-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_13811987-14065075

-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_10534-T1
Valid prediction for Augustus_model.g6892.t1
Valid prediction for pasa_asmbl_41835.p1
Valid prediction for snap_scaffold_4-snap.2837-T1
Couldn't classify 6122, 6280
Sorry, prediction pasa_asmbl_41826.p1 fails validation.
(AGG)	 AC	6122-6280	GT	AGG
(TTG)	 AG	6576-6701	GT	AGG
(GGT)	 AG	6877-7047	GT	AGG
(CTG)	 AG	7192-7317	GT	AGG
(CTG)	 AG	7494-7714	GT	AGG
(GCT)	 AG	7956-8259	GT	AGG
(GAC)	 AG	8405-8512	GT	CTG
(ATC)	 AG	8629-8748	GT	AGG
(GAG)	 AG	8918-8974	GT	TGG
(GCG)	 AG	9095-9292	GT	AGG
(GGA)	 AG	9612-9647	AA	AGA
-recovered pasa_asmbl_41826.p1, terminal, 9612, 9647
-recovered pasa_asmbl_41826.p1, internal, 6576, 6701
-recovered pasa_asmbl_41826.p1, internal, 6877, 7047
-recovered pasa_asmbl_41826.p1, internal, 7192, 7317
-recovered pasa_asmbl_41826.p1, internal, 7494, 7714
-recovered pasa_asmbl_41826.p1, internal, 7956, 8259
-recovered pasa_asmbl_41826.p1, internal, 8405, 8512
-recovered pasa_asmbl_41826.p1, internal, 8629, 8748
-recovered pasa_asmbl_41826.p1, internal, 8918, 8974
-recovered pasa_asmbl_41826.p1, internal, 9095, 9292
Valid prediction for GlimmerHMM_glimmerT_10518-T1
Valid prediction for CodingQuarry_transcript_49214-T1
Couldn't classify 181487, 181500
Sorry, prediction pasa_asmbl_41833.p1 fails validation.
(TTA)	 AA	181487-181500	GT	GAG
(GTA)	 AG	181664-181848	GT	AGG
(GTA)	 AG	182060-182172	CC	AAC
-recovered pasa_asmbl_41833.p1, terminal, 182060, 182172
-recovered pasa_asmbl_41833.p1, internal, 181664, 181848
Valid prediction for snap_scaffold_4-snap.2840-T1
Valid prediction for GlimmerHMM_glimmerT_10531-T1
Valid prediction for snap_scaffold_4-snap.2843-T1
Valid prediction for GlimmerHMM_glimmerT_10538-T1
Valid prediction for snap_scaffold_4-snap.2852-T1
Valid prediction for snap_scaffold_4-snap.2856-T1
Valid prediction for HiQ_model.g6885.t1
Valid prediction for Augustus_model.g6888.t1
Valid prediction for pasa_asmbl_41834.p1
Valid prediction for snap_scaffold_4-snap.2842-T1
Valid prediction for GlimmerHMM_glimmerT_10532-T1
Valid prediction for CodingQuarry_transcript_49213-T1
Valid prediction for GlimmerHMM_glimmerT_10543-T1
Valid prediction for GlimmerHMM_glimmerT_10544-T1
Valid prediction for snap_scaffold_4-snap.2847-T1
Valid prediction for GlimmerHMM_glimmerT_10522-T1
Valid prediction for GlimmerHMM_glimmerT_10536-T1
Valid prediction for GlimmerHMM_glimmerT_10530-T1
Valid prediction for snap_scaffold_4-snap.2854-T1
Valid prediction for pasa_asmbl_41829.p1
Valid prediction for snap_scaffold_4-snap.2866-T1
Valid prediction for snap_scaffold_4-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_10523-T1
Valid prediction for snap_scaffold_4-snap.2841-T1
Valid prediction for HiQ_model.g6897.t1
Valid prediction for GlimmerHMM_glimmerT_10520-T1
Valid prediction for GlimmerHMM_glimmerT_10528-T1
Valid prediction for GlimmerHMM_glimmerT_10525-T1
Valid prediction for Augustus_model.g6887.t1
Valid prediction for snap_scaffold_4-snap.2839-T1
Valid prediction for snap_scaffold_4-snap.2849-T1
Valid prediction for Augustus_model.g6882.t1
Couldn't classify 74437, 75159
Sorry, prediction pasa_asmbl_43023.p1 fails validation.
