-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_13303030-13514429

-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.49674_t
Valid prediction for GeneMark_model.49656_t
Valid prediction for snap_scaffold_11-snap.2863-T1
Couldn't classify 177406, 177496
Couldn't classify 179133, 179177
Sorry, prediction pasa_asmbl_6034.p1 fails validation.
(CTT)	 CA	177406-177496	GT	AGG
(ATC)	 AG	177790-177959	GT	AGG
(GTG)	 AG	179133-179177	CA	CCC
-recovered pasa_asmbl_6034.p1, internal, 177790, 177959
Valid prediction for snap_scaffold_11-snap.2874-T1
Valid prediction for GlimmerHMM_glimmerT_28775-T1
Valid prediction for snap_scaffold_11-snap.2881-T1
Valid prediction for GeneMark_model.49679_t
Valid prediction for GlimmerHMM_glimmerT_28767-T1
Valid prediction for snap_scaffold_11-snap.2859-T1
Valid prediction for snap_scaffold_11-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_28774-T1
Valid prediction for snap_scaffold_11-snap.2856-T1
Valid prediction for GeneMark_model.49650_t
Couldn't classify 80111, 80112
Sorry, prediction CodingQuarry_transcript_8258-T1 fails validation.
(ATG)	 TG	80111-80112	GT	ATG
(GGA)	 AG	80197-80251	GT	AGG
(TCG)	 AG	80354-80470	GT	CAG
(GTG)	 AG	80555-80722	GT	AGG
(GCT)	 AG	81019-81093	AC	AAA
-recovered CodingQuarry_transcript_8258-T1, terminal, 81019, 81093
-recovered CodingQuarry_transcript_8258-T1, internal, 80197, 80251
-recovered CodingQuarry_transcript_8258-T1, internal, 80354, 80470
-recovered CodingQuarry_transcript_8258-T1, internal, 80555, 80722
Valid prediction for GeneMark_model.49647_t
Valid prediction for GlimmerHMM_glimmerT_28769-T1
Valid prediction for GeneMark_model.49681_t
Valid prediction for GeneMark_model.49665_t
Valid prediction for GeneMark_model.49682_t
Valid prediction for GeneMark_model.49661_t
Valid prediction for GlimmerHMM_glimmerT_28764-T1
Valid prediction for snap_scaffold_11-snap.2869-T1
Valid prediction for snap_scaffold_11-snap.2849-T1
Valid prediction for pasa_asmbl_6029.p1
Valid prediction for snap_scaffold_11-snap.2860-T1
Valid prediction for GeneMark_model.49640_t
Valid prediction for CodingQuarry_transcript_8261-T1
Valid prediction for GeneMark_model.49676_t
Valid prediction for GlimmerHMM_glimmerT_28753-T1
Valid prediction for GeneMark_model.49654_t
Valid prediction for GeneMark_model.49653_t
Valid prediction for GlimmerHMM_glimmerT_28751-T1
Valid prediction for Augustus_model.g19206.t1
Valid prediction for snap_scaffold_11-snap.2865-T1
Valid prediction for snap_scaffold_11-snap.2847-T1
Valid prediction for snap_scaffold_11-snap.2876-T1
Valid prediction for Augustus_model.g19195.t1
Couldn't classify 82972, 83092
Couldn't classify 83238, 83268
Sorry, prediction CodingQuarry_transcript_8259-T1 fails validation.
(ATG)	 GT	81419-81493	GT	TGG
(GTT)	 AG	81571-81639	GT	AGG
(GAG)	 AG	82082-82166	GT	AGG
(ATG)	 AG	82330-82839	GT	AGG
(GGT)	 AG	82972-83092	GA	AGG
(GTT)	 CA	83238-83268	AG	GAA
-recovered CodingQuarry_transcript_8259-T1, initial, 81419, 81493
add_exon() Sorry, CodingQuarry_transcript_8259-T1 82330-82839-initial-1 is invalid.
