-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_10650773-10853797

-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 pasa_asmbl_12327.p1
Valid prediction for GeneMark_model.60655_t
Valid prediction for snap_scaffold_14-snap.2233-T1
Valid prediction for CodingQuarry_transcript_15773-T1
Valid prediction for GlimmerHMM_glimmerT_35358-T1
Valid prediction for GeneMark_model.60678_t
Valid prediction for snap_scaffold_14-snap.2232-T1
Valid prediction for Augustus_model.g23778.t1
Valid prediction for Augustus_model.g23779.t1
Valid prediction for GeneMark_model.60651_t
Valid prediction for GlimmerHMM_glimmerT_35366-T1
Valid prediction for snap_scaffold_14-snap.2208-T1
Valid prediction for snap_scaffold_14-snap.2207-T1
Valid prediction for snap_scaffold_14-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_35355-T1
Valid prediction for GlimmerHMM_glimmerT_35365-T1
Valid prediction for GlimmerHMM_glimmerT_35344-T1
Valid prediction for GlimmerHMM_glimmerT_35342-T1
Valid prediction for GeneMark_model.60659_t
Valid prediction for snap_scaffold_14-snap.2230-T1
Valid prediction for GeneMark_model.60668_t
Valid prediction for snap_scaffold_14-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_35360-T1
Valid prediction for GeneMark_model.60666_t
Valid prediction for snap_scaffold_14-snap.2229-T1
Valid prediction for GlimmerHMM_glimmerT_35359-T1
Valid prediction for GeneMark_model.60664_t
Valid prediction for GeneMark_model.60671_t
Valid prediction for GlimmerHMM_glimmerT_35362-T1
Valid prediction for GlimmerHMM_glimmerT_35341-T1
Valid prediction for Augustus_model.g23776.t1
Valid prediction for Augustus_model.g23770.t1
Valid prediction for GeneMark_model.60676_t
Valid prediction for HiQ_model.g23772.t1
Valid prediction for snap_scaffold_14-snap.2237-T1
Valid prediction for snap_scaffold_14-snap.2211-T1
Valid prediction for snap_scaffold_14-snap.2204-T1
Valid prediction for GeneMark_model.60669_t
Valid prediction for GlimmerHMM_glimmerT_35345-T1
Valid prediction for snap_scaffold_14-snap.2235-T1
Valid prediction for GeneMark_model.60650_t
Valid prediction for snap_scaffold_14-snap.2210-T1
Valid prediction for GeneMark_model.60680_t
Valid prediction for GeneMark_model.60662_t
Valid prediction for snap_scaffold_14-snap.2222-T1
Couldn't classify 158996, 159083
Couldn't classify 159431, 159571
Sorry, prediction pasa_asmbl_12727.p1 fails validation.
(CTG)	 GG	158996-159083	GT	TGG
(AGA)	 AG	159204-159295	GT	AGG
(CCT)	 AG	159431-159571	GT	AGG
-recovered pasa_asmbl_12727.p1, internal, 159204, 159295
-recovered pasa_asmbl_12727.p1, internal, 159431, 159571
Couldn't classify 123834, 123907
Couldn't classify 124334, 124380
Sorry, prediction pasa_asmbl_12677.p1 fails validation.
(TTC)	 AG	123834-123907	GT	AGG
(CTG)	 AG	124017-124240	GT	AGG
(CCT)	 AG	124334-124380	CT	GCC
-recovered pasa_asmbl_12677.p1, internal, 123834, 123907
-recovered pasa_asmbl_12677.p1, internal, 124017, 124240
Couldn't classify 41617, 41755
Sorry, prediction pasa_asmbl_12323.p1 fails validation.
(CCA)	 CG	41617-41755	GT	ACG
(AAC)	 AG	42438-42551	GT	GGG
(ATT)	 AG	42932-43032	GT	GGG
(GTC)	 AG	43419-43472	AC	GAA
-recovered pasa_asmbl_12323.p1, terminal, 43419, 43472
-recovered pasa_asmbl_12323.p1, internal, 42438, 42551
-recovered pasa_asmbl_12323.p1, internal, 42932, 43032
Couldn't classify 160173, 160316
Sorry, prediction pasa_asmbl_12330.p1 fails validation.
(GCT)	 AA	160173-160316	GT	AGG
(GAG)	 AG	160574-160660	GC	AGG
(GCT)	 AG	160682-160784	GT	AGG
(CCT)	 AG	161024-161179	GT	AAG
(GTG)	 AG	161495-161663	GT	ATG
(GAC)	 AG	161824-161873	GT	CTG
(CTC)	 AG	161969-162121	GT	AGG
(ATG)	 AG	162522-162742	GT	AGG
(AAA)	 AG	162907-163047	AA	AGA
add_exon() Sorry, pasa_asmbl_12330.p1 162522-162742-initial-1 is invalid.
-recovered pasa_asmbl_12330.p1, initial, 162522, 162742
-recovered pasa_asmbl_12330.p1, terminal, 162907, 163047
-recovered pasa_asmbl_12330.p1, internal, 160574, 160660
-recovered pasa_asmbl_12330.p1, internal, 160682, 160784
-recovered pasa_asmbl_12330.p1, internal, 161024, 161179
-recovered pasa_asmbl_12330.p1, internal, 161495, 161663
-recovered pasa_asmbl_12330.p1, internal, 161824, 161873
-recovered pasa_asmbl_12330.p1, internal, 161969, 162121
-recovered pasa_asmbl_12330.p1, internal, 162522, 162742
