-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_3414282-3577641

-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 Augustus_model.g11771.t1
Valid prediction for GeneMark_model.29671_t
Valid prediction for snap_scaffold_7-snap.838-T1
Valid prediction for snap_scaffold_7-snap.845-T1
Valid prediction for GlimmerHMM_glimmerT_17597-T1
Valid prediction for GeneMark_model.29659_t
Valid prediction for snap_scaffold_7-snap.818-T1
Valid prediction for GeneMark_model.29649_t
Valid prediction for snap_scaffold_7-snap.825-T1
Valid prediction for snap_scaffold_7-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_17598-T1
Valid prediction for snap_scaffold_7-snap.839-T1
Valid prediction for GeneMark_model.29679_t
Couldn't classify 70985, 71317
Sorry, prediction pasa_asmbl_50354.p1 fails validation.
(GCC)	 AA	70985-71317	CT	ATC
Valid prediction for GeneMark_model.29655_t
Valid prediction for snap_scaffold_7-snap.819-T1
Valid prediction for Augustus_model.g11765.t1
Couldn't classify 16010, 16180
Sorry, prediction pasa_asmbl_50568.p1 fails validation.
(CTG)	 TC	16010-16180	GT	CAG
(GTG)	 AG	16503-16591	GT	ACG
(GTG)	 AG	16704-16732	GT	TCG
(CCT)	 AG	17950-18083	GT	AGG
(CGC)	 AG	18166-18249	GT	AGG
(ACT)	 AG	18369-18454	GT	AGG
(CAC)	 AG	18687-18810	GT	GGG
(GTG)	 AG	18914-18984	GT	AGG
(ACA)	 AG	19114-19216	CC	GAC
-recovered pasa_asmbl_50568.p1, terminal, 19114, 19216
-recovered pasa_asmbl_50568.p1, internal, 16503, 16591
-recovered pasa_asmbl_50568.p1, internal, 16704, 16732
-recovered pasa_asmbl_50568.p1, internal, 17950, 18083
-recovered pasa_asmbl_50568.p1, internal, 18166, 18249
-recovered pasa_asmbl_50568.p1, internal, 18369, 18454
-recovered pasa_asmbl_50568.p1, internal, 18687, 18810
-recovered pasa_asmbl_50568.p1, internal, 18914, 18984
Valid prediction for Augustus_model.g11773.t1
Valid prediction for snap_scaffold_7-snap.835-T1
Valid prediction for Augustus_model.g11774.t1
Valid prediction for GeneMark_model.29647_t
Valid prediction for GeneMark_model.29673_t
Valid prediction for snap_scaffold_7-snap.844-T1
Valid prediction for GeneMark_model.29657_t
Valid prediction for GlimmerHMM_glimmerT_17588-T1
Valid prediction for GeneMark_model.29666_t
Valid prediction for snap_scaffold_7-snap.834-T1
Valid prediction for GlimmerHMM_glimmerT_17603-T1
Valid prediction for snap_scaffold_7-snap.846-T1
Valid prediction for snap_scaffold_7-snap.830-T1
Couldn't classify 159327, 159368
Sorry, prediction pasa_asmbl_50573.p1 fails validation.
(ATG)	 GA	158365-158598	GT	TGG
(GTC)	 AG	158810-159004	GT	CAG
(GTG)	 AG	159327-159368	AT	GCA
-recovered pasa_asmbl_50573.p1, initial, 158365, 158598
-recovered pasa_asmbl_50573.p1, internal, 158810, 159004
Valid prediction for GeneMark_model.29650_t
Valid prediction for snap_scaffold_7-snap.832-T1
Valid prediction for Augustus_model.g11759.t1
Valid prediction for GlimmerHMM_glimmerT_17581-T1
Valid prediction for GlimmerHMM_glimmerT_17578-T1
Valid prediction for Augustus_model.g11779.t1
Couldn't classify 27518, 27794
Sorry, prediction pasa_asmbl_50570.p1 fails validation.
