-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_11604397-11790688

-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_5-snap.2171-T1
Valid prediction for pasa_asmbl_44425.p1
Valid prediction for GlimmerHMM_glimmerT_12969-T1
Couldn't classify 152998, 153636
Sorry, prediction pasa_asmbl_44428.p1 fails validation.
(CCC)	 CA	152998-153636	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_12977-T1
Valid prediction for GlimmerHMM_glimmerT_12972-T1
Valid prediction for snap_scaffold_5-snap.2192-T1
Valid prediction for snap_scaffold_5-snap.2182-T1
Couldn't classify 11521, 11606
Couldn't classify 12447, 12491
Sorry, prediction pasa_asmbl_45085.p1 fails validation.
(CAG)	 CC	11521-11606	GT	ATG
(GAG)	 AG	11687-11761	GT	AGG
(GTA)	 AG	12015-12117	GT	AGG
(GTG)	 AG	12212-12358	GT	AGG
(AAC)	 AG	12447-12491	GG	CAG
-recovered pasa_asmbl_45085.p1, internal, 11687, 11761
-recovered pasa_asmbl_45085.p1, internal, 12015, 12117
-recovered pasa_asmbl_45085.p1, internal, 12212, 12358
Valid prediction for GeneMark_model.21921_t
Valid prediction for snap_scaffold_5-snap.2189-T1
Valid prediction for CodingQuarry_transcript_52134-T1
Valid prediction for GeneMark_model.21925_t
Valid prediction for GlimmerHMM_glimmerT_12987-T1
Valid prediction for snap_scaffold_5-snap.2194-T1
Valid prediction for Augustus_model.g8651.t1
Valid prediction for snap_scaffold_5-snap.2166-T1
Valid prediction for snap_scaffold_5-snap.2186-T1
Valid prediction for pasa_asmbl_44426.p1
Valid prediction for CodingQuarry_transcript_52133-T1
Valid prediction for GeneMark_model.21936_t
Valid prediction for GeneMark_model.21927_t
Valid prediction for GlimmerHMM_glimmerT_12975-T1
Valid prediction for GeneMark_model.21919_t
Valid prediction for GeneMark_model.21934_t
Valid prediction for snap_scaffold_5-snap.2167-T1
Valid prediction for snap_scaffold_5-snap.2190-T1
Valid prediction for Augustus_model.g8652.t1
Valid prediction for GeneMark_model.21940_t
Valid prediction for Augustus_model.g8643.t1
Valid prediction for Augustus_model.g8638.t1
Valid prediction for Augustus_model.g8640.t1
Valid prediction for GeneMark_model.21948_t
Valid prediction for snap_scaffold_5-snap.2165-T1
Valid prediction for snap_scaffold_5-snap.2187-T1
Valid prediction for snap_scaffold_5-snap.2178-T1
Valid prediction for GeneMark_model.21945_t
Valid prediction for GlimmerHMM_glimmerT_12992-T1
Valid prediction for HiQ_model.g8644.t1
Valid prediction for GeneMark_model.21949_t
Valid prediction for snap_scaffold_5-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_12991-T1
Valid prediction for GlimmerHMM_glimmerT_12971-T1
Valid prediction for Augustus_model.g8653.t1
Valid prediction for Augustus_model.g8641.t1
Valid prediction for GlimmerHMM_glimmerT_12984-T1
Valid prediction for CodingQuarry_transcript_52135-T1
Valid prediction for GlimmerHMM_glimmerT_12981-T1
Valid prediction for GlimmerHMM_glimmerT_12990-T1
Valid prediction for snap_scaffold_5-snap.2180-T1
Valid prediction for GeneMark_model.21924_t
Valid prediction for GeneMark_model.21932_t
Valid prediction for snap_scaffold_5-snap.2191-T1
Valid prediction for snap_scaffold_5-snap.2172-T1
Valid prediction for snap_scaffold_5-snap.2184-T1
Couldn't classify 167195, 167222
Couldn't classify 168321, 168376
Sorry, prediction pasa_asmbl_45070.p1 fails validation.
(GCC)	 AT	167195-167222	GT	TGG
(ATG)	 AG	167347-167475	GT	GGG
(ATG)	 AG	168045-168170	GT	AGG
(ATG)	 AG	168321-168376	TC	GGT
-recovered pasa_asmbl_45070.p1, initial, 167347, 167475
add_exon() Sorry, pasa_asmbl_45070.p1 168045-168170-initial-1 is invalid.
-recovered pasa_asmbl_45070.p1, initial, 168045, 168170
-recovered pasa_asmbl_45070.p1, internal, 167347, 167475
-recovered pasa_asmbl_45070.p1, internal, 168045, 168170
Valid prediction for Augustus_model.g8639.t1
Valid prediction for GlimmerHMM_glimmerT_12976-T1
Valid prediction for snap_scaffold_5-snap.2164-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.21920_t
Valid prediction for GeneMark_model.21946_t
Valid prediction for GeneMark_model.21943_t
Couldn't classify 163883, 163958
Couldn't classify 164016, 164341
Sorry, prediction CodingQuarry_transcript_52130-T1 fails validation.
(ATG)	 TC	163883-163958	CT	ACC
(CTG)	 AC	164016-164341	AA	GAA
Valid prediction for GeneMark_model.21926_t
Valid prediction for GlimmerHMM_glimmerT_12993-T1
Valid prediction for Augustus_model.g8650.t1
Valid prediction for GeneMark_model.21930_t
Valid prediction for Augustus_model.g8649.t1
Valid prediction for CodingQuarry_transcript_52136-T1
Valid prediction for Augustus_model.g8646.t1
Valid prediction for GeneMark_model.21937_t
Valid prediction for GlimmerHMM_glimmerT_12974-T1
Valid prediction for CodingQuarry_transcript_52132-T1
Valid prediction for GeneMark_model.21931_t
Valid prediction for pasa_asmbl_45799.p1
Valid prediction for GeneMark_model.21941_t