Valid prediction for snap_scaffold_14-snap.2213-T1
Valid prediction for pasa_asmbl_12318.p1
Valid prediction for snap_scaffold_14-snap.2238-T1
Valid prediction for snap_scaffold_14-snap.2220-T1
Valid prediction for snap_scaffold_14-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_35364-T1
Valid prediction for GeneMark_model.60652_t
Valid prediction for snap_scaffold_14-snap.2228-T1
Valid prediction for GeneMark_model.60654_t
Valid prediction for Augustus_model.g23773.t1
Valid prediction for Augustus_model.g23783.t1
Valid prediction for Augustus_model.g23784.t1
Valid prediction for CodingQuarry_transcript_15772-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_14-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_35354-T1
Valid prediction for snap_scaffold_14-snap.2225-T1
Valid prediction for GlimmerHMM_glimmerT_35361-T1
Valid prediction for GeneMark_model.60658_t
Valid prediction for HiQ_model.g23771.t1
Valid prediction for GlimmerHMM_glimmerT_35349-T1
Valid prediction for GeneMark_model.60665_t
Valid prediction for Augustus_model.g23768.t1
Valid prediction for snap_scaffold_14-snap.2224-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2209-T1
Valid prediction for GlimmerHMM_glimmerT_35353-T1
Valid prediction for CodingQuarry_transcript_15770-T1
Valid prediction for GlimmerHMM_glimmerT_35340-T1
Valid prediction for GlimmerHMM_glimmerT_35348-T1
Valid prediction for snap_scaffold_14-snap.2218-T1
Valid prediction for GlimmerHMM_glimmerT_35339-T1
Valid prediction for Augustus_model.g23769.t1
Valid prediction for GlimmerHMM_glimmerT_35357-T1
Valid prediction for GeneMark_model.60672_t
Valid prediction for snap_scaffold_14-snap.2226-T1
Couldn't classify 139587, 140020
Sorry, prediction pasa_asmbl_13422.p1 fails validation.
(ACC)	 TC	139587-140020	GT	AGG
(GAA)	 AG	140947-141487	CA	GAC
-recovered pasa_asmbl_13422.p1, terminal, 140947, 141487
Valid prediction for GeneMark_model.60670_t
Valid prediction for Augustus_model.g23777.t1
Valid prediction for GeneMark_model.60674_t
Valid prediction for snap_scaffold_14-snap.2216-T1
Valid prediction for snap_scaffold_14-snap.2223-T1
Valid prediction for Augustus_model.g23781.t1
Valid prediction for snap_scaffold_14-snap.2206-T1
Valid prediction for pasa_asmbl_13420.p1
Valid prediction for GeneMark_model.60661_t
Valid prediction for snap_scaffold_14-snap.2215-T1
Valid prediction for snap_scaffold_14-snap.2214-T1
Valid prediction for Augustus_model.g23774.t1
Valid prediction for GeneMark_model.60663_t
Valid prediction for GeneMark_model.60648_t
Valid prediction for snap_scaffold_14-snap.2205-T1
Valid prediction for GeneMark_model.60677_t
Valid prediction for Augustus_model.g23782.t1
Valid prediction for snap_scaffold_14-snap.2236-T1
Valid prediction for GlimmerHMM_glimmerT_35352-T1
Valid prediction for GeneMark_model.60673_t
Valid prediction for GeneMark_model.60667_t
Valid prediction for GlimmerHMM_glimmerT_35347-T1
Valid prediction for GlimmerHMM_glimmerT_35350-T1
Valid prediction for GeneMark_model.60649_t
Valid prediction for GeneMark_model.60653_t
Valid prediction for snap_scaffold_14-snap.2234-T1
Valid prediction for HiQ_model.g23775.t1
Valid prediction for GlimmerHMM_glimmerT_35343-T1
Valid prediction for GlimmerHMM_glimmerT_35363-T1
Valid prediction for snap_scaffold_14-snap.2212-T1
Valid prediction for GlimmerHMM_glimmerT_35346-T1
Valid prediction for snap_scaffold_14-snap.2231-T1
Valid prediction for Augustus_model.g23780.t1
Valid prediction for CodingQuarry_transcript_15771-T1
Valid prediction for GeneMark_model.60656_t
Valid prediction for GeneMark_model.60657_t
Valid prediction for GeneMark_model.60660_t
Valid prediction for GeneMark_model.60679_t
Valid prediction for GlimmerHMM_glimmerT_35356-T1
Valid prediction for GlimmerHMM_glimmerT_35351-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6602, rend_intergenic: 2529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53188, rend_intergenic: 50275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54096, rend_intergenic: 53364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177935, rend_intergenic: 173599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181632, rend_intergenic: 181472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203025
-exon list size: 587


