-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_13655771-13823742

-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.2720-T1
Valid prediction for snap_scaffold_10-snap.2732-T1
Valid prediction for snap_scaffold_10-snap.2740-T1
Valid prediction for Augustus_model.g17641.t1
Valid prediction for snap_scaffold_10-snap.2741-T1
Couldn't classify 49914, 50318
Sorry, prediction pasa_asmbl_4886.p1 fails validation.
(TCA)	 TG	49914-50318	CC	GAC
Valid prediction for Augustus_model.g17655.t1
Valid prediction for GlimmerHMM_glimmerT_26274-T1
Valid prediction for GlimmerHMM_glimmerT_26270-T1
Valid prediction for CodingQuarry_transcript_5629-T1
Valid prediction for GlimmerHMM_glimmerT_26285-T1
Valid prediction for Augustus_model.g17647.t1
Valid prediction for snap_scaffold_10-snap.2739-T1
Valid prediction for snap_scaffold_10-snap.2721-T1
Valid prediction for GlimmerHMM_glimmerT_26293-T1
Valid prediction for GeneMark_model.45052_t
Valid prediction for snap_scaffold_10-snap.2734-T1
Valid prediction for GeneMark_model.45039_t
Valid prediction for snap_scaffold_10-snap.2731-T1
Valid prediction for Augustus_model.g17645.t1
Valid prediction for GeneMark_model.45042_t
Valid prediction for snap_scaffold_10-snap.2715-T1
Valid prediction for snap_scaffold_10-snap.2714-T1
Valid prediction for HiQ_model.g17652.t1
Valid prediction for snap_scaffold_10-snap.2722-T1
Valid prediction for Augustus_model.g17640.t1
Valid prediction for snap_scaffold_10-snap.2748-T1
Valid prediction for GeneMark_model.45069_t
Valid prediction for GeneMark_model.45046_t
Valid prediction for GlimmerHMM_glimmerT_26289-T1
Valid prediction for snap_scaffold_10-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_26284-T1
Valid prediction for GlimmerHMM_glimmerT_26287-T1
Valid prediction for snap_scaffold_10-snap.2733-T1
Valid prediction for snap_scaffold_10-snap.2726-T1
Valid prediction for snap_scaffold_10-snap.2730-T1
Valid prediction for snap_scaffold_10-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_26279-T1
Valid prediction for GlimmerHMM_glimmerT_26276-T1
Valid prediction for GeneMark_model.45056_t
Valid prediction for GeneMark_model.45054_t
Valid prediction for GeneMark_model.45071_t
Couldn't classify 122393, 122833
Sorry, prediction pasa_asmbl_4890.p1 fails validation.
(TCT)	 GG	122393-122833	GT	AGG
(TTG)	 AG	123349-123557	GT	GAG
(TGC)	 AG	126144-126178	GT	AGG
(GCG)	 AG	127494-127643	GT	CGG
(GAG)	 AG	128063-128127	GT	TGG
(CTC)	 AG	128272-128388	GT	AGG
(GAT)	 AG	128727-128806	GT	GGG
(AAC)	 AG	129017-129098	GT	AGG
(ACA)	 AG	129370-129462	GT	AGG
(TAT)	 AG	130446-130592	GT	AGG
(GAG)	 AG	131228-131403	GT	AAG
(GTG)	 AG	131656-131754	GT	AAG
(GAT)	 AG	132196-132284	GT	AGG
(GCC)	 AG	132978-133168	GT	AAG
add_exon() Sorry, pasa_asmbl_4890.p1 132196-132284-terminal-2 is invalid.
-recovered pasa_asmbl_4890.p1, terminal, 132196, 132284
-recovered pasa_asmbl_4890.p1, terminal, 132978, 133168
-recovered pasa_asmbl_4890.p1, internal, 123349, 123557
-recovered pasa_asmbl_4890.p1, internal, 126144, 126178
-recovered pasa_asmbl_4890.p1, internal, 127494, 127643
-recovered pasa_asmbl_4890.p1, internal, 128063, 128127
-recovered pasa_asmbl_4890.p1, internal, 128272, 128388
-recovered pasa_asmbl_4890.p1, internal, 128727, 128806
-recovered pasa_asmbl_4890.p1, internal, 129017, 129098
-recovered pasa_asmbl_4890.p1, internal, 129370, 129462
-recovered pasa_asmbl_4890.p1, internal, 130446, 130592
-recovered pasa_asmbl_4890.p1, internal, 131228, 131403
-recovered pasa_asmbl_4890.p1, internal, 131656, 131754
-recovered pasa_asmbl_4890.p1, internal, 132196, 132284
-recovered pasa_asmbl_4890.p1, internal, 132978, 133168
Valid prediction for Augustus_model.g17644.t1
Valid prediction for snap_scaffold_10-snap.2746-T1
Valid prediction for GeneMark_model.45063_t
Valid prediction for Augustus_model.g17649.t1
Valid prediction for snap_scaffold_10-snap.2712-T1
Valid prediction for GeneMark_model.45065_t
Valid prediction for snap_scaffold_10-snap.2716-T1
Valid prediction for GeneMark_model.45040_t
Valid prediction for GeneMark_model.45049_t
Valid prediction for GlimmerHMM_glimmerT_26269-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.2744-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g17642.t1
Valid prediction for snap_scaffold_10-snap.2727-T1
Valid prediction for GlimmerHMM_glimmerT_26277-T1
Valid prediction for GlimmerHMM_glimmerT_26288-T1
Valid prediction for GeneMark_model.45050_t
Valid prediction for snap_scaffold_10-snap.2738-T1
Valid prediction for GeneMark_model.45067_t
