-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_3020428-3237147

-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_18-snap.610-T1
Valid prediction for snap_scaffold_18-snap.635-T1
Valid prediction for CodingQuarry_transcript_23654-T1
Valid prediction for GlimmerHMM_glimmerT_42972-T1
Couldn't classify 183819, 184361
Sorry, prediction pasa_asmbl_20471.p1 fails validation.
(TCC)	 TG	183819-184361	TA	GAT
Valid prediction for Augustus_model.g28747.t1
Valid prediction for GeneMark_model.74232_t
Valid prediction for snap_scaffold_18-snap.632-T1
Valid prediction for snap_scaffold_18-snap.618-T1
Couldn't classify 181900, 182229
Sorry, prediction pasa_asmbl_20469.p1 fails validation.
(CAT)	 AG	181900-182229	AC	ACA
Valid prediction for Augustus_model.g28741.t1
Valid prediction for GeneMark_model.74231_t
Valid prediction for GlimmerHMM_glimmerT_42966-T1
Valid prediction for HiQ_model.g28739.t1
Valid prediction for GeneMark_model.74220_t
Valid prediction for Augustus_model.g28737.t1
Valid prediction for Augustus_model.g28743.t1
Valid prediction for snap_scaffold_18-snap.623-T1
Valid prediction for GeneMark_model.74212_t
Valid prediction for Augustus_model.g28744.t1
Valid prediction for snap_scaffold_18-snap.634-T1
Valid prediction for GlimmerHMM_glimmerT_42965-T1
Valid prediction for GlimmerHMM_glimmerT_42977-T1
Valid prediction for GeneMark_model.74235_t
Valid prediction for snap_scaffold_18-snap.629-T1
Valid prediction for GeneMark_model.74229_t
Valid prediction for GlimmerHMM_glimmerT_42963-T1
Valid prediction for pasa_asmbl_20473.p1
Valid prediction for Augustus_model.g28748.t1
Valid prediction for GlimmerHMM_glimmerT_42975-T1
Valid prediction for GlimmerHMM_glimmerT_42973-T1
Valid prediction for snap_scaffold_18-snap.624-T1
Valid prediction for HiQ_model.g28750.t1
Valid prediction for Augustus_model.g28745.t1
Valid prediction for pasa_asmbl_20478.p1
Valid prediction for snap_scaffold_18-snap.626-T1
Valid prediction for snap_scaffold_18-snap.630-T1
Valid prediction for GeneMark_model.74234_t
Couldn't classify 186662, 187357
Sorry, prediction pasa_asmbl_20472.p1 fails validation.
(GGT)	 AT	186662-187357	AA	GGA
Valid prediction for GlimmerHMM_glimmerT_42971-T1
Valid prediction for GlimmerHMM_glimmerT_42980-T1
Valid prediction for snap_scaffold_18-snap.611-T1
Valid prediction for snap_scaffold_18-snap.609-T1
Valid prediction for snap_scaffold_18-snap.620-T1
Couldn't classify 192157, 192492
Sorry, prediction pasa_asmbl_20474.p1 fails validation.
(TGT)	 AC	192157-192492	GG	AGG
Couldn't classify 73402, 74056
Couldn't classify 74211, 74221
Sorry, prediction CodingQuarry_transcript_23656-T1 fails validation.
(ATG)	 CA	73402-74056	GG	CTG
(GGA)	 CA	74211-74221	GG	GAG
Valid prediction for GeneMark_model.74213_t
Valid prediction for snap_scaffold_18-snap.607-T1
Valid prediction for snap_scaffold_18-snap.616-T1
Valid prediction for snap_scaffold_18-snap.631-T1
Couldn't classify 193231, 193271
Sorry, prediction pasa_asmbl_20476.p1 fails validation.
(GTG)	 GG	193231-193271	GT	AGG
(CGA)	 AG	193376-193428	GT	AGG
(GGA)	 AG	193508-194778	CC	GAC
-recovered pasa_asmbl_20476.p1, terminal, 193508, 194778
-recovered pasa_asmbl_20476.p1, internal, 193376, 193428
Valid prediction for GlimmerHMM_glimmerT_42976-T1
Valid prediction for snap_scaffold_18-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_42970-T1
Valid prediction for snap_scaffold_18-snap.633-T1
Valid prediction for GlimmerHMM_glimmerT_42960-T1
Valid prediction for GlimmerHMM_glimmerT_42979-T1
Couldn't classify 176323, 176374
Couldn't classify 176559, 177268
Sorry, prediction pasa_asmbl_20467.p1 fails validation.
(CTG)	 AA	176323-176374	GT	TGG
(AAT)	 AG	176559-177268	AG	ACA
Valid prediction for CodingQuarry_transcript_23661-T1
Couldn't classify 192568, 193056
Sorry, prediction pasa_asmbl_20475.p1 fails validation.
(GGT)	 CT	192568-193056	GA	AGG
Valid prediction for GeneMark_model.74226_t
Valid prediction for pasa_asmbl_20461.p1
Valid prediction for GeneMark_model.74228_t
Couldn't classify 177593, 179338
Sorry, prediction pasa_asmbl_20468.p1 fails validation.
(CAT)	 CA	177593-179338	GT	AGG
Valid prediction for Augustus_model.g28736.t1
Valid prediction for GeneMark_model.74207_t
Couldn't classify 57011, 57165
Sorry, prediction pasa_asmbl_20462.p1 fails validation.
