-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_484161-704246

-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_13-snap.128-T1
Valid prediction for snap_scaffold_13-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_30979-T1
Valid prediction for snap_scaffold_13-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_30985-T1
Valid prediction for GlimmerHMM_glimmerT_30994-T1
Valid prediction for snap_scaffold_13-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_30977-T1
Valid prediction for Augustus_model.g20565.t1
Valid prediction for snap_scaffold_13-snap.100-T1
Valid prediction for pasa_asmbl_10483.p1
Couldn't classify 165719, 165779
Sorry, prediction pasa_asmbl_10496.p1 fails validation.
(CTC)	 CT	165719-165779	GT	TGG
(TGA)	 AG	166418-166479	GT	AGG
(AGC)	 AG	166603-166731	GT	AGG
(GTG)	 AG	166868-166966	GT	AGG
(GAC)	 AG	167073-167155	GT	AGG
(TGA)	 AG	167309-167435	GT	AGG
(GTG)	 AG	167524-167619	GT	AAG
(GGT)	 AG	167739-167861	GT	AGG
(GTA)	 AG	167967-168131	GT	AGG
(GTG)	 AG	168257-168382	GA	AGG
-recovered pasa_asmbl_10496.p1, terminal, 167073, 167155
-recovered pasa_asmbl_10496.p1, terminal, 168257, 168382
-recovered pasa_asmbl_10496.p1, internal, 166418, 166479
-recovered pasa_asmbl_10496.p1, internal, 166603, 166731
-recovered pasa_asmbl_10496.p1, internal, 166868, 166966
-recovered pasa_asmbl_10496.p1, internal, 167073, 167155
-recovered pasa_asmbl_10496.p1, internal, 167309, 167435
-recovered pasa_asmbl_10496.p1, internal, 167524, 167619
-recovered pasa_asmbl_10496.p1, internal, 167739, 167861
-recovered pasa_asmbl_10496.p1, internal, 167967, 168131
Valid prediction for GlimmerHMM_glimmerT_30983-T1
Valid prediction for GlimmerHMM_glimmerT_30987-T1
Valid prediction for HiQ_model.g20560.t1
Valid prediction for Augustus_model.g20570.t1
Valid prediction for GlimmerHMM_glimmerT_30998-T1
Valid prediction for HiQ_model.g20563.t1
Valid prediction for CodingQuarry_transcript_12849-T1
Valid prediction for GlimmerHMM_glimmerT_30993-T1
Valid prediction for pasa_asmbl_10499.p1
Valid prediction for snap_scaffold_13-snap.129-T1
Valid prediction for GlimmerHMM_glimmerT_30989-T1
Valid prediction for CodingQuarry_transcript_12840-T1
Couldn't classify 170331, 170516
Sorry, prediction pasa_asmbl_10497.p1 fails validation.
(CGG)	 AG	170331-170516	GT	AAG
(GTG)	 AG	171108-171314	GT	AGG
(ATC)	 AG	171386-171745	TG	GAT
-recovered pasa_asmbl_10497.p1, terminal, 171386, 171745
-recovered pasa_asmbl_10497.p1, internal, 170331, 170516
-recovered pasa_asmbl_10497.p1, internal, 171108, 171314
Valid prediction for CodingQuarry_transcript_12848-T1
Valid prediction for GlimmerHMM_glimmerT_30981-T1
Valid prediction for HiQ_model.g20571.t1
Valid prediction for HiQ_model.g20572.t1
Valid prediction for GlimmerHMM_glimmerT_30974-T1
Valid prediction for Augustus_model.g20567.t1
Valid prediction for snap_scaffold_13-snap.123-T1
Valid prediction for CodingQuarry_transcript_12842-T1
Valid prediction for GlimmerHMM_glimmerT_30971-T1
Valid prediction for snap_scaffold_13-snap.121-T1
Valid prediction for GlimmerHMM_glimmerT_30976-T1
Valid prediction for GlimmerHMM_glimmerT_30969-T1
Valid prediction for GlimmerHMM_glimmerT_30992-T1
Valid prediction for snap_scaffold_13-snap.106-T1
Valid prediction for snap_scaffold_13-snap.126-T1
Valid prediction for Augustus_model.g20569.t1
Valid prediction for CodingQuarry_transcript_12839-T1
Valid prediction for CodingQuarry_transcript_12844-T1
Valid prediction for HiQ_model.g20562.t1
Valid prediction for snap_scaffold_13-snap.122-T1
Valid prediction for GlimmerHMM_glimmerT_30995-T1
Valid prediction for CodingQuarry_transcript_12841-T1
Valid prediction for snap_scaffold_13-snap.118-T1
Valid prediction for snap_scaffold_13-snap.124-T1
Valid prediction for CodingQuarry_transcript_12843-T1
Valid prediction for pasa_asmbl_10485.p1
Valid prediction for snap_scaffold_13-snap.113-T1
Valid prediction for pasa_asmbl_10498.p1
Valid prediction for GlimmerHMM_glimmerT_31000-T1
Valid prediction for snap_scaffold_13-snap.104-T1
Valid prediction for snap_scaffold_13-snap.116-T1
Valid prediction for GlimmerHMM_glimmerT_30972-T1
Valid prediction for snap_scaffold_13-snap.108-T1
Valid prediction for Augustus_model.g20559.t1
Valid prediction for snap_scaffold_13-snap.117-T1
Valid prediction for Augustus_model.g20574.t1
Valid prediction for Augustus_model.g20568.t1