(GTT)	 CC	74437-75159	TA	AAT
Valid prediction for HiQ_model.g6902.t1
Valid prediction for HiQ_model.g6903.t1
Valid prediction for snap_scaffold_4-snap.2859-T1
Valid prediction for snap_scaffold_4-snap.2865-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10529-T1
Valid prediction for Augustus_model.g6894.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_4-snap.2863-T1
Valid prediction for snap_scaffold_4-snap.2844-T1
Valid prediction for GlimmerHMM_glimmerT_10545-T1
Valid prediction for pasa_asmbl_43025.p1
Valid prediction for GlimmerHMM_glimmerT_10539-T1
Valid prediction for snap_scaffold_4-snap.2838-T1
Valid prediction for snap_scaffold_4-snap.2861-T1
Valid prediction for snap_scaffold_4-snap.2860-T1
Valid prediction for snap_scaffold_4-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_10537-T1
Valid prediction for GlimmerHMM_glimmerT_10542-T1
Valid prediction for snap_scaffold_4-snap.2845-T1
Valid prediction for snap_scaffold_4-snap.2862-T1
Valid prediction for GlimmerHMM_glimmerT_10535-T1
Valid prediction for HiQ_model.g6896.t1
Valid prediction for Augustus_model.g6883.t1
Couldn't classify 236478, 236642
Sorry, prediction pasa_asmbl_43011.p1 fails validation.
(GGG)	 CA	236478-236642	GT	CGG
(ATG)	 AG	237080-237182	GT	GGG
(GTT)	 AG	237385-237531	GT	GAG
(TCT)	 AG	237644-237775	GT	CGG
(AAT)	 AG	237947-238075	GT	ACG
(AGT)	 AG	238296-238421	GT	AGG
(AGC)	 AG	238671-238880	GT	AGG
(ATG)	 AG	238966-239075	GT	AGG
(AAC)	 AG	239236-239362	GT	AGG
(GAG)	 AG	239540-239602	GT	AGG
(AGC)	 AG	239813-240007	GT	AGG
(AAC)	 AG	240710-240852	CA	GAC
-recovered pasa_asmbl_43011.p1, initial, 237080, 237182
-recovered pasa_asmbl_43011.p1, initial, 238966, 239075
-recovered pasa_asmbl_43011.p1, terminal, 240710, 240852
-recovered pasa_asmbl_43011.p1, internal, 237080, 237182
-recovered pasa_asmbl_43011.p1, internal, 237385, 237531
-recovered pasa_asmbl_43011.p1, internal, 237644, 237775
-recovered pasa_asmbl_43011.p1, internal, 237947, 238075
-recovered pasa_asmbl_43011.p1, internal, 238296, 238421
-recovered pasa_asmbl_43011.p1, internal, 238671, 238880
-recovered pasa_asmbl_43011.p1, internal, 238966, 239075
-recovered pasa_asmbl_43011.p1, internal, 239236, 239362
-recovered pasa_asmbl_43011.p1, internal, 239540, 239602
-recovered pasa_asmbl_43011.p1, internal, 239813, 240007
Valid prediction for GlimmerHMM_glimmerT_10526-T1
Valid prediction for snap_scaffold_4-snap.2867-T1
Valid prediction for GlimmerHMM_glimmerT_10540-T1
Valid prediction for CodingQuarry_transcript_49210-T1
Couldn't classify 187920, 188099
Sorry, prediction pasa_asmbl_43019.p1 fails validation.
