-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_11388128-11666469

-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 GlimmerHMM_glimmerT_10265-T1
Valid prediction for snap_scaffold_4-snap.2482-T1
Valid prediction for snap_scaffold_4-snap.2498-T1
Valid prediction for GlimmerHMM_glimmerT_10254-T1
Valid prediction for GlimmerHMM_glimmerT_10261-T1
Valid prediction for snap_scaffold_4-snap.2495-T1
Valid prediction for GlimmerHMM_glimmerT_10252-T1
Valid prediction for snap_scaffold_4-snap.2477-T1
Valid prediction for Augustus_model.g6681.t1
Valid prediction for GlimmerHMM_glimmerT_10250-T1
Valid prediction for GlimmerHMM_glimmerT_10255-T1
Valid prediction for snap_scaffold_4-snap.2487-T1
Valid prediction for snap_scaffold_4-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_10249-T1
Valid prediction for GlimmerHMM_glimmerT_10272-T1
Valid prediction for GlimmerHMM_glimmerT_10257-T1
Valid prediction for GlimmerHMM_glimmerT_10263-T1
Valid prediction for snap_scaffold_4-snap.2470-T1
Valid prediction for snap_scaffold_4-snap.2471-T1
Valid prediction for Augustus_model.g6677.t1
Valid prediction for GlimmerHMM_glimmerT_10269-T1
Valid prediction for GlimmerHMM_glimmerT_10260-T1
Valid prediction for GlimmerHMM_glimmerT_10259-T1
Valid prediction for snap_scaffold_4-snap.2478-T1
Valid prediction for snap_scaffold_4-snap.2475-T1
Sorry, intron length (6) is less than minimum required (10)

-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_4-snap.2472-T1
Valid prediction for snap_scaffold_4-snap.2492-T1
Valid prediction for snap_scaffold_4-snap.2483-T1
Valid prediction for snap_scaffold_4-snap.2489-T1
Valid prediction for HiQ_model.g6679.t1
Valid prediction for snap_scaffold_4-snap.2500-T1
Valid prediction for Augustus_model.g6671.t1
Valid prediction for snap_scaffold_4-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_10247-T1
Valid prediction for snap_scaffold_4-snap.2474-T1
Valid prediction for snap_scaffold_4-snap.2493-T1
Valid prediction for GlimmerHMM_glimmerT_10258-T1
Valid prediction for Augustus_model.g6674.t1
Valid prediction for snap_scaffold_4-snap.2469-T1
Valid prediction for snap_scaffold_4-snap.2496-T1
Valid prediction for snap_scaffold_4-snap.2479-T1
Valid prediction for snap_scaffold_4-snap.2499-T1
Valid prediction for GlimmerHMM_glimmerT_10267-T1
Couldn't classify 254072, 254212
Sorry, prediction pasa_asmbl_42884.p1 fails validation.
(ACC)	 CG	254072-254212	GT	AGG
(GAC)	 AG	255439-255534	GT	TGG
(TGG)	 AG	256957-257105	GT	AGG
(ACC)	 AG	257275-257447	GT	TGG
(ATC)	 AG	257558-257688	GT	AGG
(AAA)	 AG	257874-257997	GT	CCG
(AGT)	 AG	258174-258418	GT	AGG
(ATT)	 AG	258694-258832	GT	AGG
(GCC)	 AG	259864-259990	GT	AGG
(ATG)	 AG	261857-262061	GT	AGG
(TGT)	 AG	262357-262551	GT	AGG
(TGC)	 AG	262744-262977	GT	AGG
(TGC)	 AG	263286-263433	GT	AGG
(ATA)	 AG	263527-263642	GT	AGG
-recovered pasa_asmbl_42884.p1, initial, 261857, 262061
-recovered pasa_asmbl_42884.p1, terminal, 263527, 263642
-recovered pasa_asmbl_42884.p1, internal, 255439, 255534
-recovered pasa_asmbl_42884.p1, internal, 256957, 257105
-recovered pasa_asmbl_42884.p1, internal, 257275, 257447
-recovered pasa_asmbl_42884.p1, internal, 257558, 257688
-recovered pasa_asmbl_42884.p1, internal, 257874, 257997
-recovered pasa_asmbl_42884.p1, internal, 258174, 258418
-recovered pasa_asmbl_42884.p1, internal, 258694, 258832
-recovered pasa_asmbl_42884.p1, internal, 259864, 259990
-recovered pasa_asmbl_42884.p1, internal, 261857, 262061
-recovered pasa_asmbl_42884.p1, internal, 262357, 262551
-recovered pasa_asmbl_42884.p1, internal, 262744, 262977
-recovered pasa_asmbl_42884.p1, internal, 263286, 263433
-recovered pasa_asmbl_42884.p1, internal, 263527, 263642
Valid prediction for Augustus_model.g6678.t1
Valid prediction for snap_scaffold_4-snap.2481-T1
Valid prediction for GlimmerHMM_glimmerT_10270-T1
Couldn't classify 109298, 109453
Sorry, prediction pasa_asmbl_42886.p1 fails validation.
(ACC)	 CA	109298-109453	GT	TGG
(GGT)	 AG	110979-111972	GT	AGG
(ATC)	 AG	112185-112260	GT	AGG
(CAC)	 AG	113616-113673	TC	GAT
add_exon() Sorry, pasa_asmbl_42886.p1 110979-111972-terminal-3 is invalid.
-recovered pasa_asmbl_42886.p1, terminal, 110979, 111972
-recovered pasa_asmbl_42886.p1, terminal, 113616, 113673
-recovered pasa_asmbl_42886.p1, internal, 110979, 111972
-recovered pasa_asmbl_42886.p1, internal, 112185, 112260
Valid prediction for snap_scaffold_4-snap.2488-T1
Valid prediction for GlimmerHMM_glimmerT_10245-T1
Valid prediction for Augustus_model.g6672.t1
Valid prediction for snap_scaffold_4-snap.2484-T1
Valid prediction for snap_scaffold_4-snap.2486-T1
Valid prediction for snap_scaffold_4-snap.2468-T1
Valid prediction for Augustus_model.g6673.t1
Valid prediction for HiQ_model.g6670.t1
Valid prediction for GlimmerHMM_glimmerT_10246-T1
Valid prediction for GlimmerHMM_glimmerT_10268-T1
Valid prediction for GlimmerHMM_glimmerT_10248-T1
Valid prediction for Augustus_model.g6680.t1
Valid prediction for Augustus_model.g6676.t1
Valid prediction for GlimmerHMM_glimmerT_10271-T1
Valid prediction for Augustus_model.g6682.t1
Valid prediction for snap_scaffold_4-snap.2491-T1
Valid prediction for GlimmerHMM_glimmerT_10262-T1
Valid prediction for snap_scaffold_4-snap.2480-T1
Valid prediction for snap_scaffold_4-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_10253-T1
Valid prediction for snap_scaffold_4-snap.2494-T1
Valid prediction for Augustus_model.g6675.t1
Valid prediction for GlimmerHMM_glimmerT_10266-T1
Valid prediction for GlimmerHMM_glimmerT_10264-T1
Valid prediction for GlimmerHMM_glimmerT_10256-T1
Valid prediction for GlimmerHMM_glimmerT_10251-T1
Valid prediction for snap_scaffold_4-snap.2476-T1
Valid prediction for snap_scaffold_4-snap.2497-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19700, rend_intergenic: 17395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 278342
-exon list size: 226


