-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_13764392-13958636

-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 GeneMark_model.61376_t
Valid prediction for GeneMark_model.61384_t
Valid prediction for snap_scaffold_14-snap.2860-T1
Valid prediction for GeneMark_model.61388_t
Valid prediction for GeneMark_model.61381_t
Valid prediction for GeneMark_model.61370_t
Valid prediction for GlimmerHMM_glimmerT_35805-T1
Valid prediction for GlimmerHMM_glimmerT_35812-T1
Valid prediction for CodingQuarry_transcript_15874-T1
Valid prediction for GeneMark_model.61380_t
Valid prediction for HiQ_model.g24112.t1
Valid prediction for HiQ_model.g24114.t1
Valid prediction for GlimmerHMM_glimmerT_35815-T1
Valid prediction for GeneMark_model.61386_t
Valid prediction for GlimmerHMM_glimmerT_35809-T1
Couldn't classify 96336, 97343
Sorry, prediction pasa_asmbl_12491.p1 fails validation.
(GGA)	 GT	96336-97343	AT	AGA
Valid prediction for snap_scaffold_14-snap.2882-T1
Valid prediction for pasa_asmbl_12494.p1
Valid prediction for GlimmerHMM_glimmerT_35811-T1
Valid prediction for GlimmerHMM_glimmerT_35808-T1
Valid prediction for CodingQuarry_transcript_15870-T1
Valid prediction for GlimmerHMM_glimmerT_35807-T1
Valid prediction for snap_scaffold_14-snap.2866-T1
Valid prediction for HiQ_model.g24113.t1
Valid prediction for pasa_asmbl_12502.p1
Valid prediction for snap_scaffold_14-snap.2875-T1
Valid prediction for snap_scaffold_14-snap.2873-T1
Valid prediction for GeneMark_model.61369_t
Valid prediction for snap_scaffold_14-snap.2865-T1
Valid prediction for snap_scaffold_14-snap.2876-T1
Valid prediction for CodingQuarry_transcript_15873-T1
Valid prediction for GlimmerHMM_glimmerT_35804-T1
Valid prediction for GlimmerHMM_glimmerT_35816-T1
Valid prediction for snap_scaffold_14-snap.2863-T1
Valid prediction for GeneMark_model.61366_t
Valid prediction for GlimmerHMM_glimmerT_35817-T1
Valid prediction for HiQ_model.g24109.t1
Valid prediction for GeneMark_model.61392_t
Valid prediction for Augustus_model.g24107.t1
Valid prediction for snap_scaffold_14-snap.2871-T1
Valid prediction for snap_scaffold_14-snap.2868-T1
Valid prediction for GeneMark_model.61368_t
Valid prediction for GlimmerHMM_glimmerT_35810-T1
Valid prediction for GeneMark_model.61372_t
Valid prediction for GeneMark_model.61390_t
Valid prediction for GlimmerHMM_glimmerT_35806-T1
Valid prediction for snap_scaffold_14-snap.2859-T1
Valid prediction for snap_scaffold_14-snap.2861-T1
Valid prediction for GeneMark_model.61375_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_14-snap.2874-T1
Valid prediction for snap_scaffold_14-snap.2879-T1
Valid prediction for GeneMark_model.61385_t
Valid prediction for CodingQuarry_transcript_15872-T1
Valid prediction for pasa_asmbl_13640.p1
Valid prediction for GlimmerHMM_glimmerT_35813-T1
Valid prediction for GeneMark_model.61391_t
Couldn't classify 46693, 47760
Sorry, prediction pasa_asmbl_13650.p1 fails validation.
(ATC)	 AG	46693-47760	CA	TGC
Valid prediction for snap_scaffold_14-snap.2878-T1
Valid prediction for snap_scaffold_14-snap.2872-T1
Valid prediction for snap_scaffold_14-snap.2857-T1
Valid prediction for GeneMark_model.61389_t
Valid prediction for snap_scaffold_14-snap.2880-T1
Valid prediction for Augustus_model.g24108.t1
Valid prediction for HiQ_model.g24110.t1
Valid prediction for Augustus_model.g24118.t1
Valid prediction for GeneMark_model.61367_t
Valid prediction for GeneMark_model.61374_t
Valid prediction for GeneMark_model.61379_t
Valid prediction for GlimmerHMM_glimmerT_35818-T1
Valid prediction for GeneMark_model.61371_t
Valid prediction for snap_scaffold_14-snap.2864-T1
Valid prediction for Augustus_model.g24117.t1
Valid prediction for snap_scaffold_14-snap.2867-T1
Valid prediction for GlimmerHMM_glimmerT_35819-T1
