-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_5667436-5920862

-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_16-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_39230-T1
Valid prediction for snap_scaffold_16-snap.1124-T1
Valid prediction for HiQ_model.g26360.t1
Valid prediction for Augustus_model.g26355.t1
Valid prediction for snap_scaffold_16-snap.1139-T1
Valid prediction for GeneMark_model.67185_t
Valid prediction for snap_scaffold_16-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_39239-T1
Valid prediction for snap_scaffold_16-snap.1130-T1
Valid prediction for pasa_asmbl_17015.p1
Valid prediction for GeneMark_model.67191_t
Valid prediction for GlimmerHMM_glimmerT_39242-T1
Valid prediction for GlimmerHMM_glimmerT_39222-T1
Valid prediction for snap_scaffold_16-snap.1122-T1
Valid prediction for CodingQuarry_transcript_19934-T1
Valid prediction for GlimmerHMM_glimmerT_39229-T1
Valid prediction for GeneMark_model.67173_t
Valid prediction for GeneMark_model.67188_t
Valid prediction for snap_scaffold_16-snap.1116-T1
Valid prediction for GeneMark_model.67164_t
Valid prediction for GeneMark_model.67170_t
Valid prediction for GlimmerHMM_glimmerT_39231-T1
Valid prediction for snap_scaffold_16-snap.1118-T1
Valid prediction for GeneMark_model.67175_t
Valid prediction for GeneMark_model.67172_t
Valid prediction for snap_scaffold_16-snap.1135-T1
Valid prediction for GlimmerHMM_glimmerT_39223-T1
Valid prediction for GeneMark_model.67187_t
Valid prediction for GeneMark_model.67166_t
Valid prediction for HiQ_model.g26358.t1
Valid prediction for Augustus_model.g26354.t1
Valid prediction for GeneMark_model.67195_t
Valid prediction for snap_scaffold_16-snap.1119-T1
Valid prediction for snap_scaffold_16-snap.1117-T1
Valid prediction for snap_scaffold_16-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_39225-T1
Valid prediction for snap_scaffold_16-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_39233-T1
Valid prediction for GlimmerHMM_glimmerT_39220-T1
Valid prediction for GlimmerHMM_glimmerT_39247-T1
Valid prediction for GlimmerHMM_glimmerT_39232-T1
Valid prediction for snap_scaffold_16-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_39224-T1
Valid prediction for snap_scaffold_16-snap.1115-T1
Valid prediction for Augustus_model.g26356.t1
Valid prediction for GeneMark_model.67168_t
Valid prediction for GeneMark_model.67193_t
Valid prediction for CodingQuarry_transcript_19933-T1
Valid prediction for Augustus_model.g26359.t1
Valid prediction for GeneMark_model.67163_t
Valid prediction for GlimmerHMM_glimmerT_39243-T1
Couldn't classify 129451, 129796
Sorry, prediction pasa_asmbl_17022.p1 fails validation.
(ATG)	 TT	127371-127389	GT	AGG
(ACG)	 AG	128377-128458	GT	AGG
(TGA)	 AG	128705-128753	GT	AAG
(AAT)	 AG	129148-129221	GT	AGG
(CGG)	 AG	129451-129796	TC	GCT
-recovered pasa_asmbl_17022.p1, initial, 127371, 127389
-recovered pasa_asmbl_17022.p1, internal, 128377, 128458
-recovered pasa_asmbl_17022.p1, internal, 128705, 128753
-recovered pasa_asmbl_17022.p1, internal, 129148, 129221
Valid prediction for GlimmerHMM_glimmerT_39227-T1
Valid prediction for snap_scaffold_16-snap.1123-T1
Valid prediction for GeneMark_model.67176_t
Valid prediction for GeneMark_model.67178_t
Valid prediction for GeneMark_model.67190_t
Valid prediction for HiQ_model.g26367.t1
Valid prediction for GlimmerHMM_glimmerT_39235-T1
Valid prediction for snap_scaffold_16-snap.1112-T1
Valid prediction for snap_scaffold_16-snap.1140-T1
Valid prediction for GeneMark_model.67171_t
Valid prediction for snap_scaffold_16-snap.1127-T1
Couldn't classify 134992, 135137
Sorry, prediction pasa_asmbl_17023.p1 fails validation.
(ATG)	 TT	127371-127389	GT	AGG
(ACG)	 AG	128377-128458	GT	AGG
(TGA)	 AG	128705-128753	GT	AAG
(AAT)	 AG	129148-129221	GT	AGG
(CGG)	 AG	129451-129742	GT	AAG
(GTT)	 AG	131782-131910	GT	AGG
(GTT)	 AG	132147-132315	GT	AGG
(AAC)	 AG	132514-132740	GT	AGG
(CAG)	 AG	133569-133920	GT	AGG
(TGC)	 AG	134992-135137	CC	TCC
-recovered pasa_asmbl_17023.p1, initial, 127371, 127389
add_exon() Sorry, pasa_asmbl_17023.p1 132147-132315-terminal-3 is invalid.
-recovered pasa_asmbl_17023.p1, terminal, 132147, 132315
-recovered pasa_asmbl_17023.p1, internal, 128377, 128458
-recovered pasa_asmbl_17023.p1, internal, 128705, 128753
-recovered pasa_asmbl_17023.p1, internal, 129148, 129221
-recovered pasa_asmbl_17023.p1, internal, 129451, 129742
-recovered pasa_asmbl_17023.p1, internal, 131782, 131910
-recovered pasa_asmbl_17023.p1, internal, 132147, 132315
-recovered pasa_asmbl_17023.p1, internal, 132514, 132740
-recovered pasa_asmbl_17023.p1, internal, 133569, 133920
Valid prediction for CodingQuarry_transcript_19932-T1
