-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_13222989-13379806

-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.61273_t
Valid prediction for snap_scaffold_14-snap.2769-T1
Valid prediction for GeneMark_model.61248_t
Valid prediction for snap_scaffold_14-snap.2755-T1
Valid prediction for snap_scaffold_14-snap.2748-T1
Valid prediction for GeneMark_model.61269_t
Valid prediction for GlimmerHMM_glimmerT_35749-T1
Valid prediction for GlimmerHMM_glimmerT_35735-T1
Valid prediction for snap_scaffold_14-snap.2766-T1
Valid prediction for GeneMark_model.61255_t
Valid prediction for GlimmerHMM_glimmerT_35739-T1
Valid prediction for GlimmerHMM_glimmerT_35734-T1
Valid prediction for snap_scaffold_14-snap.2761-T1
Valid prediction for GeneMark_model.61245_t
Valid prediction for GeneMark_model.61260_t
Valid prediction for GeneMark_model.61231_t
Valid prediction for snap_scaffold_14-snap.2747-T1
Valid prediction for Augustus_model.g24056.t1
Valid prediction for GlimmerHMM_glimmerT_35725-T1
Valid prediction for snap_scaffold_14-snap.2759-T1
Valid prediction for GeneMark_model.61264_t
Valid prediction for snap_scaffold_14-snap.2742-T1
Valid prediction for GeneMark_model.61233_t
Valid prediction for GeneMark_model.61228_t
Valid prediction for GeneMark_model.61250_t
Valid prediction for GeneMark_model.61242_t
Valid prediction for Augustus_model.g24055.t1
Valid prediction for snap_scaffold_14-snap.2743-T1
Valid prediction for GeneMark_model.61239_t
Valid prediction for Augustus_model.g24058.t1
Valid prediction for GeneMark_model.61244_t
Valid prediction for snap_scaffold_14-snap.2757-T1
Couldn't classify 92858, 93015
Sorry, prediction pasa_asmbl_12457.p2 fails validation.
(ATG)	 GC	91418-91694	GT	ACG
(TGC)	 AG	92858-93015	CC	GTC
-recovered pasa_asmbl_12457.p2, initial, 91418, 91694
Valid prediction for GeneMark_model.61258_t
Valid prediction for GlimmerHMM_glimmerT_35741-T1
Valid prediction for GeneMark_model.61272_t
Valid prediction for snap_scaffold_14-snap.2739-T1
Valid prediction for snap_scaffold_14-snap.2751-T1
Valid prediction for snap_scaffold_14-snap.2754-T1
Valid prediction for snap_scaffold_14-snap.2750-T1
Valid prediction for Augustus_model.g24051.t1
Valid prediction for GeneMark_model.61270_t
Valid prediction for GlimmerHMM_glimmerT_35742-T1
Valid prediction for GeneMark_model.61237_t
Valid prediction for GlimmerHMM_glimmerT_35729-T1
Valid prediction for snap_scaffold_14-snap.2752-T1
Valid prediction for GeneMark_model.61247_t
Valid prediction for GeneMark_model.61235_t
Valid prediction for Augustus_model.g24060.t1
Valid prediction for GeneMark_model.61240_t
Valid prediction for GlimmerHMM_glimmerT_35732-T1
Valid prediction for snap_scaffold_14-snap.2763-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2762-T1
Valid prediction for GeneMark_model.61262_t
Valid prediction for Augustus_model.g24061.t1
Couldn't classify 58821, 59016
Sorry, prediction pasa_asmbl_12454.p1 fails validation.
