-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_15218303-15366859

-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 snap_scaffold_10-snap.3104-T1
Valid prediction for snap_scaffold_10-snap.3090-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.45589_t
Valid prediction for snap_scaffold_10-snap.3093-T1
Valid prediction for snap_scaffold_10-snap.3099-T1
Couldn't classify 91014, 91511
Sorry, prediction pasa_asmbl_4952.p1 fails validation.
(ACA)	 CC	91014-91511	AA	GAA
Valid prediction for GeneMark_model.45579_t
Valid prediction for GeneMark_model.45601_t
Valid prediction for GeneMark_model.45577_t
Valid prediction for snap_scaffold_10-snap.3077-T1
Valid prediction for GlimmerHMM_glimmerT_26506-T1
Valid prediction for GeneMark_model.45591_t
Valid prediction for GeneMark_model.45583_t
Valid prediction for GeneMark_model.45608_t
Valid prediction for GeneMark_model.45581_t
Valid prediction for snap_scaffold_10-snap.3103-T1
Valid prediction for GlimmerHMM_glimmerT_26508-T1
Valid prediction for Augustus_model.g17766.t1
Valid prediction for GeneMark_model.45573_t
Valid prediction for GeneMark_model.45576_t
Valid prediction for GlimmerHMM_glimmerT_26514-T1
Valid prediction for snap_scaffold_10-snap.3088-T1
Valid prediction for GlimmerHMM_glimmerT_26502-T1
Valid prediction for GeneMark_model.45571_t
Valid prediction for snap_scaffold_10-snap.3078-T1
Valid prediction for Augustus_model.g17776.t1
Valid prediction for GeneMark_model.45567_t
Valid prediction for GeneMark_model.45610_t
Valid prediction for GeneMark_model.45603_t
Valid prediction for GeneMark_model.45605_t
Valid prediction for Augustus_model.g17778.t1
Valid prediction for GeneMark_model.45585_t
Valid prediction for GeneMark_model.45587_t
Valid prediction for snap_scaffold_10-snap.3082-T1
Valid prediction for GeneMark_model.45598_t
Valid prediction for Augustus_model.g17769.t1
Valid prediction for snap_scaffold_10-snap.3073-T1
Valid prediction for GeneMark_model.45593_t
Valid prediction for GeneMark_model.45604_t
Valid prediction for GeneMark_model.45569_t
Valid prediction for GeneMark_model.45574_t
Valid prediction for snap_scaffold_10-snap.3080-T1
Valid prediction for GeneMark_model.45595_t
Valid prediction for GlimmerHMM_glimmerT_26504-T1
Valid prediction for GlimmerHMM_glimmerT_26503-T1
Valid prediction for snap_scaffold_10-snap.3097-T1
Valid prediction for snap_scaffold_10-snap.3105-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 CodingQuarry_transcript_5644-T1
Valid prediction for GeneMark_model.45588_t
Couldn't classify 63536, 63787
Sorry, prediction pasa_asmbl_3880.p2 fails validation.
(ATG)	 AC	63021-63128	GT	CGG
(TCT)	 AG	63536-63787	GA	CCG
-recovered pasa_asmbl_3880.p2, initial, 63021, 63128
Valid prediction for GeneMark_model.45600_t
Valid prediction for CodingQuarry_transcript_5643-T1
Valid prediction for snap_scaffold_10-snap.3095-T1
Valid prediction for GeneMark_model.45582_t
Valid prediction for GlimmerHMM_glimmerT_26511-T1
Valid prediction for GeneMark_model.45606_t
Valid prediction for snap_scaffold_10-snap.3087-T1
Valid prediction for Augustus_model.g17775.t1
Valid prediction for GeneMark_model.45568_t
Valid prediction for snap_scaffold_10-snap.3102-T1
Valid prediction for GeneMark_model.45586_t
Valid prediction for snap_scaffold_10-snap.3074-T1
Valid prediction for snap_scaffold_10-snap.3085-T1
Valid prediction for GeneMark_model.45607_t
Couldn't classify 60350, 60467
Couldn't classify 62388, 62535
Sorry, prediction pasa_asmbl_3881.p1 fails validation.
(TAC)	 AG	60350-60467	GT	GGG
(GCG)	 AG	61333-61483	GT	AAG
(CAT)	 AG	62388-62535	AA	AGA
-recovered pasa_asmbl_3881.p1, internal, 60350, 60467
-recovered pasa_asmbl_3881.p1, internal, 61333, 61483
Valid prediction for GeneMark_model.45575_t
Valid prediction for pasa_asmbl_3878.p1
Valid prediction for snap_scaffold_10-snap.3086-T1
Valid prediction for snap_scaffold_10-snap.3083-T1
Valid prediction for GeneMark_model.45612_t
Valid prediction for GeneMark_model.45594_t
Valid prediction for GlimmerHMM_glimmerT_26501-T1
Valid prediction for snap_scaffold_10-snap.3092-T1
Valid prediction for snap_scaffold_10-snap.3096-T1
Valid prediction for snap_scaffold_10-snap.3079-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g17777.t1
Valid prediction for snap_scaffold_10-snap.3075-T1
Valid prediction for Augustus_model.g17779.t1
Valid prediction for Augustus_model.g17772.t1
Valid prediction for GlimmerHMM_glimmerT_26517-T1
Couldn't classify 64186, 64260
Sorry, prediction pasa_asmbl_3879.p1 fails validation.
(ACT)	 TC	64186-64260	GT	GGG
(ATG)	 AG	64551-64685	GT	AAG
(GCA)	 AG	65506-65721	TT	AGT
-recovered pasa_asmbl_3879.p1, initial, 64551, 64685
-recovered pasa_asmbl_3879.p1, terminal, 65506, 65721
-recovered pasa_asmbl_3879.p1, internal, 64551, 64685
Valid prediction for GeneMark_model.45570_t
Valid prediction for GlimmerHMM_glimmerT_26512-T1
Valid prediction for GlimmerHMM_glimmerT_26513-T1
Valid prediction for pasa_asmbl_4003.p1
Valid prediction for GlimmerHMM_glimmerT_26516-T1
Valid prediction for GlimmerHMM_glimmerT_26515-T1
Valid prediction for snap_scaffold_10-snap.3084-T1
Valid prediction for GeneMark_model.45572_t
Valid prediction for Augustus_model.g17780.t1
Valid prediction for snap_scaffold_10-snap.3081-T1
Valid prediction for Augustus_model.g17768.t1
Valid prediction for GeneMark_model.45578_t
Couldn't classify 141404, 141535
Couldn't classify 141947, 142102
Sorry, prediction pasa_asmbl_3995.p1 fails validation.
(GAG)	 GG	141404-141535	GT	AGG
(GGG)	 AG	141768-141845	GT	TGG
(AGT)	 AG	141947-142102	AC	AGA
-recovered pasa_asmbl_3995.p1, internal, 141768, 141845
Valid prediction for Augustus_model.g17773.t1
Valid prediction for GlimmerHMM_glimmerT_26518-T1
Valid prediction for Augustus_model.g17782.t1
Valid prediction for GeneMark_model.45596_t
Valid prediction for GlimmerHMM_glimmerT_26510-T1
Valid prediction for GlimmerHMM_glimmerT_26521-T1
Valid prediction for snap_scaffold_10-snap.3089-T1
Valid prediction for GlimmerHMM_glimmerT_26507-T1
Valid prediction for Augustus_model.g17767.t1
Valid prediction for GlimmerHMM_glimmerT_26509-T1
Valid prediction for snap_scaffold_10-snap.3106-T1
Valid prediction for GeneMark_model.45602_t
Valid prediction for snap_scaffold_10-snap.3094-T1
Valid prediction for snap_scaffold_10-snap.3100-T1
Valid prediction for snap_scaffold_10-snap.3107-T1
Valid prediction for GeneMark_model.45592_t
Valid prediction for GeneMark_model.45580_t
Valid prediction for snap_scaffold_10-snap.3076-T1
Valid prediction for GeneMark_model.45597_t
Valid prediction for snap_scaffold_10-snap.3091-T1
Valid prediction for GeneMark_model.45584_t
Valid prediction for Augustus_model.g17770.t1
Valid prediction for GeneMark_model.45609_t
Valid prediction for GlimmerHMM_glimmerT_26519-T1
Valid prediction for snap_scaffold_10-snap.3101-T1
Valid prediction for snap_scaffold_10-snap.3098-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g17771.t1
Valid prediction for HiQ_model.g17774.t1
Valid prediction for Augustus_model.g17781.t1
Valid prediction for snap_scaffold_10-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_26520-T1
Valid prediction for GeneMark_model.45590_t
Valid prediction for GlimmerHMM_glimmerT_26505-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 23437, rend_intergenic: 23434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30343, rend_intergenic: 27027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33896, rend_intergenic: 31229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38319, rend_intergenic: 34439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38624, rend_intergenic: 38472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43760, rend_intergenic: 39580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49762, rend_intergenic: 46016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71670, rend_intergenic: 68142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79590, rend_intergenic: 71730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110618, rend_intergenic: 108341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116361, rend_intergenic: 112691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136450, rend_intergenic: 133065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148557
-exon list size: 569