(GGC)	 CA	187920-188099	GT	TGG
(ACA)	 AG	188447-188467	GT	TGG
(AAT)	 AG	189405-189522	GT	TGG
(AGT)	 AG	189815-189986	GT	GTG
(CAT)	 AG	190377-190445	GT	AGG
(CAT)	 AG	192380-192430	GT	TGG
(GCC)	 AG	193913-194339	AG	AAA
-recovered pasa_asmbl_43019.p1, terminal, 193913, 194339
-recovered pasa_asmbl_43019.p1, internal, 188447, 188467
-recovered pasa_asmbl_43019.p1, internal, 189405, 189522
-recovered pasa_asmbl_43019.p1, internal, 189815, 189986
-recovered pasa_asmbl_43019.p1, internal, 190377, 190445
-recovered pasa_asmbl_43019.p1, internal, 192380, 192430
Valid prediction for GlimmerHMM_glimmerT_10527-T1
Valid prediction for CodingQuarry_transcript_49211-T1
Valid prediction for Augustus_model.g6900.t1
Valid prediction for snap_scaffold_4-snap.2855-T1
Valid prediction for HiQ_model.g6891.t1
Valid prediction for Augustus_model.g6895.t1
Valid prediction for Augustus_model.g6893.t1
Valid prediction for Augustus_model.g6884.t1
Valid prediction for snap_scaffold_4-snap.2857-T1
Valid prediction for GlimmerHMM_glimmerT_10533-T1
Valid prediction for Augustus_model.g6899.t1
Valid prediction for Augustus_model.g6905.t1
Valid prediction for Augustus_model.g6904.t1
Valid prediction for snap_scaffold_4-snap.2868-T1
Valid prediction for Augustus_model.g6889.t1
Valid prediction for Augustus_model.g6901.t1
Valid prediction for GlimmerHMM_glimmerT_10521-T1
Valid prediction for HiQ_model.g6898.t1
Couldn't classify 231071, 231162
Sorry, prediction pasa_asmbl_43538.p1 fails validation.
(ATG)	 TA	230312-230409	GT	AGG
(TTT)	 AG	230564-230665	GT	AGG
(GGT)	 AG	230765-230865	GT	CCG
(CTC)	 AG	231071-231162	GG	GTG
-recovered pasa_asmbl_43538.p1, initial, 230312, 230409
-recovered pasa_asmbl_43538.p1, internal, 230564, 230665
-recovered pasa_asmbl_43538.p1, internal, 230765, 230865
Valid prediction for CodingQuarry_transcript_49207-T1
Valid prediction for snap_scaffold_4-snap.2858-T1
Valid prediction for snap_scaffold_4-snap.2848-T1
Valid prediction for Augustus_model.g6890.t1
Valid prediction for snap_scaffold_4-snap.2851-T1
Valid prediction for snap_scaffold_4-snap.2850-T1
Couldn't classify 234271, 234518
Couldn't classify 236204, 236284
Sorry, prediction pasa_asmbl_43015.p1 fails validation.
(GCC)	 CA	234271-234518	GT	CTG
(TTG)	 AG	235124-235229	GT	CGG
(GGT)	 AG	235318-235454	GT	AGG
(GTG)	 AG	235571-235783	GT	AGG
(CTG)	 AG	235915-236089	GT	CGG
(GGG)	 AG	236204-236284	GA	TGG
-recovered pasa_asmbl_43015.p1, internal, 235124, 235229
-recovered pasa_asmbl_43015.p1, internal, 235318, 235454
-recovered pasa_asmbl_43015.p1, internal, 235571, 235783
-recovered pasa_asmbl_43015.p1, internal, 235915, 236089
Valid prediction for snap_scaffold_4-snap.2846-T1
Valid prediction for Augustus_model.g6886.t1
Valid prediction for GlimmerHMM_glimmerT_10519-T1
Valid prediction for CodingQuarry_transcript_49209-T1
Valid prediction for CodingQuarry_transcript_49205-T1
Valid prediction for GlimmerHMM_glimmerT_10524-T1
Valid prediction for GlimmerHMM_glimmerT_10541-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19517, rend_intergenic: 18839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81143, rend_intergenic: 76063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253089
-exon list size: 317


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 19517, rend_intergenic: 18839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81143, rend_intergenic: 76063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support