-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_14844559-15000881

-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_9-snap.3021-T1
Valid prediction for snap_scaffold_9-snap.3008-T1
Valid prediction for snap_scaffold_9-snap.3033-T1
Valid prediction for snap_scaffold_9-snap.3009-T1
Valid prediction for GlimmerHMM_glimmerT_23405-T1
Valid prediction for snap_scaffold_9-snap.3003-T1
Valid prediction for GlimmerHMM_glimmerT_23387-T1
Valid prediction for snap_scaffold_9-snap.3012-T1
Valid prediction for Augustus_model.g15579.t1
Valid prediction for GlimmerHMM_glimmerT_23392-T1
Valid prediction for GlimmerHMM_glimmerT_23394-T1
Valid prediction for snap_scaffold_9-snap.3004-T1
Valid prediction for snap_scaffold_9-snap.3002-T1
Valid prediction for GlimmerHMM_glimmerT_23408-T1
Valid prediction for Augustus_model.g15586.t1
Valid prediction for snap_scaffold_9-snap.3017-T1
Valid prediction for snap_scaffold_9-snap.3020-T1
Valid prediction for GlimmerHMM_glimmerT_23407-T1
Valid prediction for snap_scaffold_9-snap.3030-T1
Valid prediction for Augustus_model.g15580.t1
Valid prediction for Augustus_model.g15581.t1
Valid prediction for snap_scaffold_9-snap.3018-T1
Valid prediction for snap_scaffold_9-snap.3015-T1
Valid prediction for snap_scaffold_9-snap.3016-T1
Valid prediction for GlimmerHMM_glimmerT_23385-T1
Valid prediction for snap_scaffold_9-snap.3028-T1
Valid prediction for snap_scaffold_9-snap.3013-T1
Valid prediction for snap_scaffold_9-snap.3032-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_9-snap.3026-T1
Valid prediction for GlimmerHMM_glimmerT_23396-T1
Valid prediction for GlimmerHMM_glimmerT_23399-T1
Valid prediction for snap_scaffold_9-snap.3005-T1
Valid prediction for Augustus_model.g15583.t1
Valid prediction for snap_scaffold_9-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_23397-T1
Valid prediction for GlimmerHMM_glimmerT_23390-T1
Valid prediction for snap_scaffold_9-snap.3029-T1
Couldn't classify 28376, 28406
Sorry, prediction pasa_asmbl_55775.p1 fails validation.
(AGC)	 TT	28376-28406	GT	AGG
(AGG)	 AG	28989-29118	GT	GTG
(GTA)	 AG	29504-29653	GT	TGG
(CTT)	 AG	30566-30635	GT	AGG
(CTG)	 AG	30926-31036	GT	CTG
(AAC)	 AG	31284-31379	GT	AGG
(TGC)	 AG	31534-31668	GT	AGG
(AAA)	 AG	31822-31921	GT	AGG
(GCG)	 AG	32337-32491	GT	AGG
(GTG)	 AG	32588-32713	GT	AGG
(GGT)	 AG	32858-32989	GT	AGG
(GAT)	 AG	33214-33281	GT	AGG
(GTG)	 AG	33447-33535	GT	AGG
(ATG)	 AG	33711-33808	GT	CTG
(GGT)	 AG	34082-34169	GT	CTG
(GGG)	 AG	34522-34617	GT	CGG
(GGG)	 AG	34893-35023	GT	GGG
(GCC)	 AG	35376-35501	CA	AGC
add_exon() Sorry, pasa_asmbl_55775.p1 33711-33808-initial-1 is invalid.