building trellis

0.2    
0.4    
0.5    
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0.9    
1.1    
1.2    
1.4    
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2.1    
2.3    
2.5    
2.6    
2.8    
3.0    
3.2    
3.3    
3.5    
3.7    
3.9    
4.0    
4.2    
4.4    
4.6    
4.7    
4.9    
5.1    
5.3    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.7    
6.8    
7.0    
7.2    
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7.5    
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7.9    
8.1    
8.2    
8.4    
8.6    
8.8    
8.9    
9.1    
9.3    
9.5    
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9.8    
10.0    
10.2    
10.3    
10.5    
10.7    
10.9    
11.0    
11.2    
11.4    
11.6    
11.7    
11.9    
12.1    
12.3    
12.4    
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    
15.8    
15.9    
16.1    
16.3    
16.5    
16.6    
16.8    
17.0    
17.2    
17.3    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.6    
18.7    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.4    
21.5    
21.7    
21.9    
22.1    
22.2    
22.4    
22.6    
22.8    
22.9    
23.1    
23.3    
23.5    
23.6    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.7    
25.9    
26.1    
26.3    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.8    
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    
30.5    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.1    
37.3    
37.5    
37.7    
37.8    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.8    
39.9    
40.1    
40.3    
40.5    
40.6    
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    
44.0    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.4    
45.5    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.2    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.9    
56.0    
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    
59.4    
59.5    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.9    
63.0    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.5    
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    
72.2    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.2    
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    
87.6    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 23437, rend_intergenic: 23434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30343, rend_intergenic: 27027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33896, rend_intergenic: 31229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38319, rend_intergenic: 34439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38624, rend_intergenic: 38472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43760, rend_intergenic: 39580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49762, rend_intergenic: 46016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71670, rend_intergenic: 68142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79590, rend_intergenic: 71730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110618, rend_intergenic: 108341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116361, rend_intergenic: 112691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136450, rend_intergenic: 133065  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