-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_14529012-14656940

-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.2809-T1
Valid prediction for Augustus_model.g21882.t1
Valid prediction for snap_scaffold_13-snap.2806-T1
Valid prediction for GlimmerHMM_glimmerT_32810-T1
Valid prediction for GlimmerHMM_glimmerT_32804-T1
Valid prediction for GlimmerHMM_glimmerT_32795-T1
Valid prediction for snap_scaffold_13-snap.2794-T1
Valid prediction for snap_scaffold_13-snap.2785-T1
Valid prediction for Augustus_model.g21887.t1
Valid prediction for snap_scaffold_13-snap.2807-T1
Valid prediction for GlimmerHMM_glimmerT_32796-T1
Valid prediction for GlimmerHMM_glimmerT_32801-T1
Valid prediction for Augustus_model.g21890.t1
Valid prediction for snap_scaffold_13-snap.2800-T1
Couldn't classify 122066, 122139
Sorry, prediction pasa_asmbl_11462.p1 fails validation.
(GAA)	 GA	122066-122139	GT	GGG
(GGG)	 AG	122558-122724	GT	TGG
(GAG)	 AG	122974-123224	GT	AGG
(GTG)	 AG	123337-123539	GT	AGG
(TGC)	 AG	123981-124233	GT	CGG
(GCT)	 AG	124416-124615	GT	AGG
(GAG)	 AG	125006-125051	GT	AGG
(GTG)	 AG	125282-125311	AT	AGA
-recovered pasa_asmbl_11462.p1, terminal, 125282, 125311
-recovered pasa_asmbl_11462.p1, internal, 122558, 122724
-recovered pasa_asmbl_11462.p1, internal, 122974, 123224
-recovered pasa_asmbl_11462.p1, internal, 123337, 123539
-recovered pasa_asmbl_11462.p1, internal, 123981, 124233
-recovered pasa_asmbl_11462.p1, internal, 124416, 124615
-recovered pasa_asmbl_11462.p1, internal, 125006, 125051
Valid prediction for snap_scaffold_13-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_32811-T1
Valid prediction for GlimmerHMM_glimmerT_32797-T1
Valid prediction for snap_scaffold_13-snap.2786-T1
Valid prediction for GlimmerHMM_glimmerT_32805-T1
Valid prediction for snap_scaffold_13-snap.2797-T1
Valid prediction for snap_scaffold_13-snap.2798-T1
Valid prediction for Augustus_model.g21889.t1
Valid prediction for snap_scaffold_13-snap.2799-T1
Valid prediction for snap_scaffold_13-snap.2791-T1
Valid prediction for snap_scaffold_13-snap.2793-T1
Couldn't classify 121267, 121453
Sorry, prediction pasa_asmbl_11461.p1 fails validation.
(ATG)	 CC	117995-118144	GT	AGG
(GAG)	 AG	118391-118522	GT	AGG
(GTT)	 AG	118813-119009	GT	AAG
(ACT)	 AG	121267-121453	GT	CGG
-recovered pasa_asmbl_11461.p1, initial, 117995, 118144
-recovered pasa_asmbl_11461.p1, internal, 118391, 118522
-recovered pasa_asmbl_11461.p1, internal, 118813, 119009
-recovered pasa_asmbl_11461.p1, internal, 121267, 121453
Valid prediction for snap_scaffold_13-snap.2803-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.2795-T1
Valid prediction for snap_scaffold_13-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_32799-T1
Valid prediction for snap_scaffold_13-snap.2802-T1
Valid prediction for GlimmerHMM_glimmerT_32800-T1
Valid prediction for snap_scaffold_13-snap.2787-T1
Valid prediction for snap_scaffold_13-snap.2790-T1
Valid prediction for snap_scaffold_13-snap.2792-T1
Valid prediction for HiQ_model.g21885.t1
Valid prediction for GlimmerHMM_glimmerT_32807-T1
Valid prediction for GlimmerHMM_glimmerT_32803-T1
Valid prediction for Augustus_model.g21881.t1
Valid prediction for snap_scaffold_13-snap.2784-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g21884.t1
Valid prediction for GlimmerHMM_glimmerT_32802-T1
Valid prediction for GlimmerHMM_glimmerT_32809-T1
Couldn't classify 82315, 82597
Sorry, prediction pasa_asmbl_10320.p1 fails validation.
(CTG)	 CT	82315-82597	GT	AGG
(GCT)	 AG	82864-83078	AC	AGA
-recovered pasa_asmbl_10320.p1, terminal, 82864, 83078
Valid prediction for CodingQuarry_transcript_13315-T1
Valid prediction for GlimmerHMM_glimmerT_32808-T1
Valid prediction for GlimmerHMM_glimmerT_32798-T1
Valid prediction for snap_scaffold_13-snap.2804-T1
Valid prediction for snap_scaffold_13-snap.2808-T1
Valid prediction for HiQ_model.g21888.t1
Valid prediction for GlimmerHMM_glimmerT_32806-T1
Couldn't classify 72098, 72369
Couldn't classify 75358, 75474
Sorry, prediction pasa_asmbl_10203.p1 fails validation.
(ACC)	 CG	72098-72369	GT	CGG
(TGA)	 AG	74059-74179	GT	AGG
(GAA)	 AG	74342-74371	GT	AGG
(CTG)	 AG	75358-75474	GT	AGG
-recovered pasa_asmbl_10203.p1, internal, 74059, 74179
-recovered pasa_asmbl_10203.p1, internal, 74342, 74371
-recovered pasa_asmbl_10203.p1, internal, 75358, 75474
Valid prediction for HiQ_model.g21883.t1
Valid prediction for snap_scaffold_13-snap.2796-T1
Valid prediction for snap_scaffold_13-snap.2789-T1
Valid prediction for snap_scaffold_13-snap.2805-T1
Valid prediction for Augustus_model.g21886.t1
Valid prediction for pasa_asmbl_10198.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25346, rend_intergenic: 21031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32574, rend_intergenic: 30535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50298, rend_intergenic: 46053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52623, rend_intergenic: 50957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74444, rend_intergenic: 63953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88688, rend_intergenic: 76922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98620, rend_intergenic: 90467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102829, rend_intergenic: 98729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108867, rend_intergenic: 103328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115355, rend_intergenic: 109909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122705, rend_intergenic: 117995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 127929
-exon list size: 236