-recovered pasa_asmbl_55775.p1, initial, 33711, 33808
-recovered pasa_asmbl_55775.p1, terminal, 35376, 35501
-recovered pasa_asmbl_55775.p1, internal, 28989, 29118
-recovered pasa_asmbl_55775.p1, internal, 29504, 29653
-recovered pasa_asmbl_55775.p1, internal, 30566, 30635
-recovered pasa_asmbl_55775.p1, internal, 30926, 31036
-recovered pasa_asmbl_55775.p1, internal, 31284, 31379
-recovered pasa_asmbl_55775.p1, internal, 31534, 31668
-recovered pasa_asmbl_55775.p1, internal, 31822, 31921
-recovered pasa_asmbl_55775.p1, internal, 32337, 32491
-recovered pasa_asmbl_55775.p1, internal, 32588, 32713
-recovered pasa_asmbl_55775.p1, internal, 32858, 32989
-recovered pasa_asmbl_55775.p1, internal, 33214, 33281
-recovered pasa_asmbl_55775.p1, internal, 33447, 33535
-recovered pasa_asmbl_55775.p1, internal, 33711, 33808
-recovered pasa_asmbl_55775.p1, internal, 34082, 34169
-recovered pasa_asmbl_55775.p1, internal, 34522, 34617
-recovered pasa_asmbl_55775.p1, internal, 34893, 35023
Valid prediction for snap_scaffold_9-snap.3023-T1
Valid prediction for snap_scaffold_9-snap.3034-T1
Valid prediction for snap_scaffold_9-snap.3010-T1
Valid prediction for snap_scaffold_9-snap.3022-T1
Valid prediction for Augustus_model.g15585.t1
Valid prediction for GlimmerHMM_glimmerT_23401-T1
Valid prediction for snap_scaffold_9-snap.3006-T1
Valid prediction for snap_scaffold_9-snap.3014-T1
Valid prediction for HiQ_model.g15587.t1
Valid prediction for GlimmerHMM_glimmerT_23388-T1
Valid prediction for GlimmerHMM_glimmerT_23393-T1
Valid prediction for snap_scaffold_9-snap.3011-T1
Valid prediction for HiQ_model.g15584.t1
Valid prediction for GlimmerHMM_glimmerT_23400-T1
Valid prediction for GlimmerHMM_glimmerT_23404-T1
Valid prediction for Augustus_model.g15582.t1
Valid prediction for snap_scaffold_9-snap.3019-T1
Valid prediction for Augustus_model.g15577.t1
Valid prediction for snap_scaffold_9-snap.3007-T1
Valid prediction for GlimmerHMM_glimmerT_23389-T1
Valid prediction for GlimmerHMM_glimmerT_23391-T1
Valid prediction for snap_scaffold_9-snap.3031-T1
Valid prediction for GlimmerHMM_glimmerT_23406-T1
Valid prediction for snap_scaffold_9-snap.3027-T1
Valid prediction for Augustus_model.g15588.t1
Valid prediction for Augustus_model.g15578.t1
Valid prediction for GlimmerHMM_glimmerT_23395-T1
Valid prediction for pasa_asmbl_55507.p1
Valid prediction for CodingQuarry_transcript_62409-T1
Valid prediction for GlimmerHMM_glimmerT_23398-T1
Valid prediction for GlimmerHMM_glimmerT_23402-T1
Valid prediction for GlimmerHMM_glimmerT_23403-T1
Valid prediction for snap_scaffold_9-snap.3024-T1
Valid prediction for GlimmerHMM_glimmerT_23386-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14823, rend_intergenic: 12559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30957, rend_intergenic: 29026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40614, rend_intergenic: 31057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46844, rend_intergenic: 45189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64358, rend_intergenic: 47019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85435, rend_intergenic: 80938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120333, rend_intergenic: 111622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132791, rend_intergenic: 124089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153246, rend_intergenic: 148056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156323
-exon list size: 248


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.4    
4.8    
5.2    
5.6    
6.0    
6.4    
6.8    
7.2    
7.6    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.8    
13.2    
13.6    
14.0    
14.4    
14.8    
15.2    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
18.0    
18.4    
18.8    
19.2    
19.6    
20.0    
20.4    
20.8    
21.2    
21.6    
22.0    
22.4    
22.8    
23.2    
23.6    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.4    
26.8    
27.2    
27.6    
28.0    
28.4    
28.8    
29.2    
29.6    
30.0    
30.4    
30.8    
31.2    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.6    
36.0    
36.4    
36.8    
37.2    
37.6    
38.0    
38.4    
38.8    
39.2    
39.6    
40.0    
40.4    
40.8    
41.2    
41.6    
42.0    
42.4    
42.8    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
46.0    
46.4    
46.8    
47.2    
47.6    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.4    
52.8    
53.2    
53.6    
54.0    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.2    
57.6    
58.0    
58.4    
58.8    
59.2    
59.6    
60.0    
60.4    
60.8    
61.2    
61.6    
62.0    
62.4    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.8    
69.2    
69.6    
70.0    
70.4    
70.8    
71.2    
71.6    
72.0    
72.4    
72.8    
73.2    
73.6    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.4    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.2    
79.6    
80.0    
80.4    
80.8    
81.2    
81.6    
82.0    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.8    
85.2    
85.6    
86.0    
86.4    
86.8    
87.2    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.4    
92.8    
93.2    
93.6    
94.0    
94.4    
94.8    
95.2    
95.6    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 14823, rend_intergenic: 12559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30957, rend_intergenic: 29026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40614, rend_intergenic: 31057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46844, rend_intergenic: 45189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64358, rend_intergenic: 47019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85435, rend_intergenic: 80938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120333, rend_intergenic: 111622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132791, rend_intergenic: 124089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153246, rend_intergenic: 148056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support