(ATG)	 AA	57834-57934	GC	AGG
(CGG)	 AG	58821-59016	GC	GGG
-recovered pasa_asmbl_12454.p1, initial, 57834, 57934
-recovered pasa_asmbl_12454.p1, internal, 58821, 59016
Valid prediction for GeneMark_model.61275_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 GeneMark_model.61265_t
Valid prediction for GlimmerHMM_glimmerT_35726-T1
Valid prediction for Augustus_model.g24062.t1
Valid prediction for Augustus_model.g24057.t1
Valid prediction for Augustus_model.g24059.t1
Valid prediction for Augustus_model.g24052.t1
Valid prediction for GeneMark_model.61271_t
Valid prediction for Augustus_model.g24054.t1
Valid prediction for GeneMark_model.61253_t
Valid prediction for snap_scaffold_14-snap.2767-T1
Valid prediction for CodingQuarry_transcript_15851-T1
Valid prediction for snap_scaffold_14-snap.2764-T1
Valid prediction for GeneMark_model.61274_t
Valid prediction for GlimmerHMM_glimmerT_35744-T1
Valid prediction for GeneMark_model.61229_t
Valid prediction for GlimmerHMM_glimmerT_35748-T1
Valid prediction for snap_scaffold_14-snap.2768-T1
Valid prediction for GlimmerHMM_glimmerT_35737-T1
Valid prediction for GeneMark_model.61251_t
Valid prediction for GeneMark_model.61241_t
Valid prediction for Augustus_model.g24066.t1
Valid prediction for Augustus_model.g24067.t1
Valid prediction for CodingQuarry_transcript_15852-T1
Valid prediction for GeneMark_model.61254_t
Valid prediction for GeneMark_model.61243_t
Valid prediction for GlimmerHMM_glimmerT_35736-T1
Valid prediction for snap_scaffold_14-snap.2745-T1
Valid prediction for snap_scaffold_14-snap.2736-T1
Valid prediction for GeneMark_model.61230_t
Valid prediction for GeneMark_model.61236_t
Valid prediction for Augustus_model.g24064.t1
Valid prediction for HiQ_model.g24063.t1
Valid prediction for snap_scaffold_14-snap.2753-T1
Valid prediction for GlimmerHMM_glimmerT_35740-T1
Valid prediction for snap_scaffold_14-snap.2744-T1
Valid prediction for snap_scaffold_14-snap.2737-T1
Valid prediction for snap_scaffold_14-snap.2740-T1
Valid prediction for Augustus_model.g24053.t1
Valid prediction for snap_scaffold_14-snap.2765-T1
Valid prediction for GeneMark_model.61249_t
Valid prediction for GeneMark_model.61256_t
Valid prediction for GeneMark_model.61268_t
Valid prediction for GlimmerHMM_glimmerT_35746-T1
Valid prediction for GlimmerHMM_glimmerT_35728-T1
Valid prediction for GeneMark_model.61252_t
Valid prediction for GeneMark_model.61257_t
Valid prediction for GeneMark_model.61246_t
Valid prediction for GlimmerHMM_glimmerT_35724-T1
Couldn't classify 36855, 37183
Sorry, prediction pasa_asmbl_13619.p1 fails validation.
(ACA)	 TC	36855-37183	GT	AGG
(CAA)	 AG	37446-37764	AA	AAA
-recovered pasa_asmbl_13619.p1, terminal, 37446, 37764
Valid prediction for GlimmerHMM_glimmerT_35743-T1
Valid prediction for snap_scaffold_14-snap.2760-T1
Valid prediction for snap_scaffold_14-snap.2758-T1
Valid prediction for Augustus_model.g24065.t1
Valid prediction for GlimmerHMM_glimmerT_35750-T1
Valid prediction for GlimmerHMM_glimmerT_35747-T1
Valid prediction for GeneMark_model.61232_t
Valid prediction for pasa_asmbl_13616.p1
Valid prediction for GeneMark_model.61238_t
Valid prediction for GlimmerHMM_glimmerT_35751-T1
Valid prediction for snap_scaffold_14-snap.2746-T1
Valid prediction for Augustus_model.g24050.t1
Valid prediction for snap_scaffold_14-snap.2741-T1
Valid prediction for GlimmerHMM_glimmerT_35731-T1
Valid prediction for GeneMark_model.61234_t
Valid prediction for GlimmerHMM_glimmerT_35730-T1
Valid prediction for snap_scaffold_14-snap.2772-T1
Valid prediction for GeneMark_model.61266_t
Valid prediction for GlimmerHMM_glimmerT_35733-T1
Valid prediction for snap_scaffold_14-snap.2756-T1
Valid prediction for snap_scaffold_14-snap.2770-T1
Valid prediction for GeneMark_model.61263_t
Valid prediction for snap_scaffold_14-snap.2738-T1
Valid prediction for Augustus_model.g24049.t1
Valid prediction for GlimmerHMM_glimmerT_35745-T1
Valid prediction for snap_scaffold_14-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_35738-T1
Valid prediction for snap_scaffold_14-snap.2771-T1
Valid prediction for GeneMark_model.61276_t
Couldn't classify 38235, 38365
Sorry, prediction pasa_asmbl_13618.p1 fails validation.