(TCC)	 TC	27518-27794	GT	CGG
(GCT)	 AG	28720-28902	GT	AGG
(GTA)	 AG	29566-29780	GG	AGG
-recovered pasa_asmbl_50570.p1, terminal, 29566, 29780
-recovered pasa_asmbl_50570.p1, internal, 28720, 28902
Valid prediction for GeneMark_model.29652_t
Valid prediction for GlimmerHMM_glimmerT_17591-T1
Valid prediction for snap_scaffold_7-snap.820-T1
Valid prediction for Augustus_model.g11781.t1
Valid prediction for snap_scaffold_7-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_17590-T1
Valid prediction for snap_scaffold_7-snap.851-T1
Valid prediction for GlimmerHMM_glimmerT_17584-T1
Valid prediction for GlimmerHMM_glimmerT_17582-T1
Valid prediction for GlimmerHMM_glimmerT_17602-T1
Valid prediction for Augustus_model.g11767.t1
Valid prediction for snap_scaffold_7-snap.827-T1
Valid prediction for snap_scaffold_7-snap.836-T1
Valid prediction for GlimmerHMM_glimmerT_17596-T1
Valid prediction for GlimmerHMM_glimmerT_17605-T1
Valid prediction for GlimmerHMM_glimmerT_17587-T1
Valid prediction for snap_scaffold_7-snap.837-T1
Valid prediction for Augustus_model.g11785.t1
Valid prediction for Augustus_model.g11761.t1
Valid prediction for GeneMark_model.29672_t
Valid prediction for Augustus_model.g11772.t1
Valid prediction for GeneMark_model.29660_t
Valid prediction for snap_scaffold_7-snap.831-T1
Valid prediction for HiQ_model.g11758.t1
Valid prediction for GlimmerHMM_glimmerT_17609-T1
Valid prediction for Augustus_model.g11755.t1
Valid prediction for Augustus_model.g11780.t1
Valid prediction for Augustus_model.g11782.t1
Valid prediction for GlimmerHMM_glimmerT_17593-T1
Valid prediction for Augustus_model.g11787.t1
Valid prediction for Augustus_model.g11763.t1
Valid prediction for snap_scaffold_7-snap.823-T1
Valid prediction for GlimmerHMM_glimmerT_17604-T1
Valid prediction for GeneMark_model.29662_t

-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_7-snap.828-T1
Valid prediction for Augustus_model.g11770.t1
Valid prediction for Augustus_model.g11768.t1
Valid prediction for GlimmerHMM_glimmerT_17599-T1
Valid prediction for snap_scaffold_7-snap.833-T1
Valid prediction for GeneMark_model.29680_t
Valid prediction for GeneMark_model.29670_t
Valid prediction for GeneMark_model.29676_t
Valid prediction for GlimmerHMM_glimmerT_17586-T1
Valid prediction for Augustus_model.g11766.t1
Valid prediction for snap_scaffold_7-snap.840-T1
Valid prediction for GlimmerHMM_glimmerT_17589-T1
Valid prediction for pasa_asmbl_50400.p1
Valid prediction for CodingQuarry_transcript_57311-T1
Valid prediction for Augustus_model.g11784.t1
Valid prediction for snap_scaffold_7-snap.841-T1
Couldn't classify 15139, 15274
Sorry, prediction pasa_asmbl_49613.p2 fails validation.
(ATG)	 GG	13838-13986	GT	TGG
(GTT)	 AG	14411-14545	GT	GAG
(GTT)	 AG	15139-15274	GG	CGG
-recovered pasa_asmbl_49613.p2, initial, 13838, 13986
add_exon() Sorry, pasa_asmbl_49613.p2 14411-14545-terminal-1 is invalid.
-recovered pasa_asmbl_49613.p2, terminal, 14411, 14545
-recovered pasa_asmbl_49613.p2, internal, 14411, 14545
Valid prediction for GlimmerHMM_glimmerT_17592-T1
Valid prediction for Augustus_model.g11757.t1
Valid prediction for Augustus_model.g11764.t1
Valid prediction for GlimmerHMM_glimmerT_17585-T1
Couldn't classify 50724, 51149
Sorry, prediction pasa_asmbl_49612.p1 fails validation.
