-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_1895009-2137515

-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_12-snap.424-T1
Valid prediction for snap_scaffold_12-snap.422-T1
Valid prediction for snap_scaffold_12-snap.415-T1
Valid prediction for GeneMark_model.51003_t
Valid prediction for Augustus_model.g19644.t1
Valid prediction for GeneMark_model.50994_t
Valid prediction for snap_scaffold_12-snap.426-T1
Valid prediction for snap_scaffold_12-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_29531-T1
Valid prediction for Augustus_model.g19647.t1
Valid prediction for snap_scaffold_12-snap.419-T1
Valid prediction for snap_scaffold_12-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_29535-T1
Valid prediction for GeneMark_model.50988_t
Valid prediction for snap_scaffold_12-snap.408-T1
Valid prediction for GeneMark_model.50976_t
Valid prediction for Augustus_model.g19633.t1
Valid prediction for HiQ_model.g19650.t1
Valid prediction for GeneMark_model.50989_t
Valid prediction for snap_scaffold_12-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_29521-T1
Valid prediction for Augustus_model.g19645.t1
Valid prediction for Augustus_model.g19642.t1
Valid prediction for snap_scaffold_12-snap.439-T1
Valid prediction for GeneMark_model.50972_t
Valid prediction for snap_scaffold_12-snap.401-T1
Valid prediction for GeneMark_model.50967_t
Valid prediction for GeneMark_model.50969_t
Valid prediction for GeneMark_model.50982_t
Valid prediction for GeneMark_model.50992_t
Valid prediction for GeneMark_model.50986_t
Valid prediction for snap_scaffold_12-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_29528-T1
Valid prediction for GeneMark_model.50987_t
Valid prediction for Augustus_model.g19648.t1
Valid prediction for GlimmerHMM_glimmerT_29530-T1
Valid prediction for GeneMark_model.50980_t
Valid prediction for snap_scaffold_12-snap.436-T1
Valid prediction for GeneMark_model.51006_t
Valid prediction for snap_scaffold_12-snap.434-T1
Couldn't classify 209403, 209495
Couldn't classify 210315, 210872
Sorry, prediction pasa_asmbl_8445.p1 fails validation.
(CAC)	 TG	209403-209495	GT	CGG
(TCC)	 AG	210315-210872	GA	GGG
Valid prediction for GeneMark_model.50998_t
Valid prediction for snap_scaffold_12-snap.425-T1
Valid prediction for snap_scaffold_12-snap.418-T1
Valid prediction for snap_scaffold_12-snap.435-T1
Valid prediction for snap_scaffold_12-snap.427-T1
Valid prediction for snap_scaffold_12-snap.430-T1
Valid prediction for GlimmerHMM_glimmerT_29533-T1
Valid prediction for GeneMark_model.51001_t
Valid prediction for GlimmerHMM_glimmerT_29534-T1
Valid prediction for Augustus_model.g19646.t1
Valid prediction for snap_scaffold_12-snap.403-T1
Valid prediction for GeneMark_model.50978_t
Valid prediction for GlimmerHMM_glimmerT_29519-T1
Valid prediction for GeneMark_model.51008_t
Valid prediction for GeneMark_model.50996_t
Valid prediction for snap_scaffold_12-snap.433-T1
Valid prediction for snap_scaffold_12-snap.420-T1
Couldn't classify 216484, 216554
Sorry, prediction pasa_asmbl_8447.p1 fails validation.
