-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_1662814-1733696

-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 GlimmerHMM_glimmerT_51724-T1
Valid prediction for Augustus_model.g34756.t1
Valid prediction for GeneMark_model.89897_t
Valid prediction for snap_scaffold_23-snap.281-T1
Valid prediction for GlimmerHMM_glimmerT_51726-T1
Valid prediction for GeneMark_model.89886_t
Valid prediction for snap_scaffold_23-snap.285-T1
Valid prediction for GeneMark_model.89888_t
Valid prediction for snap_scaffold_23-snap.266-T1
Valid prediction for GeneMark_model.89895_t
Valid prediction for GeneMark_model.89905_t
Valid prediction for Augustus_model.g34758.t1
Valid prediction for CodingQuarry_transcript_35490-T1
Valid prediction for GeneMark_model.89893_t
Valid prediction for snap_scaffold_23-snap.288-T1
Valid prediction for GeneMark_model.89898_t
Valid prediction for snap_scaffold_23-snap.273-T1
Valid prediction for GlimmerHMM_glimmerT_51725-T1
Valid prediction for GeneMark_model.89900_t
Valid prediction for GeneMark_model.89907_t
Valid prediction for snap_scaffold_23-snap.280-T1
Valid prediction for GlimmerHMM_glimmerT_51728-T1
Valid prediction for Augustus_model.g34754.t1
Valid prediction for Augustus_model.g34757.t1
Valid prediction for snap_scaffold_23-snap.275-T1
Valid prediction for snap_scaffold_23-snap.271-T1
Valid prediction for GeneMark_model.89903_t
Valid prediction for GlimmerHMM_glimmerT_51722-T1
Valid prediction for GeneMark_model.89884_t
Valid prediction for Augustus_model.g34749.t1
Valid prediction for GeneMark_model.89889_t
Valid prediction for GlimmerHMM_glimmerT_51718-T1
Valid prediction for snap_scaffold_23-snap.277-T1
Valid prediction for Augustus_model.g34759.t1
Valid prediction for snap_scaffold_23-snap.282-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 GeneMark_model.89908_t
Valid prediction for GeneMark_model.89899_t
Valid prediction for GlimmerHMM_glimmerT_51719-T1
Couldn't classify 58283, 58428
Couldn't classify 62135, 62277
Sorry, prediction pasa_asmbl_31386.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_31386.p1, internal, 59463, 59594
-recovered pasa_asmbl_31386.p1, internal, 59960, 60087
Valid prediction for snap_scaffold_23-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_51721-T1
Valid prediction for GeneMark_model.89890_t
Valid prediction for GeneMark_model.89891_t
Valid prediction for GeneMark_model.89885_t
Valid prediction for snap_scaffold_23-snap.267-T1
Valid prediction for GeneMark_model.89902_t
Valid prediction for CodingQuarry_transcript_35492-T1
Valid prediction for GeneMark_model.89896_t
Valid prediction for snap_scaffold_23-snap.279-T1
Valid prediction for Augustus_model.g34752.t1
Valid prediction for snap_scaffold_23-snap.270-T1
Valid prediction for GeneMark_model.89892_t
Valid prediction for GlimmerHMM_glimmerT_51723-T1
Valid prediction for snap_scaffold_23-snap.284-T1
Valid prediction for HiQ_model.g34755.t1
Valid prediction for snap_scaffold_23-snap.268-T1
Valid prediction for GeneMark_model.89904_t
Valid prediction for GeneMark_model.89887_t
Valid prediction for CodingQuarry_transcript_35491-T1
Valid prediction for HiQ_model.g34753.t1
Valid prediction for Augustus_model.g34750.t1
Valid prediction for GlimmerHMM_glimmerT_51720-T1
Valid prediction for snap_scaffold_23-snap.272-T1
Valid prediction for pasa_asmbl_31391.p1
Valid prediction for snap_scaffold_23-snap.276-T1
Valid prediction for GeneMark_model.89906_t
Valid prediction for GlimmerHMM_glimmerT_51727-T1
Valid prediction for GeneMark_model.89894_t
Couldn't classify 55246, 55442
Sorry, prediction pasa_asmbl_31388.p1 fails validation.
(ATG)	 AA	54875-55016	GT	AGG
(TGG)	 AG	55246-55442	GT	GGG
-recovered pasa_asmbl_31388.p1, initial, 54875, 55016
-recovered pasa_asmbl_31388.p1, internal, 55246, 55442
Valid prediction for snap_scaffold_23-snap.283-T1
Valid prediction for pasa_asmbl_31389.p1
Valid prediction for GlimmerHMM_glimmerT_51717-T1
Valid prediction for snap_scaffold_23-snap.287-T1
Valid prediction for snap_scaffold_23-snap.269-T1
Valid prediction for snap_scaffold_23-snap.286-T1
Valid prediction for Augustus_model.g34751.t1
Valid prediction for snap_scaffold_23-snap.274-T1
Valid prediction for snap_scaffold_23-snap.278-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7222, rend_intergenic: 1941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13376, rend_intergenic: 11149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24031, rend_intergenic: 22769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28853, rend_intergenic: 25933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34019, rend_intergenic: 32036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50215, rend_intergenic: 45776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51082, rend_intergenic: 50411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55579, rend_intergenic: 51365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60863, rend_intergenic: 55915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68339, rend_intergenic: 63969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 70883
-exon list size: 353


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    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.4    
19.7    
20.0    
20.3    
20.6    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
40.0    
40.3    
40.6    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.4    
59.7    
60.0    
60.3    
60.6    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.4    
79.7    
80.0    
80.3    
80.6    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
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 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 7222, rend_intergenic: 1941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13376, rend_intergenic: 11149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24031, rend_intergenic: 22769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28853, rend_intergenic: 25933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34019, rend_intergenic: 32036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50215, rend_intergenic: 45776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51082, rend_intergenic: 50411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55579, rend_intergenic: 51365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60863, rend_intergenic: 55915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68339, rend_intergenic: 63969  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