-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_18056240-18301141

-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_2-snap.3536-T1
Valid prediction for snap_scaffold_2-snap.3533-T1
Valid prediction for Augustus_model.g3706.t1
Valid prediction for snap_scaffold_2-snap.3530-T1
Valid prediction for snap_scaffold_2-snap.3541-T1
Valid prediction for snap_scaffold_2-snap.3509-T1
Valid prediction for snap_scaffold_2-snap.3539-T1
Valid prediction for snap_scaffold_2-snap.3531-T1
Valid prediction for snap_scaffold_2-snap.3516-T1
Valid prediction for snap_scaffold_2-snap.3543-T1
Valid prediction for snap_scaffold_2-snap.3538-T1
Valid prediction for GlimmerHMM_glimmerT_5507-T1
Valid prediction for GlimmerHMM_glimmerT_5491-T1
Valid prediction for GlimmerHMM_glimmerT_5512-T1
Valid prediction for GlimmerHMM_glimmerT_5508-T1
Valid prediction for snap_scaffold_2-snap.3542-T1
Valid prediction for GlimmerHMM_glimmerT_5496-T1
Valid prediction for GlimmerHMM_glimmerT_5511-T1
Valid prediction for snap_scaffold_2-snap.3532-T1
Valid prediction for GlimmerHMM_glimmerT_5490-T1
Valid prediction for GlimmerHMM_glimmerT_5488-T1
Valid prediction for Augustus_model.g3705.t1
Valid prediction for snap_scaffold_2-snap.3545-T1
Valid prediction for GlimmerHMM_glimmerT_5500-T1
Valid prediction for snap_scaffold_2-snap.3548-T1
Valid prediction for GlimmerHMM_glimmerT_5509-T1
Valid prediction for pasa_asmbl_25221.p1
Valid prediction for snap_scaffold_2-snap.3524-T1
Valid prediction for Augustus_model.g3702.t1
Valid prediction for snap_scaffold_2-snap.3512-T1
Valid prediction for GlimmerHMM_glimmerT_5495-T1
Valid prediction for GlimmerHMM_glimmerT_5501-T1
Valid prediction for snap_scaffold_2-snap.3521-T1
Valid prediction for GlimmerHMM_glimmerT_5485-T1
Valid prediction for GlimmerHMM_glimmerT_5497-T1
Valid prediction for snap_scaffold_2-snap.3546-T1
Valid prediction for snap_scaffold_2-snap.3523-T1
Valid prediction for GlimmerHMM_glimmerT_5505-T1
Valid prediction for GlimmerHMM_glimmerT_5504-T1
Valid prediction for Augustus_model.g3703.t1
Valid prediction for Augustus_model.g3704.t1
Valid prediction for HiQ_model.g3701.t1
Valid prediction for snap_scaffold_2-snap.3526-T1
Valid prediction for GlimmerHMM_glimmerT_5499-T1
Valid prediction for snap_scaffold_2-snap.3518-T1
Valid prediction for GlimmerHMM_glimmerT_5492-T1
Valid prediction for GlimmerHMM_glimmerT_5486-T1
Valid prediction for GlimmerHMM_glimmerT_5502-T1
Valid prediction for snap_scaffold_2-snap.3549-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 Augustus_model.g3707.t1
Valid prediction for snap_scaffold_2-snap.3534-T1
Valid prediction for CodingQuarry_transcript_28837-T1
Valid prediction for snap_scaffold_2-snap.3525-T1
Valid prediction for snap_scaffold_2-snap.3513-T1
Valid prediction for GlimmerHMM_glimmerT_5510-T1
Valid prediction for GlimmerHMM_glimmerT_5506-T1
Valid prediction for snap_scaffold_2-snap.3535-T1
Couldn't classify 5166, 5360
Couldn't classify 11214, 11503
Sorry, prediction pasa_asmbl_23772.p1 fails validation.
(CTG)	 GT	5166-5360	GT	AGG
(GAA)	 AG	5484-5655	GT	AGG
(ATC)	 AG	7165-7229	GT	ACG
(GAT)	 AG	7816-7932	GT	AGG
(GAG)	 AG	10727-10940	GT	TGG
(AGC)	 AG	11214-11503	TG	GGT
add_exon() Sorry, pasa_asmbl_23772.p1 5484-5655-terminal-3 is invalid.
-recovered pasa_asmbl_23772.p1, terminal, 5484, 5655
-recovered pasa_asmbl_23772.p1, internal, 5484, 5655
-recovered pasa_asmbl_23772.p1, internal, 7165, 7229
-recovered pasa_asmbl_23772.p1, internal, 7816, 7932
-recovered pasa_asmbl_23772.p1, internal, 10727, 10940
Valid prediction for snap_scaffold_2-snap.3514-T1
Valid prediction for snap_scaffold_2-snap.3508-T1
Valid prediction for snap_scaffold_2-snap.3510-T1
Valid prediction for GlimmerHMM_glimmerT_5498-T1
Valid prediction for snap_scaffold_2-snap.3511-T1
Valid prediction for GlimmerHMM_glimmerT_5489-T1
Couldn't classify 15094, 15179
Couldn't classify 18431, 18586
Sorry, prediction pasa_asmbl_23771.p1 fails validation.
(AGG)	 AT	15094-15179	GT	AGG
(TCC)	 AG	15501-15587	GT	AGG
(TCA)	 AG	16485-16633	GT	CGG
(GGA)	 AG	17483-17570	GT	AGG
(GAA)	 AG	18033-18165	GT	AGG
(TCC)	 AG	18431-18586	AA	GTA
-recovered pasa_asmbl_23771.p1, internal, 15501, 15587
-recovered pasa_asmbl_23771.p1, internal, 16485, 16633
-recovered pasa_asmbl_23771.p1, internal, 17483, 17570
-recovered pasa_asmbl_23771.p1, internal, 18033, 18165
Valid prediction for snap_scaffold_2-snap.3522-T1
Valid prediction for snap_scaffold_2-snap.3520-T1
Valid prediction for snap_scaffold_2-snap.3547-T1
Valid prediction for Augustus_model.g3708.t1
Valid prediction for snap_scaffold_2-snap.3537-T1
Valid prediction for snap_scaffold_2-snap.3540-T1
Valid prediction for snap_scaffold_2-snap.3529-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3517-T1
Valid prediction for GlimmerHMM_glimmerT_5487-T1
Valid prediction for snap_scaffold_2-snap.3515-T1
Valid prediction for snap_scaffold_2-snap.3527-T1
Couldn't classify 33958, 34086
Couldn't classify 38772, 38933
Sorry, prediction pasa_asmbl_23770.p1 fails validation.
(CAC)	 GT	33958-34086	GT	TGG
(GTG)	 AG	35619-35750	GT	GGG
(ACC)	 AG	36750-36926	GT	AGG
(GGC)	 AG	38772-38933	GT	CAG
-recovered pasa_asmbl_23770.p1, internal, 35619, 35750
-recovered pasa_asmbl_23770.p1, internal, 36750, 36926
-recovered pasa_asmbl_23770.p1, internal, 38772, 38933
Valid prediction for snap_scaffold_2-snap.3528-T1
Valid prediction for GlimmerHMM_glimmerT_5493-T1
Valid prediction for GlimmerHMM_glimmerT_5503-T1
Valid prediction for snap_scaffold_2-snap.3519-T1
Valid prediction for snap_scaffold_2-snap.3507-T1
Valid prediction for snap_scaffold_2-snap.3544-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5494-T1
Couldn't classify 44137, 44439
Sorry, prediction pasa_asmbl_24051.p1 fails validation.
(TGT)	 GC	44137-44439	GG	AAG

