GT	AGG
(GGG)	 AG	221496-221639	GT	TAG
(ACA)	 AG	221750-221953	GT	TGG
(GTC)	 AG	222032-222171	GT	AGG
(GTG)	 AG	222406-222628	GT	AGG
(GAC)	 AG	222745-222992	TG	AAT
add_exon() Sorry, pasa_asmbl_3323.p1 222406-222628-terminal-3 is invalid.
-recovered pasa_asmbl_3323.p1, terminal, 222406, 222628
-recovered pasa_asmbl_3323.p1, terminal, 222745, 222992
-recovered pasa_asmbl_3323.p1, internal, 221496, 221639
-recovered pasa_asmbl_3323.p1, internal, 221750, 221953
-recovered pasa_asmbl_3323.p1, internal, 222032, 222171
-recovered pasa_asmbl_3323.p1, internal, 222406, 222628
Valid prediction for Augustus_model.g16709.t1
Valid prediction for snap_scaffold_10-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_25107-T1
Couldn't classify 180995, 181012
Couldn't classify 181748, 181954
Sorry, prediction pasa_asmbl_3320.p1 fails validation.
(TGG)	 AA	180995-181012	GT	TGG
(GGA)	 AG	181439-181510	GT	AGG
(GAG)	 AG	181748-181954	AC	GGA
-recovered pasa_asmbl_3320.p1, internal, 181439, 181510
Valid prediction for snap_scaffold_10-snap.1666-T1
Valid prediction for Augustus_model.g16708.t1
Valid prediction for snap_scaffold_10-snap.1643-T1
Valid prediction for snap_scaffold_10-snap.1667-T1
Valid prediction for Augustus_model.g16713.t1
Valid prediction for GlimmerHMM_glimmerT_25079-T1
Valid prediction for snap_scaffold_10-snap.1638-T1
Valid prediction for Augustus_model.g16716.t1
Valid prediction for Augustus_model.g16711.t1
Valid prediction for GlimmerHMM_glimmerT_25100-T1
Valid prediction for snap_scaffold_10-snap.1659-T1
Valid prediction for HiQ_model.g16696.t1
Valid prediction for snap_scaffold_10-snap.1673-T1
Valid prediction for GlimmerHMM_glimmerT_25095-T1
Valid prediction for snap_scaffold_10-snap.1642-T1
Valid prediction for Augustus_model.g16701.t1
Valid prediction for GlimmerHMM_glimmerT_25111-T1
Valid prediction for GlimmerHMM_glimmerT_25113-T1
Valid prediction for GlimmerHMM_glimmerT_25110-T1
Valid prediction for GlimmerHMM_glimmerT_25106-T1
Valid prediction for GlimmerHMM_glimmerT_25096-T1
Valid prediction for GlimmerHMM_glimmerT_25082-T1
Valid prediction for GlimmerHMM_glimmerT_25114-T1
Valid prediction for HiQ_model.g16704.t1
Valid prediction for GlimmerHMM_glimmerT_25084-T1
Valid prediction for Augustus_model.g16706.t1
Couldn't classify 61741, 61917
Sorry, prediction pasa_asmbl_3313.p1 fails validation.
(ATG)	 AG	59780-60006	GT	AGG
(CTC)	 AG	60239-60434	GT	AGG
(AAG)	 AG	60674-60767	GT	AGG
(CAA)	 AG	61342-61449	GT	AGG
(GAA)	 AG	61541-61653	GT	AAG
(GAC)	 AG	61741-61917	TT	GCT
-recovered pasa_asmbl_3313.p1, initial, 59780, 60006
add_exon() Sorry, pasa_asmbl_3313.p1 60674-60767-terminal-3 is invalid.