(GGA)	 GA	216484-216554	GT	CTG
(GTT)	 AG	216790-216895	GT	AGG
(TTG)	 AG	217019-217109	GT	AGG
(CGT)	 AG	217227-217297	GT	ATG
(GTC)	 AG	217602-217729	GT	AGG
(GGA)	 AG	217858-218044	GT	AGG
(GAG)	 AG	218516-218623	GT	AGG
(CTG)	 AG	218738-218849	GT	AGG
(GTG)	 AG	219082-219139	GT	AGG
(AGA)	 AG	219353-219432	GT	ATG
(ATA)	 AG	219769-219859	GT	AGG
(CGA)	 AG	220187-220340	GT	AGG
-recovered pasa_asmbl_8447.p1, terminal, 220187, 220340
-recovered pasa_asmbl_8447.p1, internal, 216790, 216895
-recovered pasa_asmbl_8447.p1, internal, 217019, 217109
-recovered pasa_asmbl_8447.p1, internal, 217227, 217297
-recovered pasa_asmbl_8447.p1, internal, 217602, 217729
-recovered pasa_asmbl_8447.p1, internal, 217858, 218044
-recovered pasa_asmbl_8447.p1, internal, 218516, 218623
-recovered pasa_asmbl_8447.p1, internal, 218738, 218849
-recovered pasa_asmbl_8447.p1, internal, 219082, 219139
-recovered pasa_asmbl_8447.p1, internal, 219353, 219432
-recovered pasa_asmbl_8447.p1, internal, 219769, 219859
-recovered pasa_asmbl_8447.p1, internal, 220187, 220340
Valid prediction for GeneMark_model.50984_t
Valid prediction for GeneMark_model.51005_t
Valid prediction for snap_scaffold_12-snap.431-T1
Valid prediction for CodingQuarry_transcript_10108-T1
Valid prediction for Augustus_model.g19649.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_12-snap.421-T1
Valid prediction for GeneMark_model.50983_t
Valid prediction for snap_scaffold_12-snap.414-T1
Valid prediction for GlimmerHMM_glimmerT_29520-T1
Valid prediction for snap_scaffold_12-snap.411-T1
Valid prediction for Augustus_model.g19651.t1
Valid prediction for GeneMark_model.50977_t
Valid prediction for GlimmerHMM_glimmerT_29532-T1
Valid prediction for Augustus_model.g19640.t1
Valid prediction for snap_scaffold_12-snap.429-T1
Valid prediction for snap_scaffold_12-snap.438-T1
Couldn't classify 147978, 148041
Sorry, prediction pasa_asmbl_7453.p1 fails validation.
(CCT)	 AT	147978-148041	GT	CGG
(CGT)	 AG	148172-148325	GT	GGG
(GGA)	 AG	148713-148825	GT	AGG
(CTT)	 AG	148995-149107	GT	AGG
(AGC)	 AG	149680-149788	GT	TGG
(GAA)	 AG	150154-150229	GT	GGG
(CCG)	 AG	150495-150651	CG	AGC
-recovered pasa_asmbl_7453.p1, terminal, 150495, 150651
-recovered pasa_asmbl_7453.p1, internal, 148172, 148325
-recovered pasa_asmbl_7453.p1, internal, 148713, 148825
-recovered pasa_asmbl_7453.p1, internal, 148995, 149107
-recovered pasa_asmbl_7453.p1, internal, 149680, 149788
-recovered pasa_asmbl_7453.p1, internal, 150154, 150229
Valid prediction for GeneMark_model.50975_t
Valid prediction for GeneMark_model.50991_t
Valid prediction for GlimmerHMM_glimmerT_29526-T1
Valid prediction for GeneMark_model.50971_t
Valid prediction for snap_scaffold_12-snap.432-T1
Valid prediction for GeneMark_model.51002_t
Couldn't classify 202391, 202476
Couldn't classify 202685, 202907
Sorry, prediction pasa_asmbl_8365.p1 fails validation.
(AGC)	 GC	202391-202476	GT	AAG
(GAA)	 AG	202685-202907	GG	TAG
Valid prediction for CodingQuarry_transcript_10105-T1
Valid prediction for Augustus_model.g19635.t1
Valid prediction for GlimmerHMM_glimmerT_29529-T1
Valid prediction for Augustus_model.g19636.t1
Valid prediction for snap_scaffold_12-snap.407-T1
Valid prediction for CodingQuarry_transcript_10107-T1
Valid prediction for GeneMark_model.50968_t
Valid prediction for snap_scaffold_12-snap.413-T1
Valid prediction for GeneMark_model.50999_t
Valid prediction for snap_scaffold_12-snap.405-T1
Valid prediction for GeneMark_model.50979_t
Valid prediction for GlimmerHMM_glimmerT_29525-T1
Valid prediction for Augustus_model.g19638.t1
Valid prediction for snap_scaffold_12-snap.402-T1
Valid prediction for GeneMark_model.50990_t
Valid prediction for GeneMark_model.50981_t
Valid prediction for GeneMark_model.51007_t
Valid prediction for GlimmerHMM_glimmerT_29522-T1
Valid prediction for GeneMark_model.51004_t
Valid prediction for GlimmerHMM_glimmerT_29524-T1
Couldn't classify 179711, 179895
Sorry, prediction pasa_asmbl_7442.p1 fails validation.