(CTT)	 CT	38235-38365	GT	AGG
(GCC)	 AG	38464-38566	GT	AGG
(ACT)	 AG	38680-38748	GT	AGG
(GTC)	 AG	38952-39093	GT	AGG
(AGC)	 AG	39334-39470	GT	AGG
(TAT)	 AG	39617-39738	GT	AGG
(GAT)	 AG	39899-40003	GT	AGG
(CGA)	 AG	40098-40186	GT	CGG
(CCT)	 AG	40317-40408	GT	AGG
(GTT)	 AG	40652-40768	GT	CTG
(GTG)	 AG	40968-41039	GT	AGG
(GTT)	 AG	41139-41312	GT	AGG
(GGT)	 AG	41440-41531	GT	AGG
(ACC)	 AG	41737-41836	GT	CAG
(GTA)	 AG	41938-42002	GT	CAG
(GAT)	 AG	42258-42373	GT	AGG
(ATG)	 AG	43232-43350	CC	GAC
-recovered pasa_asmbl_13618.p1, terminal, 39899, 40003
-recovered pasa_asmbl_13618.p1, terminal, 43232, 43350
-recovered pasa_asmbl_13618.p1, internal, 38464, 38566
-recovered pasa_asmbl_13618.p1, internal, 38680, 38748
-recovered pasa_asmbl_13618.p1, internal, 38952, 39093
-recovered pasa_asmbl_13618.p1, internal, 39334, 39470
-recovered pasa_asmbl_13618.p1, internal, 39617, 39738
-recovered pasa_asmbl_13618.p1, internal, 39899, 40003
-recovered pasa_asmbl_13618.p1, internal, 40098, 40186
-recovered pasa_asmbl_13618.p1, internal, 40317, 40408
-recovered pasa_asmbl_13618.p1, internal, 40652, 40768
-recovered pasa_asmbl_13618.p1, internal, 40968, 41039
-recovered pasa_asmbl_13618.p1, internal, 41139, 41312
-recovered pasa_asmbl_13618.p1, internal, 41440, 41531
-recovered pasa_asmbl_13618.p1, internal, 41737, 41836
-recovered pasa_asmbl_13618.p1, internal, 41938, 42002
-recovered pasa_asmbl_13618.p1, internal, 42258, 42373
Valid prediction for GeneMark_model.61261_t
Valid prediction for GeneMark_model.61259_t
Valid prediction for GlimmerHMM_glimmerT_35727-T1
Valid prediction for GeneMark_model.61267_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5703, rend_intergenic: 5050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6894, rend_intergenic: 6633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17614, rend_intergenic: 16444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29484, rend_intergenic: 18456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66712, rend_intergenic: 66214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70317, rend_intergenic: 67434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81848, rend_intergenic: 79361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92990, rend_intergenic: 86738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98347, rend_intergenic: 96229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111493, rend_intergenic: 104826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117871, rend_intergenic: 114813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129175, rend_intergenic: 125592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137221, rend_intergenic: 129615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156818
-exon list size: 683


building trellis

0.1    
0.3    
0.4    
0.6    
0.7    
0.9    
1.0    
1.2    
1.3    
1.5    
1.6    
1.8    
1.9    
2.0    
2.2    
2.3    
2.5    
2.6    
2.8    
2.9    
3.1    
3.2    
3.4    
3.5    
3.6    
3.8    
3.9    
4.1    
4.2    
4.4    
4.5    
4.7    
4.8    
5.0    
5.1    
5.3    
5.4    
5.5    
5.7    
5.8    
6.0    
6.1    
6.3    
6.4    
6.6    
6.7    
6.9    
7.0    
7.2    
7.3    
7.4    
7.6    
7.7    
7.9    
8.0    
8.2    
8.3    
8.5    
8.6    
8.8    
8.9    
9.1    
9.2    
9.3    
9.5    
9.6    
9.8    
9.9    
10.1    
10.2    
10.4    
10.5    
10.7    
10.8    
10.9    
11.1    
11.2    
11.4    
11.5    
11.7    
11.8    
12.0    
12.1    
12.3    
12.4    
12.6    
12.7    
12.8    
13.0    
13.1    
13.3    
13.4    
13.6    
13.7    
13.9    
14.0    
14.2    
14.3    
14.5    
14.6    
14.7    
14.9    
15.0    
15.2    
15.3    
15.5    
15.6    
15.8    
15.9    
16.1    
16.2    
16.4    
16.5    
16.6    
16.8    
16.9    
17.1    
17.2    
17.4    
17.5    
17.7    
17.8    
