-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_1604829-1733696

-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_23-snap.268-T1
Valid prediction for snap_scaffold_23-snap.245-T1
Valid prediction for Augustus_model.g33741.t1
Valid prediction for snap_scaffold_23-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_50526-T1
Valid prediction for Augustus_model.g33744.t1
Valid prediction for CodingQuarry_transcript_35559-T1
Valid prediction for GlimmerHMM_glimmerT_50525-T1
Valid prediction for GlimmerHMM_glimmerT_50505-T1
Valid prediction for Augustus_model.g33751.t1
Valid prediction for Augustus_model.g33755.t1
Valid prediction for Augustus_model.g33753.t1
Valid prediction for GlimmerHMM_glimmerT_50520-T1
Valid prediction for snap_scaffold_23-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_50506-T1
Valid prediction for Augustus_model.g33740.t1
Valid prediction for Augustus_model.g33754.t1
Valid prediction for snap_scaffold_23-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_50523-T1
Valid prediction for snap_scaffold_23-snap.248-T1
Valid prediction for pasa_asmbl_31348.p1
Valid prediction for snap_scaffold_23-snap.254-T1
Valid prediction for snap_scaffold_23-snap.247-T1
Valid prediction for GlimmerHMM_glimmerT_50509-T1
Valid prediction for snap_scaffold_23-snap.275-T1
Valid prediction for snap_scaffold_23-snap.257-T1
Valid prediction for Augustus_model.g33742.t1
Valid prediction for GlimmerHMM_glimmerT_50514-T1
Valid prediction for snap_scaffold_23-snap.283-T1
Valid prediction for GlimmerHMM_glimmerT_50528-T1
Valid prediction for GlimmerHMM_glimmerT_50515-T1
Valid prediction for GlimmerHMM_glimmerT_50516-T1
Valid prediction for snap_scaffold_23-snap.266-T1
Valid prediction for snap_scaffold_23-snap.259-T1
Valid prediction for Augustus_model.g33746.t1
Valid prediction for GlimmerHMM_glimmerT_50508-T1
Valid prediction for GlimmerHMM_glimmerT_50511-T1
Valid prediction for snap_scaffold_23-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_50522-T1
Valid prediction for snap_scaffold_23-snap.279-T1
Valid prediction for snap_scaffold_23-snap.282-T1
Valid prediction for CodingQuarry_transcript_35558-T1
Valid prediction for snap_scaffold_23-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_50527-T1
Valid prediction for snap_scaffold_23-snap.270-T1
Valid prediction for snap_scaffold_23-snap.261-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_23-snap.277-T1
Valid prediction for Augustus_model.g33747.t1
Valid prediction for Augustus_model.g33743.t1
Valid prediction for snap_scaffold_23-snap.260-T1
Valid prediction for snap_scaffold_23-snap.250-T1
Valid prediction for CodingQuarry_transcript_35557-T1
Couldn't classify 80465, 80603
Couldn't classify 80977, 81089
Sorry, prediction pasa_asmbl_30664.p1 fails validation.
(GAG)	 AG	80465-80603	GT	AGG
(ATT)	 AG	80778-80891	GT	AGG
(AAA)	 AG	80977-81089	GG	AAG
-recovered pasa_asmbl_30664.p1, internal, 80465, 80603
-recovered pasa_asmbl_30664.p1, internal, 80778, 80891
Valid prediction for GlimmerHMM_glimmerT_50513-T1
Valid prediction for snap_scaffold_23-snap.265-T1
Valid prediction for Augustus_model.g33749.t1
Valid prediction for snap_scaffold_23-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_50512-T1
Valid prediction for snap_scaffold_23-snap.256-T1
Valid prediction for snap_scaffold_23-snap.269-T1
Valid prediction for snap_scaffold_23-snap.253-T1
Valid prediction for CodingQuarry_transcript_35561-T1
Valid prediction for snap_scaffold_23-snap.258-T1
Valid prediction for CodingQuarry_transcript_35560-T1
Valid prediction for pasa_asmbl_30673.p1
Valid prediction for snap_scaffold_23-snap.280-T1
Valid prediction for snap_scaffold_23-snap.255-T1
Valid prediction for GlimmerHMM_glimmerT_50507-T1
Valid prediction for snap_scaffold_23-snap.264-T1
Valid prediction for Augustus_model.g33748.t1
Valid prediction for GlimmerHMM_glimmerT_50517-T1
Couldn't classify 55246, 55442
Sorry, prediction pasa_asmbl_30671.p1 fails validation.