(TCG)	 TT	57011-57165	GT	CGG
(GGT)	 AG	57741-57870	GT	AGG
(TGG)	 AG	58516-58587	AA	GAA
-recovered pasa_asmbl_20462.p1, terminal, 58516, 58587
-recovered pasa_asmbl_20462.p1, internal, 57741, 57870
Valid prediction for CodingQuarry_transcript_23653-T1
Valid prediction for GlimmerHMM_glimmerT_42961-T1
Valid prediction for GeneMark_model.74224_t
Valid prediction for HiQ_model.g28734.t1
Valid prediction for snap_scaffold_18-snap.614-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: -)Couldn't classify 5633, 6820
Sorry, prediction pasa_asmbl_19794.p1 fails validation.
(CAG)	 AC	5633-6820	CC	GAC
Valid prediction for CodingQuarry_transcript_23657-T1
Couldn't classify 20535, 21002
Sorry, prediction pasa_asmbl_19789.p1 fails validation.
(CCA)	 TC	20535-21002	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_42982-T1
Valid prediction for GeneMark_model.74221_t
Valid prediction for GeneMark_model.74237_t
Valid prediction for snap_scaffold_18-snap.638-T1
Valid prediction for snap_scaffold_18-snap.612-T1
Valid prediction for Augustus_model.g28752.t1
Valid prediction for snap_scaffold_18-snap.621-T1
Valid prediction for snap_scaffold_18-snap.608-T1
Valid prediction for GeneMark_model.74233_t
Valid prediction for GeneMark_model.74230_t
Valid prediction for snap_scaffold_18-snap.613-T1
Valid prediction for GeneMark_model.74214_t
Valid prediction for GlimmerHMM_glimmerT_42969-T1
Valid prediction for snap_scaffold_18-snap.606-T1
Valid prediction for Augustus_model.g28742.t1
Valid prediction for GeneMark_model.74236_t
Valid prediction for GlimmerHMM_glimmerT_42959-T1
Valid prediction for pasa_asmbl_19783.p1
Valid prediction for GeneMark_model.74223_t
Valid prediction for snap_scaffold_18-snap.628-T1
Valid prediction for GeneMark_model.74227_t
Couldn't classify 19101, 19203
Couldn't classify 20139, 20183
Sorry, prediction pasa_asmbl_19790.p1 fails validation.
(GTA)	 CA	19101-19203	GT	AAG
(CGG)	 AG	19595-19726	GT	AGG
(CCC)	 AG	19858-20024	GT	ATG
(TGG)	 AG	20139-20183	AA	CCA
-recovered pasa_asmbl_19790.p1, internal, 19595, 19726
-recovered pasa_asmbl_19790.p1, internal, 19858, 20024
Valid prediction for CodingQuarry_transcript_23662-T1
Valid prediction for GeneMark_model.74222_t
Valid prediction for GeneMark_model.74217_t
Valid prediction for Augustus_model.g28753.t1
Valid prediction for snap_scaffold_18-snap.625-T1
Valid prediction for GlimmerHMM_glimmerT_42964-T1
Valid prediction for GlimmerHMM_glimmerT_42962-T1
Valid prediction for GeneMark_model.74215_t
Valid prediction for HiQ_model.g28751.t1
Valid prediction for snap_scaffold_18-snap.617-T1
Valid prediction for snap_scaffold_18-snap.615-T1
Valid prediction for GlimmerHMM_glimmerT_42967-T1
Couldn't classify 3573, 3606
Couldn't classify 4581, 4676
Sorry, prediction pasa_asmbl_19795.p1 fails validation.
(ACA)	 AA	3573-3606	GT	AGG
(CAG)	 AG	3951-4156	GT	GGG
(ATG)	 AG	4317-4409	GT	GAG
(AGT)	 AG	4581-4676	GT	AGG
-recovered pasa_asmbl_19795.p1, initial, 4317, 4409
-recovered pasa_asmbl_19795.p1, internal, 3951, 4156
-recovered pasa_asmbl_19795.p1, internal, 4317, 4409
-recovered pasa_asmbl_19795.p1, internal, 4581, 4676
Valid prediction for GlimmerHMM_glimmerT_42968-T1
Valid prediction for CodingQuarry_transcript_23658-T1
Valid prediction for Augustus_model.g28746.t1
Valid prediction for GlimmerHMM_glimmerT_42981-T1
Valid prediction for snap_scaffold_18-snap.622-T1
Valid prediction for HiQ_model.g28740.t1
Valid prediction for pasa_asmbl_19779.p1
Valid prediction for snap_scaffold_18-snap.637-T1
Valid prediction for GeneMark_model.74225_t
Valid prediction for GeneMark_model.74210_t
Valid prediction for pasa_asmbl_19792.p1
Valid prediction for HiQ_model.g28749.t1
Valid prediction for GeneMark_model.74209_t
Valid prediction for snap_scaffold_18-snap.627-T1
Valid prediction for snap_scaffold_18-snap.636-T1
Valid prediction for HiQ_model.g28735.t1
Valid prediction for GlimmerHMM_glimmerT_42978-T1
Valid prediction for Augustus_model.g28738.t1
Valid prediction for snap_scaffold_18-snap.619-T1
Valid prediction for GlimmerHMM_glimmerT_42958-T1
Valid prediction for GlimmerHMM_glimmerT_42974-T1
Valid prediction for GeneMark_model.74208_t
Valid prediction for GeneMark_model.74219_t
Valid prediction for GeneMark_model.74238_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 94954, rend_intergenic: 89966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166911, rend_intergenic: 166357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216720
-exon list size: 441


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.0    
2.3    
2.5    
2.7    
2.9    
3.2    
3.4    
3.6    
3.8    
4.1    
4.3    
4.5    
4.7    
5.0    
5.2    
5.4    
5.6    
5.9    
6.1    
6.3    
6.5    
6.8    
7.0    
7.2    
7.4    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
9.9    
10.2    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.7    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
19.0    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.3    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.6    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.5    
34.8    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.2    
65.5    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.4    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 94954, rend_intergenic: 89966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166911, rend_intergenic: 166357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support