18.0    
18.1    
18.2    
18.4    
18.5    
18.7    
18.8    
19.0    
19.1    
19.3    
19.4    
19.6    
19.7    
19.9    
20.0    
20.1    
20.3    
20.4    
20.6    
20.7    
20.9    
21.0    
21.2    
21.3    
21.5    
21.6    
21.8    
21.9    
22.0    
22.2    
22.3    
22.5    
22.6    
22.8    
22.9    
23.1    
23.2    
23.4    
23.5    
23.6    
23.8    
23.9    
24.1    
24.2    
24.4    
24.5    
24.7    
24.8    
25.0    
25.1    
25.3    
25.4    
25.5    
25.7    
25.8    
26.0    
26.1    
26.3    
26.4    
26.6    
26.7    
26.9    
27.0    
27.2    
27.3    
27.4    
27.6    
27.7    
27.9    
28.0    
28.2    
28.3    
28.5    
28.6    
28.8    
28.9    
29.1    
29.2    
29.3    
29.5    
29.6    
29.8    
29.9    
30.1    
30.2    
30.4    
30.5    
30.7    
30.8    
30.9    
31.1    
31.2    
31.4    
31.5    
31.7    
31.8    
32.0    
32.1    
32.3    
32.4    
32.6    
32.7    
32.8    
33.0    
33.1    
33.3    
33.4    
33.6    
33.7    
33.9    
34.0    
34.2    
34.3    
34.5    
34.6    
34.7    
34.9    
35.0    
35.2    
35.3    
35.5    
35.6    
35.8    
35.9    
36.1    
36.2    
36.4    
36.5    
36.6    
36.8    
36.9    
37.1    
37.2    
37.4    
37.5    
37.7    
37.8    
38.0    
38.1    
38.2    
38.4    
38.5    
38.7    
38.8    
39.0    
39.1    
39.3    
39.4    
39.6    
39.7    
39.9    
40.0    
40.1    
40.3    
40.4    
40.6    
40.7    
40.9    
41.0    
41.2    
41.3    
41.5    
41.6    
41.8    
41.9    
42.0    
42.2    
42.3    
42.5    
42.6    
42.8    
42.9    
43.1    
43.2    
43.4    
43.5    
43.6    
43.8    
43.9    
44.1    
44.2    
44.4    
44.5    
44.7    
44.8    
45.0    
45.1    
45.3    
45.4    
45.5    
45.7    
45.8    
46.0    
46.1    
46.3    
46.4    
46.6    
46.7    
46.9    
47.0    
47.2    
47.3    
47.4    
47.6    
47.7    
47.9    
48.0    
48.2    
48.3    
48.5    
48.6    
48.8    
48.9    
49.1    
49.2    
49.3    
49.5    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.5    
50.7    
50.8    
50.9    
51.1    
51.2    
51.4    
51.5    
51.7    
51.8    
52.0    
52.1    
52.3    
52.4    
52.6    
52.7    
52.8    
53.0    
53.1    
53.3    
53.4    
53.6    
53.7    
53.9    
54.0    
54.2    
54.3    
54.5    
54.6    
54.7    
54.9    
55.0    
55.2    
55.3    
55.5    
55.6    
55.8    
55.9    
56.1    
56.2    
56.4    
56.5    
56.6    
56.8    
56.9    
57.1    
57.2    
57.4    
57.5    
57.7    
57.8    
58.0    
58.1    
58.2    
58.4    
58.5    
58.7    
58.8    
59.0    
59.1    
59.3    
59.4    
59.6    
59.7    
59.9    
60.0    
60.1    
60.3    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.0    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 5703, rend_intergenic: 5050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6894, rend_intergenic: 6633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17614, rend_intergenic: 16444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29484, rend_intergenic: 18456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66712, rend_intergenic: 66214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70317, rend_intergenic: 67434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81848, rend_intergenic: 79361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92990, rend_intergenic: 86738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98347, rend_intergenic: 96229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111493, rend_intergenic: 104826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117871, rend_intergenic: 114813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129175, rend_intergenic: 125592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137221, rend_intergenic: 129615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support