(ATG)	 AA	54875-55016	GT	AGG
(TGG)	 AG	55246-55442	GT	GGG
-recovered pasa_asmbl_30671.p1, initial, 54875, 55016
-recovered pasa_asmbl_30671.p1, internal, 55246, 55442
Valid prediction for snap_scaffold_23-snap.263-T1
Valid prediction for GlimmerHMM_glimmerT_50510-T1
Valid prediction for GlimmerHMM_glimmerT_50519-T1
Valid prediction for snap_scaffold_23-snap.249-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 58283, 58428
Couldn't classify 62135, 62277
Sorry, prediction pasa_asmbl_30669.p1 fails validation.
(CTG)	 CG	58283-58428	GT	GAG
(GAT)	 AG	59463-59594	GT	AGG
(CCC)	 AG	59960-60087	GT	CGG
(ACA)	 AG	62135-62277	TA	GGT
-recovered pasa_asmbl_30669.p1, internal, 59463, 59594
-recovered pasa_asmbl_30669.p1, internal, 59960, 60087
Valid prediction for GlimmerHMM_glimmerT_50518-T1
Valid prediction for Augustus_model.g33745.t1
Valid prediction for snap_scaffold_23-snap.262-T1
Couldn't classify 71112, 71217
Couldn't classify 76188, 76543
Sorry, prediction pasa_asmbl_30666.p1 fails validation.
(TCG)	 CG	71112-71217	GT	CGG
(GCG)	 AG	72546-72720	GT	AGG
(ATA)	 AG	72946-73073	GT	TGG
(GAG)	 AG	73226-73519	GT	GGG
(GTA)	 AG	76188-76543	GG	GCG
-recovered pasa_asmbl_30666.p1, internal, 72546, 72720
-recovered pasa_asmbl_30666.p1, internal, 72946, 73073
-recovered pasa_asmbl_30666.p1, internal, 73226, 73519
Valid prediction for snap_scaffold_23-snap.281-T1
Valid prediction for snap_scaffold_23-snap.267-T1
Valid prediction for pasa_asmbl_30672.p1
Valid prediction for HiQ_model.g33750.t1
Valid prediction for GlimmerHMM_glimmerT_50524-T1
Valid prediction for snap_scaffold_23-snap.251-T1
Valid prediction for snap_scaffold_23-snap.273-T1
Valid prediction for HiQ_model.g33752.t1
Couldn't classify 76634, 76880
Couldn't classify 79532, 79924
Sorry, prediction pasa_asmbl_30665.p1 fails validation.
(CCT)	 CT	76634-76880	GT	AGG
(TGG)	 AG	79114-79301	GT	AGG
(GTG)	 AG	79532-79924	CA	CCC
-recovered pasa_asmbl_30665.p1, internal, 79114, 79301
Valid prediction for GlimmerHMM_glimmerT_50521-T1
Valid prediction for snap_scaffold_23-snap.271-T1
Valid prediction for snap_scaffold_23-snap.284-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22023, rend_intergenic: 15527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31298, rend_intergenic: 25296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33520, rend_intergenic: 31615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37902, rend_intergenic: 33527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46040, rend_intergenic: 44732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47394, rend_intergenic: 47290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57985, rend_intergenic: 54633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65207, rend_intergenic: 59926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71361, rend_intergenic: 69134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86838, rend_intergenic: 83918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92004, rend_intergenic: 90021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108200, rend_intergenic: 103761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109067, rend_intergenic: 108396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113564, rend_intergenic: 109350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118848, rend_intergenic: 113634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126324, rend_intergenic: 121954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128868
-exon list size: 352


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 22023, rend_intergenic: 15527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31298, rend_intergenic: 25296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33520, rend_intergenic: 31615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37902, rend_intergenic: 33527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46040, rend_intergenic: 44732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47394, rend_intergenic: 47290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57985, rend_intergenic: 54633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65207, rend_intergenic: 59926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71361, rend_intergenic: 69134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86838, rend_intergenic: 83918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92004, rend_intergenic: 90021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108200, rend_intergenic: 103761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109067, rend_intergenic: 108396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113564, rend_intergenic: 109350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118848, rend_intergenic: 113634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126324, rend_intergenic: 121954  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