building trellis

0.4    
0.8    
1.3    
1.7    
2.1    
2.5    
2.9    
3.4    
3.8    
4.2    
4.6    
5.0    
5.5    
5.9    
6.3    
6.7    
7.1    
7.6    
8.0    
8.4    
8.8    
9.2    
9.7    
10.1    
10.5    
10.9    
11.3    
11.8    
12.2    
12.6    
13.0    
13.4    
13.9    
14.3    
14.7    
15.1    
15.5    
16.0    
16.4    
16.8    
17.2    
17.6    
18.1    
18.5    
18.9    
19.3    
19.7    
20.2    
20.6    
21.0    
21.4    
21.8    
22.3    
22.7    
23.1    
23.5    
23.9    
24.4    
24.8    
25.2    
25.6    
26.1    
26.5    
26.9    
27.3    
27.7    
28.2    
28.6    
29.0    
29.4    
29.8    
30.3    
30.7    
31.1    
31.5    
31.9    
32.4    
32.8    
33.2    
33.6    
34.0    
34.5    
34.9    
35.3    
35.7    
36.1    
36.6    
37.0    
37.4    
37.8    
38.2    
38.7    
39.1    
39.5    
39.9    
40.3    
40.8    
41.2    
41.6    
42.0    
42.4    
42.9    
43.3    
43.7    
44.1    
44.5    
45.0    
45.4    
45.8    
46.2    
46.6    
47.1    
47.5    
47.9    
48.3    
48.7    
49.2    
49.6    
50.0    
50.4    
50.8    
51.3    
51.7    
52.1    
52.5    
52.9    
53.4    
53.8    
54.2    
54.6    
55.0    
55.5    
55.9    
56.3    
56.7    
57.1    
57.6    
58.0    
58.4    
58.8    
59.2    
59.7    
60.1    
60.5    
60.9    
61.3    
61.8    
62.2    
62.6    
63.0    
63.4    
63.9    
64.3    
64.7    
65.1    
65.5    
66.0    
66.4    
66.8    
67.2    
67.6    
68.1    
68.5    
68.9    
69.3    
69.7    
70.2    
70.6    
71.0    
71.4    
71.8    
72.3    
72.7    
73.1    
73.5    
73.9    
74.4    
74.8    
75.2    
75.6    
76.1    
76.5    
76.9    
77.3    
77.7    
78.2    
78.6    
79.0    
79.4    
79.8    
80.3    
80.7    
81.1    
81.5    
81.9    
82.4    
82.8    
83.2    
83.6    
84.0    
84.5    
84.9    
85.3    
85.7    
86.1    
86.6    
87.0    
87.4    
87.8    
88.2    
88.7    
89.1    
89.5    
89.9    
90.3    
90.8    
91.2    
91.6    
92.0    
92.4    
92.9    
93.3    
93.7    
94.1    
94.5    
95.0    
95.4    
95.8    
96.2    
96.6    
97.1    
97.5    
97.9    
98.3    
98.7    
99.2    
99.6    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 25346, rend_intergenic: 21031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32574, rend_intergenic: 30535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50298, rend_intergenic: 46053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52623, rend_intergenic: 50957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74444, rend_intergenic: 63953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88688, rend_intergenic: 76922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98620, rend_intergenic: 90467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102829, rend_intergenic: 98729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108867, rend_intergenic: 103328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115355, rend_intergenic: 109909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122705, rend_intergenic: 117995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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