(GAG)	 TG	179711-179895	GT	ATG
(GAT)	 AG	180289-180445	GT	GGG
(TTC)	 AG	180711-180864	GT	CGG
(GGA)	 AG	181336-181412	GT	AGG
(CTG)	 AG	181690-181755	GT	TGG
(ATC)	 AG	183221-183373	GA	AAG
-recovered pasa_asmbl_7442.p1, terminal, 183221, 183373
-recovered pasa_asmbl_7442.p1, internal, 180289, 180445
-recovered pasa_asmbl_7442.p1, internal, 180711, 180864
-recovered pasa_asmbl_7442.p1, internal, 181336, 181412
-recovered pasa_asmbl_7442.p1, internal, 181690, 181755
Valid prediction for snap_scaffold_12-snap.409-T1
Valid prediction for GeneMark_model.50970_t
Valid prediction for snap_scaffold_12-snap.423-T1
Valid prediction for GeneMark_model.51000_t
Valid prediction for snap_scaffold_12-snap.416-T1
Valid prediction for GeneMark_model.50993_t
Valid prediction for GeneMark_model.50974_t
Valid prediction for Augustus_model.g19639.t1
Valid prediction for CodingQuarry_transcript_10106-T1
Valid prediction for GlimmerHMM_glimmerT_29523-T1
Valid prediction for GeneMark_model.50997_t
Valid prediction for snap_scaffold_12-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_29527-T1
Couldn't classify 163956, 164074
Sorry, prediction pasa_asmbl_7445.p1 fails validation.
(CTT)	 AG	163956-164074	GT	AGG
(GAT)	 AG	165013-165233	GT	CAG
(AGC)	 AG	165528-165638	GT	GAG
(AGT)	 AG	165814-165905	AA	AAA
add_exon() Sorry, pasa_asmbl_7445.p1 165528-165638-terminal-1 is invalid.
-recovered pasa_asmbl_7445.p1, terminal, 165528, 165638
-recovered pasa_asmbl_7445.p1, terminal, 165814, 165905
-recovered pasa_asmbl_7445.p1, internal, 163956, 164074
-recovered pasa_asmbl_7445.p1, internal, 165013, 165233
-recovered pasa_asmbl_7445.p1, internal, 165528, 165638
Valid prediction for HiQ_model.g19641.t1
Valid prediction for pasa_asmbl_7449.p1
Valid prediction for GeneMark_model.51009_t
Valid prediction for snap_scaffold_12-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_29536-T1
Valid prediction for snap_scaffold_12-snap.406-T1
Valid prediction for HiQ_model.g19643.t1
Valid prediction for Augustus_model.g19634.t1
Valid prediction for snap_scaffold_12-snap.412-T1
Valid prediction for Augustus_model.g19637.t1
Valid prediction for GeneMark_model.50985_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36786, rend_intergenic: 31850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139738, rend_intergenic: 138428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187801, rend_intergenic: 186188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190557, rend_intergenic: 189819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242507
-exon list size: 504


building trellis

0.2    
0.4    
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0.8    
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3.6    
3.8    
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5.9    
6.1    
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8.1    
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8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
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10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
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13.0    
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13.4    
13.6    
13.8    
14.0    
14.2    
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14.6    
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15.0    
15.2    
15.4    
15.6    
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16.4    
16.6    
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17.6    
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18.2    
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19.6    
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20.0    
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20.4    
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20.8    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 36786, rend_intergenic: 31850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139738, rend_intergenic: 138428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187801, rend_intergenic: 186188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190557, rend_intergenic: 189819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20330
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 1575 - 20330
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 6502 - 20330
-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