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.6    
3.1    
3.5    
3.9    
4.4    
4.8    
5.3    
5.7    
6.1    
6.6    
7.0    
7.5    
7.9    
8.3    
8.8    
9.2    
9.6    
10.1    
10.5    
11.0    
11.4    
11.8    
12.3    
12.7    
13.2    
13.6    
14.0    
14.5    
14.9    
15.4    
15.8    
16.2    
16.7    
17.1    
17.5    
18.0    
18.4    
18.9    
19.3    
19.7    
20.2    
20.6    
21.1    
21.5    
21.9    
22.4    
22.8    
23.2    
23.7    
24.1    
24.6    
25.0    
25.4    
25.9    
26.3    
26.8    
27.2    
27.6    
28.1    
28.5    
28.9    
29.4    
29.8    
30.3    
30.7    
31.1    
31.6    
32.0    
32.5    
32.9    
33.3    
33.8    
34.2    
34.6    
35.1    
35.5    
36.0    
36.4    
36.8    
37.3    
37.7    
38.2    
38.6    
39.0    
39.5    
39.9    
40.4    
40.8    
41.2    
41.7    
42.1    
42.5    
43.0    
43.4    
43.9    
44.3    
44.7    
45.2    
45.6    
46.1    
46.5    
46.9    
47.4    
47.8    
48.2    
48.7    
49.1    
49.6    
50.0    
50.4    
50.9    
51.3    
51.8    
52.2    
52.6    
53.1    
53.5    
53.9    
54.4    
54.8    
55.3    
55.7    
56.1    
56.6    
57.0    
57.5    
57.9    
58.3    
58.8    
59.2    
59.6    
60.1    
60.5    
61.0    
61.4    
61.8    
62.3    
62.7    
63.2    
63.6    
64.0    
64.5    
64.9    
65.4    
65.8    
66.2    
66.7    
67.1    
67.5    
68.0    
68.4    
68.9    
69.3    
69.7    
70.2    
70.6    
71.1    
71.5    
71.9    
72.4    
72.8    
73.2    
73.7    
74.1    
74.6    
75.0    
75.4    
75.9    
76.3    
76.8    
77.2    
77.6    
78.1    
78.5    
78.9    
79.4    
79.8    
80.3    
80.7    
81.1    
81.6    
82.0    
82.5    
82.9    
83.3    
83.8    
84.2    
84.6    
85.1    
85.5    
86.0    
86.4    
86.8    
87.3    
87.7    
88.2    
88.6    
89.0    
89.5    
89.9    
90.4    
90.8    
91.2    
91.7    
92.1    
92.5    
93.0    
93.4    
93.9    
94.3    
94.7    
95.2    
95.6    
96.1    
96.5    
96.9    
97.4    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 19700, rend_intergenic: 17395  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