Valid prediction for snap_scaffold_13-snap.103-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_13-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_30973-T1
Valid prediction for HiQ_model.g20566.t1
Valid prediction for Augustus_model.g20558.t1
Valid prediction for snap_scaffold_13-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_30975-T1
Valid prediction for HiQ_model.g20561.t1
Valid prediction for CodingQuarry_transcript_12850-T1
Valid prediction for GlimmerHMM_glimmerT_30978-T1
Valid prediction for HiQ_model.g20564.t1
Valid prediction for GlimmerHMM_glimmerT_30991-T1
Valid prediction for GlimmerHMM_glimmerT_30999-T1
Valid prediction for GlimmerHMM_glimmerT_31001-T1
Valid prediction for snap_scaffold_13-snap.101-T1
Valid prediction for GlimmerHMM_glimmerT_30996-T1
Valid prediction for snap_scaffold_13-snap.125-T1
Couldn't classify 28873, 29005
Sorry, prediction pasa_asmbl_9369.p1 fails validation.
(ATC)	 TC	28873-29005	GT	ACG
(TAC)	 AG	29204-29379	GT	AGG
(GTG)	 AG	29574-29780	GT	CGG
(GCT)	 AG	29898-29979	GT	CGG
(GAG)	 AG	30145-30338	GT	AGG
(AGT)	 AG	30508-30667	GT	TGG
(GTC)	 AG	31002-31159	GT	AGG
(CTG)	 AG	31277-31380	GT	AGG
(AGG)	 AG	31497-31636	GT	AGG
(TGT)	 AG	31811-32049	GG	AAG
-recovered pasa_asmbl_9369.p1, terminal, 31811, 32049
-recovered pasa_asmbl_9369.p1, internal, 29204, 29379
-recovered pasa_asmbl_9369.p1, internal, 29574, 29780
-recovered pasa_asmbl_9369.p1, internal, 29898, 29979
-recovered pasa_asmbl_9369.p1, internal, 30145, 30338
-recovered pasa_asmbl_9369.p1, internal, 30508, 30667
-recovered pasa_asmbl_9369.p1, internal, 31002, 31159
-recovered pasa_asmbl_9369.p1, internal, 31277, 31380
-recovered pasa_asmbl_9369.p1, internal, 31497, 31636
Valid prediction for CodingQuarry_transcript_12851-T1
Valid prediction for snap_scaffold_13-snap.130-T1
Valid prediction for HiQ_model.g20573.t1
Valid prediction for GlimmerHMM_glimmerT_30984-T1
Valid prediction for GlimmerHMM_glimmerT_30970-T1
Valid prediction for pasa_asmbl_9357.p1
Valid prediction for snap_scaffold_13-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_30986-T1
Valid prediction for HiQ_model.g20575.t1
Valid prediction for GlimmerHMM_glimmerT_30988-T1
Valid prediction for snap_scaffold_13-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_30982-T1
Valid prediction for GlimmerHMM_glimmerT_30990-T1
Valid prediction for GlimmerHMM_glimmerT_30980-T1
Valid prediction for snap_scaffold_13-snap.127-T1
Valid prediction for snap_scaffold_13-snap.111-T1
Valid prediction for snap_scaffold_13-snap.110-T1
Valid prediction for CodingQuarry_transcript_12847-T1
Valid prediction for snap_scaffold_13-snap.112-T1
Valid prediction for CodingQuarry_transcript_12846-T1
Valid prediction for pasa_asmbl_9364.p1
Valid prediction for GlimmerHMM_glimmerT_30997-T1
Valid prediction for CodingQuarry_transcript_12845-T1
Valid prediction for Augustus_model.g20576.t1
Valid prediction for pasa_asmbl_9358.p1
Valid prediction for snap_scaffold_13-snap.105-T1
Valid prediction for GlimmerHMM_glimmerT_31002-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13153, rend_intergenic: 11492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220086
-exon list size: 380


building trellis

0.3    
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0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
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4.5    
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5.2    
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5.8    
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7.9    
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10.7    
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11.3    
11.5    
11.8    
12.0    
12.3    
12.6    
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13.1    
13.4    
13.6    
13.9    
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14.4    
14.7    
14.9    
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15.4    
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17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
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20.4    
20.7    
20.9    
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21.5    
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22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 13153, rend_intergenic: 11492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support