-recovered pasa_asmbl_3313.p1, terminal, 60674, 60767
-recovered pasa_asmbl_3313.p1, internal, 59780, 60006
-recovered pasa_asmbl_3313.p1, internal, 60239, 60434
-recovered pasa_asmbl_3313.p1, internal, 60674, 60767
-recovered pasa_asmbl_3313.p1, internal, 61342, 61449
-recovered pasa_asmbl_3313.p1, internal, 61541, 61653
Valid prediction for snap_scaffold_10-snap.1670-T1
Valid prediction for Augustus_model.g16699.t1
Valid prediction for GlimmerHMM_glimmerT_25103-T1
Valid prediction for pasa_asmbl_3312.p1
Valid prediction for CodingQuarry_transcript_5488-T1
Valid prediction for snap_scaffold_10-snap.1632-T1
Valid prediction for snap_scaffold_10-snap.1663-T1
Valid prediction for GlimmerHMM_glimmerT_25086-T1
Valid prediction for snap_scaffold_10-snap.1636-T1
Valid prediction for snap_scaffold_10-snap.1650-T1
Valid prediction for CodingQuarry_transcript_5492-T1
Valid prediction for GlimmerHMM_glimmerT_25109-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_10-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_25080-T1
Valid prediction for GlimmerHMM_glimmerT_25085-T1
Valid prediction for GlimmerHMM_glimmerT_25093-T1
Valid prediction for snap_scaffold_10-snap.1658-T1
Valid prediction for snap_scaffold_10-snap.1633-T1
Valid prediction for CodingQuarry_transcript_5486-T1
Valid prediction for HiQ_model.g16715.t1
Valid prediction for GlimmerHMM_glimmerT_25087-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25090-T1
Valid prediction for GlimmerHMM_glimmerT_25101-T1
Valid prediction for pasa_asmbl_4594.p1
Valid prediction for GlimmerHMM_glimmerT_25112-T1
Valid prediction for pasa_asmbl_4593.p1
Valid prediction for snap_scaffold_10-snap.1664-T1
Valid prediction for HiQ_model.g16700.t1
Valid prediction for GlimmerHMM_glimmerT_25115-T1
Valid prediction for snap_scaffold_10-snap.1672-T1
Valid prediction for pasa_asmbl_4588.p1
Valid prediction for GlimmerHMM_glimmerT_25088-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.1644-T1
Valid prediction for CodingQuarry_transcript_5490-T1
Valid prediction for CodingQuarry_transcript_5484-T1
Valid prediction for GlimmerHMM_glimmerT_25102-T1
Valid prediction for CodingQuarry_transcript_5487-T1
Valid prediction for Augustus_model.g16705.t1
Valid prediction for snap_scaffold_10-snap.1674-T1
Couldn't classify 213015, 213110
Sorry, prediction pasa_asmbl_4571.p1 fails validation.
(GTA)	 GC	213015-213110	GT	AGG
(GCA)	 AG	213263-213446	GT	GGG
(GCA)	 AG	213936-213997	CC	GAC
-recovered pasa_asmbl_4571.p1, terminal, 213936, 213997
-recovered pasa_asmbl_4571.p1, internal, 213263, 213446
Valid prediction for CodingQuarry_transcript_5493-T1
Valid prediction for snap_scaffold_10-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_25116-T1
Valid prediction for snap_scaffold_10-snap.1647-T1
Valid prediction for snap_scaffold_10-snap.1641-T1
Valid prediction for snap_scaffold_10-snap.1640-T1
Valid prediction for snap_scaffold_10-snap.1649-T1
Valid prediction for snap_scaffold_10-snap.1668-T1
Valid prediction for snap_scaffold_10-snap.1669-T1
Couldn't classify 209719, 209890
Couldn't classify 210967, 210983
Sorry, prediction pasa_asmbl_4572.p1 fails validation.
(GTC)	 TG	209719-209890	GT	AGG
(TTT)	 AG	210367-210537	GT	TGG
(GCA)	 AG	210967-210983	TT	GCT
-recovered pasa_asmbl_4572.p1, internal, 210367, 210537
Valid prediction for snap_scaffold_10-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_25078-T1
Couldn't classify 58616, 58617
Sorry, prediction CodingQuarry_transcript_5491-T1 fails validation.