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.0    
2.2    
2.4    
2.5    
2.7    
2.9    
3.1    
3.2    
3.4    
3.6    
3.7    
3.9    
4.1    
4.2    
4.4    
4.6    
4.8    
4.9    
5.1    
5.3    
5.4    
5.6    
5.8    
5.9    
6.1    
6.3    
6.5    
6.6    
6.8    
7.0    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.1    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.7    
12.9    
13.1    
13.2    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.4    
14.6    
14.8    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
16.0    
16.1    
16.3    
16.5    
16.6    
16.8    
17.0    
17.1    
17.3    
17.5    
17.7    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.8    
19.0    
19.2    
19.4    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.5    
20.7    
20.9    
21.1    
21.2    
21.4    
21.6    
21.7    
21.9    
22.1    
22.2    
22.4    
22.6    
22.8    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.3    
32.4    
32.6    
32.8    
32.9    
33.1    
33.3    
33.4    
33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.6    
43.8    
44.0    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.9    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 6602, rend_intergenic: 2529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53188, rend_intergenic: 50275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54096, rend_intergenic: 53364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177935, rend_intergenic: 173599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181632, rend_intergenic: 181472  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

-building DP trellis

-building trellis in range 189269 - 203025
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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 190671 - 203025
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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 191416 - 203025
-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

-building DP trellis

-building trellis in range 191470 - 203025
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 191470 - 202519
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 191679 - 202519
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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