-recovered CodingQuarry_transcript_8259-T1, initial, 82330, 82839
-recovered CodingQuarry_transcript_8259-T1, internal, 81571, 81639
-recovered CodingQuarry_transcript_8259-T1, internal, 82082, 82166
-recovered CodingQuarry_transcript_8259-T1, internal, 82330, 82839
Valid prediction for snap_scaffold_11-snap.2878-T1
Valid prediction for CodingQuarry_transcript_8256-T1
Valid prediction for GeneMark_model.49668_t
Valid prediction for GeneMark_model.49683_t
Valid prediction for GeneMark_model.49639_t
Valid prediction for GeneMark_model.49672_t
Valid prediction for GlimmerHMM_glimmerT_28771-T1
Valid prediction for Augustus_model.g19198.t1
Valid prediction for snap_scaffold_11-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_28772-T1
Valid prediction for snap_scaffold_11-snap.2880-T1
Valid prediction for HiQ_model.g19199.t1
Valid prediction for GlimmerHMM_glimmerT_28748-T1
Valid prediction for CodingQuarry_transcript_8257-T1
Valid prediction for snap_scaffold_11-snap.2872-T1
Valid prediction for Augustus_model.g19193.t1
Valid prediction for HiQ_model.g19204.t1
Valid prediction for Augustus_model.g19207.t1
Valid prediction for Augustus_model.g19203.t1
Valid prediction for snap_scaffold_11-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_28765-T1
Valid prediction for GlimmerHMM_glimmerT_28766-T1
Valid prediction for snap_scaffold_11-snap.2882-T1
Valid prediction for GeneMark_model.49678_t
Valid prediction for GlimmerHMM_glimmerT_28754-T1
Valid prediction for Augustus_model.g19208.t1
Valid prediction for GlimmerHMM_glimmerT_28759-T1
Valid prediction for GlimmerHMM_glimmerT_28757-T1
Valid prediction for Augustus_model.g19200.t1
Valid prediction for GeneMark_model.49659_t
Valid prediction for CodingQuarry_transcript_8260-T1
Valid prediction for GeneMark_model.49643_t
Valid prediction for pasa_asmbl_6033.p1
Valid prediction for snap_scaffold_11-snap.2844-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 GeneMark_model.49671_t
Valid prediction for snap_scaffold_11-snap.2857-T1
Valid prediction for snap_scaffold_11-snap.2848-T1
Valid prediction for GlimmerHMM_glimmerT_28758-T1
Valid prediction for GeneMark_model.49664_t
Valid prediction for GeneMark_model.49673_t
Valid prediction for GeneMark_model.49667_t
Valid prediction for GlimmerHMM_glimmerT_28773-T1
Valid prediction for GlimmerHMM_glimmerT_28768-T1
Valid prediction for snap_scaffold_11-snap.2851-T1
Valid prediction for snap_scaffold_11-snap.2879-T1
Valid prediction for Augustus_model.g19196.t1
Valid prediction for GeneMark_model.49670_t
Valid prediction for GeneMark_model.49645_t
Valid prediction for GlimmerHMM_glimmerT_28762-T1
Valid prediction for GlimmerHMM_glimmerT_28750-T1
Valid prediction for GeneMark_model.49646_t
Valid prediction for snap_scaffold_11-snap.2852-T1
Valid prediction for GeneMark_model.49657_t
Valid prediction for GlimmerHMM_glimmerT_28749-T1
Valid prediction for GeneMark_model.49641_t
Valid prediction for GlimmerHMM_glimmerT_28770-T1
Valid prediction for snap_scaffold_11-snap.2875-T1
Valid prediction for GeneMark_model.49644_t
Valid prediction for Augustus_model.g19209.t1
Valid prediction for GeneMark_model.49680_t
Valid prediction for GeneMark_model.49652_t
Valid prediction for GlimmerHMM_glimmerT_28756-T1
Valid prediction for snap_scaffold_11-snap.2846-T1
Valid prediction for GeneMark_model.49651_t
Valid prediction for GlimmerHMM_glimmerT_28755-T1
Valid prediction for GeneMark_model.49655_t
Valid prediction for snap_scaffold_11-snap.2845-T1
Valid prediction for GeneMark_model.49675_t
Valid prediction for snap_scaffold_11-snap.2850-T1
Valid prediction for snap_scaffold_11-snap.2862-T1
Valid prediction for GlimmerHMM_glimmerT_28763-T1
Valid prediction for snap_scaffold_11-snap.2871-T1
Valid prediction for Augustus_model.g19202.t1
Valid prediction for snap_scaffold_11-snap.2855-T1
Valid prediction for GeneMark_model.49648_t
Valid prediction for GeneMark_model.49662_t
Valid prediction for pasa_asmbl_7107.p1
Valid prediction for snap_scaffold_11-snap.2870-T1
Valid prediction for snap_scaffold_11-snap.2873-T1
Valid prediction for Augustus_model.g19197.t1
Valid prediction for snap_scaffold_11-snap.2867-T1
Valid prediction for GeneMark_model.49686_t
Valid prediction for GeneMark_model.49642_t
Valid prediction for GeneMark_model.49666_t
Valid prediction for snap_scaffold_11-snap.2864-T1
Valid prediction for GeneMark_model.49649_t
Valid prediction for Augustus_model.g19194.t1
Valid prediction for HiQ_model.g19205.t1
Valid prediction for CodingQuarry_transcript_8262-T1
Valid prediction for GeneMark_model.49677_t