(ATG)	 AG	58616-58617	GT	ATG
(GAC)	 AG	59171-59393	GT	GTG
(CTG)	 AG	60035-60511	AC	AAA
-recovered CodingQuarry_transcript_5491-T1, terminal, 60035, 60511
-recovered CodingQuarry_transcript_5491-T1, internal, 58616, 58617
-recovered CodingQuarry_transcript_5491-T1, internal, 59171, 59393
Valid prediction for snap_scaffold_10-snap.1631-T1
Valid prediction for GlimmerHMM_glimmerT_25105-T1
Valid prediction for CodingQuarry_transcript_5485-T1
Valid prediction for Augustus_model.g16697.t1
Valid prediction for snap_scaffold_10-snap.1653-T1
Valid prediction for snap_scaffold_10-snap.1661-T1
Valid prediction for snap_scaffold_10-snap.1639-T1
Valid prediction for pasa_asmbl_4569.p1
Valid prediction for snap_scaffold_10-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_25108-T1
Valid prediction for HiQ_model.g16714.t1
Valid prediction for CodingQuarry_transcript_5482-T1
Valid prediction for GlimmerHMM_glimmerT_25097-T1
Valid prediction for Augustus_model.g16703.t1
Valid prediction for snap_scaffold_10-snap.1657-T1
Valid prediction for snap_scaffold_10-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_25099-T1
Valid prediction for snap_scaffold_10-snap.1637-T1
Valid prediction for snap_scaffold_10-snap.1634-T1
Valid prediction for HiQ_model.g16710.t1
Valid prediction for GlimmerHMM_glimmerT_25077-T1
Couldn't classify 211641, 211749
Couldn't classify 212193, 212342
Sorry, prediction pasa_asmbl_5122.p1 fails validation.
(TAC)	 GC	211641-211749	GT	AGG
(GCT)	 AG	211972-212078	GT	AGG
(AAA)	 AG	212193-212342	GT	AGG
-recovered pasa_asmbl_5122.p1, internal, 211972, 212078
-recovered pasa_asmbl_5122.p1, internal, 212193, 212342
Valid prediction for GlimmerHMM_glimmerT_25081-T1
Valid prediction for snap_scaffold_10-snap.1648-T1
Valid prediction for GlimmerHMM_glimmerT_25089-T1
Valid prediction for snap_scaffold_10-snap.1656-T1
Valid prediction for Augustus_model.g16717.t1
Valid prediction for snap_scaffold_10-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_25092-T1
Valid prediction for HiQ_model.g16707.t1
Valid prediction for HiQ_model.g16702.t1
Valid prediction for CodingQuarry_transcript_5489-T1
Valid prediction for pasa_asmbl_4591.p1
Valid prediction for pasa_asmbl_4586.p1
Valid prediction for pasa_asmbl_4574.p1
Valid prediction for GlimmerHMM_glimmerT_25094-T1
Valid prediction for CodingQuarry_transcript_5483-T1
Valid prediction for GlimmerHMM_glimmerT_25083-T1
Valid prediction for CodingQuarry_transcript_5480-T1
Valid prediction for HiQ_model.g16695.t1
Valid prediction for GlimmerHMM_glimmerT_25098-T1
Valid prediction for Augustus_model.g16698.t1
Valid prediction for snap_scaffold_10-snap.1651-T1
Valid prediction for pasa_asmbl_4585.p1
Valid prediction for snap_scaffold_10-snap.1645-T1
Valid prediction for pasa_asmbl_4577.p1
Valid prediction for GlimmerHMM_glimmerT_25091-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 100283, rend_intergenic: 79587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243927, rend_intergenic: 241489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248149
-exon list size: 383


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.6    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.8    
7.0    
7.3    
7.5    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 100283, rend_intergenic: 79587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243927, rend_intergenic: 241489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19022
-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 1 - 17654
-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 7220 - 17654