(GGG)	 AC	50724-51149	AT	AAA
Couldn't classify 2614, 2700
Sorry, prediction pasa_asmbl_49615.p1 fails validation.
(ATG)	 AG	1651-1768	GT	AGG
(CTT)	 AG	1880-2094	GT	AGG
(ATC)	 AG	2614-2700	GA	ATG
-recovered pasa_asmbl_49615.p1, initial, 1651, 1768
-recovered pasa_asmbl_49615.p1, internal, 1651, 1768
-recovered pasa_asmbl_49615.p1, internal, 1880, 2094
Valid prediction for snap_scaffold_7-snap.850-T1
Valid prediction for GeneMark_model.29658_t
Valid prediction for GlimmerHMM_glimmerT_17608-T1
Valid prediction for GlimmerHMM_glimmerT_17583-T1
Valid prediction for HiQ_model.g11786.t1
Valid prediction for GlimmerHMM_glimmerT_17594-T1
Valid prediction for snap_scaffold_7-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_17607-T1
Valid prediction for GlimmerHMM_glimmerT_17595-T1
Valid prediction for Augustus_model.g11777.t1
Valid prediction for snap_scaffold_7-snap.848-T1
Valid prediction for snap_scaffold_7-snap.821-T1
Valid prediction for GeneMark_model.29675_t
Valid prediction for HiQ_model.g11788.t1
Valid prediction for GlimmerHMM_glimmerT_17580-T1
Valid prediction for snap_scaffold_7-snap.843-T1
Valid prediction for GeneMark_model.29681_t
Valid prediction for GlimmerHMM_glimmerT_17606-T1
Valid prediction for snap_scaffold_7-snap.816-T1
Valid prediction for Augustus_model.g11762.t1
Valid prediction for Augustus_model.g11778.t1
Valid prediction for Augustus_model.g11783.t1
Valid prediction for GeneMark_model.29654_t
Valid prediction for snap_scaffold_7-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_17611-T1
Valid prediction for GlimmerHMM_glimmerT_17601-T1
Valid prediction for Augustus_model.g11756.t1
Valid prediction for Augustus_model.g11775.t1
Valid prediction for GeneMark_model.29677_t
Valid prediction for GlimmerHMM_glimmerT_17600-T1
Couldn't classify 5879, 6052
Sorry, prediction pasa_asmbl_49614.p1 fails validation.
(GCA)	 GT	5879-6052	GT	GTG
(GAT)	 AG	6433-7437	GT	GAG
-recovered pasa_asmbl_49614.p1, terminal, 6433, 7437
-recovered pasa_asmbl_49614.p1, internal, 6433, 7437
Valid prediction for snap_scaffold_7-snap.852-T1
Valid prediction for snap_scaffold_7-snap.822-T1
Valid prediction for GeneMark_model.29646_t
Valid prediction for Augustus_model.g11776.t1
Valid prediction for snap_scaffold_7-snap.824-T1
Valid prediction for snap_scaffold_7-snap.817-T1
Valid prediction for snap_scaffold_7-snap.829-T1
Valid prediction for GeneMark_model.29648_t
Valid prediction for snap_scaffold_7-snap.842-T1
Valid prediction for GeneMark_model.29653_t
Valid prediction for Augustus_model.g11760.t1
Valid prediction for GeneMark_model.29651_t
Valid prediction for GlimmerHMM_glimmerT_17610-T1
Valid prediction for snap_scaffold_7-snap.854-T1
Valid prediction for snap_scaffold_7-snap.826-T1
Valid prediction for Augustus_model.g11769.t1
Valid prediction for GlimmerHMM_glimmerT_17579-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29780, rend_intergenic: 27534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160792, rend_intergenic: 159755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163360
-exon list size: 388


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.2    
6.4    
6.7    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 29780, rend_intergenic: 27534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160792, rend_intergenic: 159755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support