Valid prediction for GeneMark_model.49685_t
Valid prediction for GeneMark_model.49660_t
Valid prediction for GlimmerHMM_glimmerT_28752-T1
Valid prediction for Augustus_model.g19201.t1
Valid prediction for snap_scaffold_11-snap.2854-T1
Valid prediction for snap_scaffold_11-snap.2861-T1
Valid prediction for GlimmerHMM_glimmerT_28761-T1
Valid prediction for GlimmerHMM_glimmerT_28760-T1
Valid prediction for snap_scaffold_11-snap.2866-T1
Valid prediction for GeneMark_model.49669_t
Valid prediction for GeneMark_model.49687_t
Valid prediction for snap_scaffold_11-snap.2858-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22742, rend_intergenic: 17899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27881, rend_intergenic: 23499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31866, rend_intergenic: 28724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57236, rend_intergenic: 51175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71535, rend_intergenic: 68865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97617, rend_intergenic: 86538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101713, rend_intergenic: 99576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105094, rend_intergenic: 104593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107297, rend_intergenic: 105106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112502, rend_intergenic: 108309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116469, rend_intergenic: 115429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130182, rend_intergenic: 123158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136412, rend_intergenic: 130627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146543, rend_intergenic: 136730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211400
-exon list size: 576


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.6    
1.7    
1.9    
2.1    
2.2    
2.4    
2.6    
2.8    
2.9    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.7    
6.9    
7.1    
7.3    
7.4    
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    
9.9    
10.0    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.2    
11.4    
11.6    
11.8    
11.9    
12.1    
12.3    
12.5    
12.6    
12.8    
13.0    
13.1    
13.3    
13.5    
13.7    
13.8    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.1    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.1    
17.3    
17.5    
17.6    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.2    
20.4    
20.6    
20.8    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.7    
22.8    
23.0    
23.2    
23.4    
23.5    
23.7    
23.9    
24.0    
24.2    
24.4    
24.6    
24.7    
24.9    
25.1    
25.3    
25.4    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.2    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.9    
42.0    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.3    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.6    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.1    
47.2    
47.4    
47.6    
47.8    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.2    
52.4    
52.6    
52.8    
52.9    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.4    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.1    
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    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 22742, rend_intergenic: 17899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27881, rend_intergenic: 23499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31866, rend_intergenic: 28724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57236, rend_intergenic: 51175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71535, rend_intergenic: 68865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97617, rend_intergenic: 86538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101713, rend_intergenic: 99576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105094, rend_intergenic: 104593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107297, rend_intergenic: 105106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112502, rend_intergenic: 108309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116469, rend_intergenic: 115429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130182, rend_intergenic: 123158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136412, rend_intergenic: 130627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146543, rend_intergenic: 136730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support