-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_7336628-7548400

-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.g2796.t1
Valid prediction for GlimmerHMM_glimmerT_4181-T1
Valid prediction for GeneMark_model.6746_t
Valid prediction for Augustus_model.g2808.t1
Valid prediction for snap_scaffold_2-snap.1599-T1
Valid prediction for GeneMark_model.6762_t
Valid prediction for snap_scaffold_2-snap.1597-T1
Valid prediction for GeneMark_model.6771_t
Valid prediction for GeneMark_model.6745_t
Valid prediction for GeneMark_model.6749_t
Valid prediction for GeneMark_model.6766_t
Valid prediction for GeneMark_model.6768_t
Valid prediction for Augustus_model.g2817.t1
Valid prediction for snap_scaffold_2-snap.1606-T1
Valid prediction for Augustus_model.g2804.t1
Valid prediction for snap_scaffold_2-snap.1594-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_4173-T1
Valid prediction for GlimmerHMM_glimmerT_4162-T1
Valid prediction for GlimmerHMM_glimmerT_4183-T1
Valid prediction for GlimmerHMM_glimmerT_4171-T1
Valid prediction for snap_scaffold_2-snap.1591-T1
Valid prediction for Augustus_model.g2806.t1
Valid prediction for GlimmerHMM_glimmerT_4164-T1
Valid prediction for GlimmerHMM_glimmerT_4175-T1
Valid prediction for Augustus_model.g2798.t1
Valid prediction for GlimmerHMM_glimmerT_4194-T1
Valid prediction for Augustus_model.g2803.t1
Valid prediction for snap_scaffold_2-snap.1589-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g2801.t1
Valid prediction for snap_scaffold_2-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_4177-T1
Valid prediction for snap_scaffold_2-snap.1605-T1
Valid prediction for snap_scaffold_2-snap.1603-T1
Valid prediction for GlimmerHMM_glimmerT_4192-T1
Valid prediction for Augustus_model.g2811.t1
Valid prediction for snap_scaffold_2-snap.1590-T1
Valid prediction for GeneMark_model.6755_t
Valid prediction for GeneMark_model.6765_t
Valid prediction for GlimmerHMM_glimmerT_4167-T1
Valid prediction for snap_scaffold_2-snap.1593-T1
Valid prediction for GeneMark_model.6742_t
Valid prediction for GlimmerHMM_glimmerT_4186-T1
Valid prediction for snap_scaffold_2-snap.1595-T1
Valid prediction for GlimmerHMM_glimmerT_4168-T1
Valid prediction for GlimmerHMM_glimmerT_4195-T1
Valid prediction for GlimmerHMM_glimmerT_4185-T1
Valid prediction for GeneMark_model.6763_t
Valid prediction for GlimmerHMM_glimmerT_4165-T1
Valid prediction for Augustus_model.g2797.t1
Valid prediction for GlimmerHMM_glimmerT_4180-T1
Valid prediction for GeneMark_model.6751_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 GlimmerHMM_glimmerT_4170-T1
Valid prediction for GeneMark_model.6761_t
Valid prediction for Augustus_model.g2815.t1
Valid prediction for Augustus_model.g2807.t1
Valid prediction for snap_scaffold_2-snap.1600-T1
Valid prediction for GlimmerHMM_glimmerT_4179-T1
Valid prediction for GlimmerHMM_glimmerT_4163-T1
Valid prediction for GeneMark_model.6741_t
Valid prediction for GlimmerHMM_glimmerT_4189-T1
Valid prediction for snap_scaffold_2-snap.1588-T1
Valid prediction for snap_scaffold_2-snap.1615-T1
Couldn't classify 69579, 69737
Sorry, prediction pasa_asmbl_23292.p1 fails validation.
