-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_13563458-13752627

-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.2724-T1
Valid prediction for GlimmerHMM_glimmerT_23212-T1
Valid prediction for Augustus_model.g15474.t1
Valid prediction for snap_scaffold_9-snap.2722-T1
Valid prediction for GlimmerHMM_glimmerT_23207-T1
Valid prediction for Augustus_model.g15475.t1
Valid prediction for snap_scaffold_9-snap.2718-T1
Valid prediction for GlimmerHMM_glimmerT_23220-T1
Valid prediction for snap_scaffold_9-snap.2726-T1
Valid prediction for snap_scaffold_9-snap.2699-T1
Valid prediction for GlimmerHMM_glimmerT_23230-T1
Valid prediction for GlimmerHMM_glimmerT_23206-T1
Valid prediction for snap_scaffold_9-snap.2708-T1
Valid prediction for snap_scaffold_9-snap.2689-T1
Valid prediction for snap_scaffold_9-snap.2713-T1
Valid prediction for GlimmerHMM_glimmerT_23234-T1
Valid prediction for snap_scaffold_9-snap.2696-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23208-T1
Valid prediction for GlimmerHMM_glimmerT_23227-T1
Valid prediction for pasa_asmbl_54505.p1
Valid prediction for HiQ_model.g15477.t1
Valid prediction for snap_scaffold_9-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_23232-T1
Valid prediction for pasa_asmbl_54510.p1
Valid prediction for snap_scaffold_9-snap.2719-T1
Valid prediction for snap_scaffold_9-snap.2709-T1
Valid prediction for Augustus_model.g15481.t1
Valid prediction for GlimmerHMM_glimmerT_23223-T1
Valid prediction for GlimmerHMM_glimmerT_23209-T1
Valid prediction for CodingQuarry_transcript_62396-T1
Couldn't classify 39504, 39641
Couldn't classify 40972, 41093
Sorry, prediction pasa_asmbl_54502.p1 fails validation.
(CAG)	 TG	39504-39641	GT	AGG
(AAA)	 AG	39805-39985	GT	AGG
(GTG)	 AG	40972-41093	TG	AGT
-recovered pasa_asmbl_54502.p1, internal, 39805, 39985
Valid prediction for snap_scaffold_9-snap.2707-T1
Valid prediction for snap_scaffold_9-snap.2693-T1
Valid prediction for Augustus_model.g15478.t1
Valid prediction for snap_scaffold_9-snap.2715-T1
Valid prediction for GlimmerHMM_glimmerT_23222-T1
Valid prediction for snap_scaffold_9-snap.2702-T1
Valid prediction for GlimmerHMM_glimmerT_23226-T1
Valid prediction for Augustus_model.g15480.t1
Valid prediction for snap_scaffold_9-snap.2691-T1
Valid prediction for snap_scaffold_9-snap.2704-T1
Couldn't classify 62645, 62827
Couldn't classify 68375, 68464
Sorry, prediction pasa_asmbl_54509.p1 fails validation.
(CGG)	 GC	62645-62827	GT	GGG
(CAG)	 AG	63000-63077	GT	TGG
(GCC)	 AG	63581-63706	GT	AGG
(GTG)	 AG	63919-64047	GT	CTG
(GTT)	 AG	64307-64441	GT	TGG
(GAC)	 AG	64683-64784	GT	AGG
(GTG)	 AG	65245-65355	GT	TGG
(CTC)	 AG	65506-65604	GT	CTG
(CAC)	 AG	65714-65756	GT	GGG
(ACC)	 AG	65908-66013	GT	AGG
(GCA)	 AG	66600-66737	GT	TTG
(GGT)	 AG	67026-67058	GT	TGG
(CAC)	 AG	68074-68188	GT	AGG
(AAG)	 AG	68375-68464	CG	GCC
-recovered pasa_asmbl_54509.p1, internal, 63000, 63077
-recovered pasa_asmbl_54509.p1, internal, 63581, 63706
-recovered pasa_asmbl_54509.p1, internal, 63919, 64047
-recovered pasa_asmbl_54509.p1, internal, 64307, 64441
-recovered pasa_asmbl_54509.p1, internal, 64683, 64784
-recovered pasa_asmbl_54509.p1, internal, 65245, 65355
-recovered pasa_asmbl_54509.p1, internal, 65506, 65604
-recovered pasa_asmbl_54509.p1, internal, 65714, 65756
-recovered pasa_asmbl_54509.p1, internal, 65908, 66013
-recovered pasa_asmbl_54509.p1, internal, 66600, 66737
-recovered pasa_asmbl_54509.p1, internal, 67026, 67058
-recovered pasa_asmbl_54509.p1, internal, 68074, 68188
Valid prediction for GlimmerHMM_glimmerT_23214-T1
Valid prediction for GlimmerHMM_glimmerT_23215-T1
Valid prediction for snap_scaffold_9-snap.2711-T1
Valid prediction for Augustus_model.g15476.t1
Valid prediction for GlimmerHMM_glimmerT_23218-T1
Valid prediction for snap_scaffold_9-snap.2721-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 Augustus_model.g15479.t1
Valid prediction for GlimmerHMM_glimmerT_23229-T1
Valid prediction for GlimmerHMM_glimmerT_23211-T1
Valid prediction for snap_scaffold_9-snap.2700-T1
Valid prediction for snap_scaffold_9-snap.2716-T1
Valid prediction for snap_scaffold_9-snap.2714-T1
Valid prediction for snap_scaffold_9-snap.2712-T1
Valid prediction for snap_scaffold_9-snap.2703-T1
Valid prediction for snap_scaffold_9-snap.2717-T1