Valid prediction for Augustus_model.g26363.t1
Valid prediction for GlimmerHMM_glimmerT_39245-T1
Valid prediction for Augustus_model.g26357.t1
Couldn't classify 140970, 141314
Sorry, prediction pasa_asmbl_17024.p1 fails validation.
(CAA)	 GC	140970-141314	GT	GGG
(GGA)	 AG	143217-143393	GT	GGG
(GTG)	 AG	144284-144490	GT	AGG
(ATG)	 AG	144835-144923	GT	AGG
(GCA)	 AG	145382-145430	GG	GAG
-recovered pasa_asmbl_17024.p1, initial, 144835, 144923
-recovered pasa_asmbl_17024.p1, terminal, 145382, 145430
-recovered pasa_asmbl_17024.p1, internal, 143217, 143393
-recovered pasa_asmbl_17024.p1, internal, 144284, 144490
-recovered pasa_asmbl_17024.p1, internal, 144835, 144923
Valid prediction for pasa_asmbl_17027.p1
Valid prediction for GeneMark_model.67165_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 snap_scaffold_16-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_39234-T1
Valid prediction for GlimmerHMM_glimmerT_39246-T1
Valid prediction for GeneMark_model.67180_t
Valid prediction for snap_scaffold_16-snap.1138-T1
Valid prediction for GeneMark_model.67183_t
Valid prediction for snap_scaffold_16-snap.1126-T1
Valid prediction for snap_scaffold_16-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_39236-T1
Valid prediction for GlimmerHMM_glimmerT_39244-T1
Valid prediction for Augustus_model.g26353.t1
Valid prediction for GeneMark_model.67169_t
Valid prediction for GeneMark_model.67194_t
Valid prediction for GeneMark_model.67192_t
Valid prediction for snap_scaffold_16-snap.1121-T1
Valid prediction for GeneMark_model.67189_t
Valid prediction for Augustus_model.g26365.t1
Valid prediction for GeneMark_model.67186_t
Valid prediction for snap_scaffold_16-snap.1132-T1
Valid prediction for snap_scaffold_16-snap.1114-T1
Valid prediction for GeneMark_model.67182_t
Valid prediction for GlimmerHMM_glimmerT_39226-T1
Valid prediction for snap_scaffold_16-snap.1133-T1
Valid prediction for Augustus_model.g26361.t1
Valid prediction for GeneMark_model.67177_t
Valid prediction for GlimmerHMM_glimmerT_39238-T1
Valid prediction for Augustus_model.g26362.t1
Valid prediction for Augustus_model.g26364.t1
Valid prediction for GlimmerHMM_glimmerT_39241-T1
Valid prediction for GlimmerHMM_glimmerT_39228-T1
Valid prediction for Augustus_model.g26366.t1
Valid prediction for GeneMark_model.67174_t
Valid prediction for GeneMark_model.67179_t
Valid prediction for GeneMark_model.67184_t
Valid prediction for GlimmerHMM_glimmerT_39237-T1
Valid prediction for GlimmerHMM_glimmerT_39240-T1
Valid prediction for GeneMark_model.67181_t
Valid prediction for GlimmerHMM_glimmerT_39221-T1
Valid prediction for snap_scaffold_16-snap.1125-T1
Valid prediction for snap_scaffold_16-snap.1129-T1
Valid prediction for GeneMark_model.67167_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 205813, rend_intergenic: 202537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235306, rend_intergenic: 219948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253427
-exon list size: 452


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
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1.5    
1.8    
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3.7    
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8.8    
9.0    
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10.1    
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10.6    
10.8    
11.0    
11.2    
11.5    
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11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
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13.9    
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14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.9    
16.1    
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16.7    
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17.6    
17.8    
18.1    
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18.9    
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19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
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22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
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 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 205813, rend_intergenic: 202537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235306, rend_intergenic: 219948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11705
-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 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

-building DP trellis

-building trellis in range 1 - 10623
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support