Valid prediction for GlimmerHMM_glimmerT_26291-T1
Valid prediction for GeneMark_model.45041_t
Valid prediction for GeneMark_model.45064_t
Valid prediction for GlimmerHMM_glimmerT_26286-T1
Valid prediction for Augustus_model.g17643.t1
Valid prediction for snap_scaffold_10-snap.2723-T1
Valid prediction for GlimmerHMM_glimmerT_26268-T1
Valid prediction for GlimmerHMM_glimmerT_26278-T1
Valid prediction for Augustus_model.g17653.t1
Valid prediction for Augustus_model.g17654.t1
Valid prediction for Augustus_model.g17650.t1
Valid prediction for snap_scaffold_10-snap.2713-T1
Valid prediction for GlimmerHMM_glimmerT_26282-T1
Valid prediction for GeneMark_model.45066_t
Valid prediction for GlimmerHMM_glimmerT_26273-T1
Valid prediction for snap_scaffold_10-snap.2743-T1
Valid prediction for GeneMark_model.45051_t
Valid prediction for snap_scaffold_10-snap.2736-T1
Valid prediction for GlimmerHMM_glimmerT_26283-T1
Valid prediction for snap_scaffold_10-snap.2729-T1
Valid prediction for GlimmerHMM_glimmerT_26275-T1
Valid prediction for snap_scaffold_10-snap.2742-T1
Valid prediction for snap_scaffold_10-snap.2735-T1
Valid prediction for snap_scaffold_10-snap.2719-T1
Valid prediction for GeneMark_model.45061_t
Valid prediction for GeneMark_model.45059_t
Valid prediction for GeneMark_model.45070_t
Valid prediction for snap_scaffold_10-snap.2737-T1
Valid prediction for CodingQuarry_transcript_5627-T1
Valid prediction for GeneMark_model.45053_t
Valid prediction for GlimmerHMM_glimmerT_26272-T1
Valid prediction for CodingQuarry_transcript_5630-T1
Valid prediction for GeneMark_model.45058_t
Valid prediction for CodingQuarry_transcript_5628-T1
Valid prediction for GeneMark_model.45060_t
Valid prediction for HiQ_model.g17651.t1
Valid prediction for GeneMark_model.45055_t
Valid prediction for GeneMark_model.45057_t
Valid prediction for snap_scaffold_10-snap.2718-T1
Valid prediction for GeneMark_model.45048_t
Valid prediction for GlimmerHMM_glimmerT_26280-T1
Valid prediction for GlimmerHMM_glimmerT_26281-T1
Valid prediction for Augustus_model.g17646.t1
Valid prediction for Augustus_model.g17648.t1
Valid prediction for GlimmerHMM_glimmerT_26271-T1
Couldn't classify 48721, 49001
Sorry, prediction pasa_asmbl_3832.p1 fails validation.
(TGC)	 TC	48721-49001	GT	AGG
(GTG)	 AG	49225-49353	GT	AAG
(TTG)	 AG	49653-49756	GT	CCG
(AGC)	 AG	49973-50087	GT	GAG
(CCC)	 AG	50316-50419	GT	TGG
(TGT)	 AG	51156-51316	TC	GAT
add_exon() Sorry, pasa_asmbl_3832.p1 49225-49353-terminal-1 is invalid.
-recovered pasa_asmbl_3832.p1, terminal, 49225, 49353
-recovered pasa_asmbl_3832.p1, terminal, 51156, 51316
-recovered pasa_asmbl_3832.p1, internal, 49225, 49353
-recovered pasa_asmbl_3832.p1, internal, 49653, 49756
-recovered pasa_asmbl_3832.p1, internal, 49973, 50087
-recovered pasa_asmbl_3832.p1, internal, 50316, 50419
Valid prediction for snap_scaffold_10-snap.2725-T1
Valid prediction for pasa_asmbl_3828.p1
Valid prediction for GeneMark_model.45068_t
Valid prediction for snap_scaffold_10-snap.2747-T1
Valid prediction for pasa_asmbl_3826.p1
Valid prediction for snap_scaffold_10-snap.2745-T1
Valid prediction for snap_scaffold_10-snap.2717-T1
Valid prediction for snap_scaffold_10-snap.2724-T1
Valid prediction for GlimmerHMM_glimmerT_26290-T1
Valid prediction for GeneMark_model.45043_t
Valid prediction for GeneMark_model.45045_t
Valid prediction for GlimmerHMM_glimmerT_26292-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61246, rend_intergenic: 60199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69446, rend_intergenic: 65442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78179, rend_intergenic: 73691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167972
-exon list size: 456


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
2.0    
2.2    
2.4    
2.6    
2.8    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.2    
5.5    
5.7    
5.9    
6.1    
6.3    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.7    
15.9    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.4    
26.6    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.2    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.6    
52.8    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.4    
73.6    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 61246, rend_intergenic: 60199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69446, rend_intergenic: 65442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78179, rend_intergenic: 73691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support