Valid prediction for GlimmerHMM_glimmerT_12988-T1
Valid prediction for GeneMark_model.21923_t
Valid prediction for GlimmerHMM_glimmerT_12994-T1
Valid prediction for GeneMark_model.21942_t
Valid prediction for CodingQuarry_transcript_52131-T1
Valid prediction for GeneMark_model.21944_t
Valid prediction for snap_scaffold_5-snap.2175-T1
Couldn't classify 57036, 57158
Couldn't classify 59707, 59811
Sorry, prediction pasa_asmbl_45808.p1 fails validation.
(TGG)	 CC	57036-57158	GT	AGG
(GTT)	 AG	57943-58057	GT	AGG
(GTT)	 AG	58201-58347	GT	TGG
(GCC)	 AG	59369-59619	GT	AGG
(GTG)	 AG	59707-59811	GT	CAG
add_exon() Sorry, pasa_asmbl_45808.p1 57943-58057-terminal-3 is invalid.
-recovered pasa_asmbl_45808.p1, terminal, 57943, 58057
-recovered pasa_asmbl_45808.p1, internal, 57943, 58057
-recovered pasa_asmbl_45808.p1, internal, 58201, 58347
-recovered pasa_asmbl_45808.p1, internal, 59369, 59619
-recovered pasa_asmbl_45808.p1, internal, 59707, 59811
Valid prediction for GlimmerHMM_glimmerT_12973-T1
Valid prediction for snap_scaffold_5-snap.2170-T1
Valid prediction for GeneMark_model.21928_t
Valid prediction for snap_scaffold_5-snap.2185-T1
Valid prediction for GlimmerHMM_glimmerT_12986-T1
Valid prediction for snap_scaffold_5-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_12982-T1
Valid prediction for GlimmerHMM_glimmerT_12979-T1
Valid prediction for snap_scaffold_5-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_12980-T1
Valid prediction for HiQ_model.g8642.t1
Valid prediction for GeneMark_model.21918_t
Valid prediction for Augustus_model.g8648.t1
Valid prediction for GlimmerHMM_glimmerT_12989-T1
Valid prediction for snap_scaffold_5-snap.2174-T1
Valid prediction for snap_scaffold_5-snap.2177-T1
Valid prediction for snap_scaffold_5-snap.2168-T1
Valid prediction for GlimmerHMM_glimmerT_12970-T1
Valid prediction for Augustus_model.g8647.t1
Valid prediction for GeneMark_model.21935_t
Valid prediction for snap_scaffold_5-snap.2169-T1
Valid prediction for GlimmerHMM_glimmerT_12983-T1
Valid prediction for GlimmerHMM_glimmerT_12978-T1
Valid prediction for GeneMark_model.21933_t
Valid prediction for GeneMark_model.21939_t
Valid prediction for snap_scaffold_5-snap.2181-T1
Valid prediction for GlimmerHMM_glimmerT_12985-T1
Valid prediction for snap_scaffold_5-snap.2183-T1
Valid prediction for GeneMark_model.21947_t
Valid prediction for Augustus_model.g8645.t1
Valid prediction for snap_scaffold_5-snap.2176-T1
Valid prediction for snap_scaffold_5-snap.2188-T1
Valid prediction for GeneMark_model.21922_t
Valid prediction for GeneMark_model.21938_t
Valid prediction for GeneMark_model.21929_t
Valid prediction for GeneMark_model.21950_t
Valid prediction for pasa_asmbl_45806.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65865, rend_intergenic: 63724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75128, rend_intergenic: 73204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80064, rend_intergenic: 76027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92894, rend_intergenic: 88870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186292
-exon list size: 451


building trellis

0.2    
0.4    
0.7    
0.9    
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3.8    
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6.8    
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8.8    
9.1    
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10.8    
11.0    
11.3    
11.5    
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11.9    
12.1    
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13.9    
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14.8    
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15.2    
15.5    
15.7    
15.9    
16.1    
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16.8    
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18.1    
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21.6    
21.9    
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23.6    
23.8    
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24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.6    
53.9    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.4    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 65865, rend_intergenic: 63724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75128, rend_intergenic: 73204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80064, rend_intergenic: 76027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92894, rend_intergenic: 88870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 173151 - 186292
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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 173151 - 183632
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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