Valid prediction for snap_scaffold_14-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_35814-T1
Couldn't classify 67081, 67270
Sorry, prediction pasa_asmbl_13647.p1 fails validation.
(TTT)	 GC	67081-67270	GT	ATG
(ACA)	 AG	67658-67962	GG	AAG
-recovered pasa_asmbl_13647.p1, terminal, 67658, 67962
Valid prediction for snap_scaffold_14-snap.2870-T1
Valid prediction for GeneMark_model.61382_t
Valid prediction for Augustus_model.g24115.t1
Valid prediction for snap_scaffold_14-snap.2869-T1
Valid prediction for GeneMark_model.61383_t
Valid prediction for GeneMark_model.61377_t
Couldn't classify 35092, 35161
Couldn't classify 37012, 37087
Sorry, prediction pasa_asmbl_13652.p1 fails validation.
(CAG)	 CT	35092-35161	GT	TGG
(GCT)	 AG	36358-36488	GT	AGG
(AGA)	 AG	36756-36868	GT	AGG
(ATT)	 AG	37012-37087	AA	GGA
-recovered pasa_asmbl_13652.p1, internal, 36358, 36488
-recovered pasa_asmbl_13652.p1, internal, 36756, 36868
Valid prediction for Augustus_model.g24116.t1
Valid prediction for pasa_asmbl_13642.p1
Valid prediction for snap_scaffold_14-snap.2862-T1
Valid prediction for Augustus_model.g24119.t1
Valid prediction for GeneMark_model.61378_t
Valid prediction for CodingQuarry_transcript_15871-T1
Valid prediction for snap_scaffold_14-snap.2858-T1
Valid prediction for GlimmerHMM_glimmerT_35820-T1
Couldn't classify 47905, 48270
Sorry, prediction pasa_asmbl_13649.p2 fails validation.
(GTC)	 CC	47905-48270	CT	AAC
Valid prediction for GeneMark_model.61387_t
Valid prediction for GeneMark_model.61373_t
Valid prediction for snap_scaffold_14-snap.2881-T1
Valid prediction for GeneMark_model.61365_t
Valid prediction for HiQ_model.g24111.t1
Valid prediction for GeneMark_model.61393_t
Couldn't classify 41931, 42160
Couldn't classify 45293, 46032
Sorry, prediction pasa_asmbl_13771.p1 fails validation.
(TAC)	 GT	41931-42160	GT	AGG
(GTT)	 AG	42723-42882	GT	ACG
(GCG)	 AG	43525-43842	GT	AGG
(AGA)	 AG	44724-44991	GT	AGG
(GAG)	 AG	45293-46032	TC	CTT
-recovered pasa_asmbl_13771.p1, internal, 42723, 42882
-recovered pasa_asmbl_13771.p1, internal, 43525, 43842
-recovered pasa_asmbl_13771.p1, internal, 44724, 44991

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22819, rend_intergenic: 17929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49041, rend_intergenic: 47679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162188, rend_intergenic: 150322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190827, rend_intergenic: 181389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194245
-exon list size: 361


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.4    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 22819, rend_intergenic: 17929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49041, rend_intergenic: 47679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162188, rend_intergenic: 150322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190827, rend_intergenic: 181389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17445
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-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 - 17056
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-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

-building DP trellis

-building trellis in range 1699 - 17056
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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 5487 - 17056
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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

-building DP trellis

-building trellis in range 5487 - 16085
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 5487 - 15757
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 5487 - 15657
-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