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37835, rend_intergenic: 26891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40003, rend_intergenic: 38666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48554, rend_intergenic: 41789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56665, rend_intergenic: 50287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58905, rend_intergenic: 58547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61994, rend_intergenic: 61504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68271, rend_intergenic: 62278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91076, rend_intergenic: 90615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115309, rend_intergenic: 91123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129418, rend_intergenic: 117579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149442, rend_intergenic: 129560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164476, rend_intergenic: 149729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175085, rend_intergenic: 171531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181979, rend_intergenic: 176664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186820, rend_intergenic: 182614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202712, rend_intergenic: 187235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220609, rend_intergenic: 205010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231422, rend_intergenic: 221654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233529, rend_intergenic: 231462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243154, rend_intergenic: 233946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244902
-exon list size: 318


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
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3.8    
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4.7    
5.0    
5.3    
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5.9    
6.2    
6.6    
6.9    
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7.5    
7.8    
8.1    
8.4    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
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26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 37835, rend_intergenic: 26891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40003, rend_intergenic: 38666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48554, rend_intergenic: 41789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56665, rend_intergenic: 50287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58905, rend_intergenic: 58547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61994, rend_intergenic: 61504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68271, rend_intergenic: 62278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91076, rend_intergenic: 90615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115309, rend_intergenic: 91123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129418, rend_intergenic: 117579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149442, rend_intergenic: 129560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164476, rend_intergenic: 149729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175085, rend_intergenic: 171531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181979, rend_intergenic: 176664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186820, rend_intergenic: 182614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202712, rend_intergenic: 187235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220609, rend_intergenic: 205010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231422, rend_intergenic: 221654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233529, rend_intergenic: 231462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243154, rend_intergenic: 233946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10182
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support