(ATG)	 TG	68375-68524	GT	AGG
(AAT)	 AG	68650-68766	GT	AGG
(GTG)	 AG	68843-68977	GT	TGG
(GGC)	 AG	69116-69232	GT	CAG
(GCC)	 AG	69579-69737	GG	AAG
-recovered pasa_asmbl_23292.p1, initial, 68375, 68524
-recovered pasa_asmbl_23292.p1, internal, 68650, 68766
-recovered pasa_asmbl_23292.p1, internal, 68843, 68977
-recovered pasa_asmbl_23292.p1, internal, 69116, 69232
Valid prediction for Augustus_model.g2800.t1
Valid prediction for Augustus_model.g2795.t1
Valid prediction for GlimmerHMM_glimmerT_4176-T1
Valid prediction for snap_scaffold_2-snap.1598-T1
Valid prediction for Augustus_model.g2818.t1
Valid prediction for GlimmerHMM_glimmerT_4174-T1
Valid prediction for snap_scaffold_2-snap.1610-T1
Valid prediction for HiQ_model.g2809.t1
Valid prediction for snap_scaffold_2-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_4182-T1
Valid prediction for GeneMark_model.6770_t
Valid prediction for GeneMark_model.6759_t
Valid prediction for Augustus_model.g2816.t1
Valid prediction for GeneMark_model.6757_t
Valid prediction for pasa_asmbl_23288.p1
Valid prediction for HiQ_model.g2813.t1
Valid prediction for GeneMark_model.6760_t
Valid prediction for snap_scaffold_2-snap.1607-T1
Valid prediction for CodingQuarry_transcript_28549-T1
Valid prediction for snap_scaffold_2-snap.1596-T1
Valid prediction for Augustus_model.g2814.t1
Valid prediction for CodingQuarry_transcript_28546-T1
Valid prediction for GlimmerHMM_glimmerT_4166-T1
Valid prediction for GeneMark_model.6753_t
Valid prediction for GeneMark_model.6769_t
Valid prediction for CodingQuarry_transcript_28545-T1
Valid prediction for GeneMark_model.6772_t
Valid prediction for Augustus_model.g2802.t1
Valid prediction for GlimmerHMM_glimmerT_4172-T1
Valid prediction for GlimmerHMM_glimmerT_4193-T1
Valid prediction for GeneMark_model.6764_t
Valid prediction for GlimmerHMM_glimmerT_4191-T1
Valid prediction for Augustus_model.g2810.t1
Valid prediction for pasa_asmbl_23277.p1
Valid prediction for snap_scaffold_2-snap.1614-T1
Valid prediction for snap_scaffold_2-snap.1612-T1
Valid prediction for GeneMark_model.6743_t
Valid prediction for GeneMark_model.6744_t
Valid prediction for GeneMark_model.6750_t
Couldn't classify 70278, 71100
Couldn't classify 71222, 71340
Sorry, prediction pasa_asmbl_24050.p1 fails validation.
(CTC)	 AT	70278-71100	GT	AAG
(AGC)	 AG	71222-71340	AG	GCA
Valid prediction for CodingQuarry_transcript_28544-T1
Valid prediction for CodingQuarry_transcript_28548-T1
Valid prediction for GeneMark_model.6752_t
Valid prediction for snap_scaffold_2-snap.1608-T1
Valid prediction for GlimmerHMM_glimmerT_4184-T1
Valid prediction for GlimmerHMM_glimmerT_4187-T1
Valid prediction for GeneMark_model.6758_t
Valid prediction for GeneMark_model.6754_t
Valid prediction for GlimmerHMM_glimmerT_4169-T1
Valid prediction for Augustus_model.g2805.t1
Valid prediction for GlimmerHMM_glimmerT_4161-T1
Valid prediction for HiQ_model.g2812.t1
Valid prediction for Augustus_model.g2799.t1
Valid prediction for GeneMark_model.6747_t
Valid prediction for snap_scaffold_2-snap.1613-T1
Valid prediction for snap_scaffold_2-snap.1609-T1
Valid prediction for snap_scaffold_2-snap.1611-T1
Valid prediction for GlimmerHMM_glimmerT_4188-T1
Valid prediction for snap_scaffold_2-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_4190-T1
Valid prediction for GeneMark_model.6748_t
Valid prediction for GeneMark_model.6756_t
Valid prediction for GeneMark_model.6767_t
Valid prediction for GlimmerHMM_glimmerT_4178-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41281, rend_intergenic: 40543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211773
-exon list size: 384


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.1    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
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    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
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    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 41281, rend_intergenic: 40543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10819
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 1 - 10697
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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