Valid prediction for snap_scaffold_9-snap.2697-T1
Valid prediction for GlimmerHMM_glimmerT_23231-T1
Valid prediction for snap_scaffold_9-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_23210-T1
Valid prediction for snap_scaffold_9-snap.2706-T1
Valid prediction for GlimmerHMM_glimmerT_23221-T1
Valid prediction for snap_scaffold_9-snap.2688-T1
Valid prediction for GlimmerHMM_glimmerT_23225-T1
Valid prediction for GlimmerHMM_glimmerT_23219-T1
Valid prediction for GlimmerHMM_glimmerT_23216-T1
Valid prediction for GlimmerHMM_glimmerT_23213-T1
Valid prediction for Augustus_model.g15482.t1
Valid prediction for snap_scaffold_9-snap.2695-T1
Valid prediction for GlimmerHMM_glimmerT_23233-T1
Valid prediction for GlimmerHMM_glimmerT_23217-T1
Valid prediction for snap_scaffold_9-snap.2690-T1
Valid prediction for snap_scaffold_9-snap.2692-T1
Valid prediction for GlimmerHMM_glimmerT_23224-T1
Valid prediction for snap_scaffold_9-snap.2694-T1
Valid prediction for GlimmerHMM_glimmerT_23228-T1
Valid prediction for snap_scaffold_9-snap.2720-T1
Valid prediction for snap_scaffold_9-snap.2710-T1
Valid prediction for snap_scaffold_9-snap.2723-T1
Valid prediction for snap_scaffold_9-snap.2701-T1
Sorry, intron length (6) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9386, rend_intergenic: 7489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12986, rend_intergenic: 10446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15829, rend_intergenic: 13013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16215, rend_intergenic: 16006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22225, rend_intergenic: 17578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26538, rend_intergenic: 22572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32621, rend_intergenic: 30939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41246, rend_intergenic: 32787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56720, rend_intergenic: 52343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64459, rend_intergenic: 57745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79400, rend_intergenic: 65327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85511, rend_intergenic: 80884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112897, rend_intergenic: 99810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123757, rend_intergenic: 121697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133702, rend_intergenic: 123910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143604, rend_intergenic: 137647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147209, rend_intergenic: 145184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159688, rend_intergenic: 156111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172670, rend_intergenic: 161166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174775, rend_intergenic: 172705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176829, rend_intergenic: 174953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189170
-exon list size: 378


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 9386, rend_intergenic: 7489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12986, rend_intergenic: 10446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15829, rend_intergenic: 13013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16215, rend_intergenic: 16006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22225, rend_intergenic: 17578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26538, rend_intergenic: 22572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32621, rend_intergenic: 30939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41246, rend_intergenic: 32787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56720, rend_intergenic: 52343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64459, rend_intergenic: 57745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79400, rend_intergenic: 65327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85511, rend_intergenic: 80884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112897, rend_intergenic: 99810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123757, rend_intergenic: 121697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133702, rend_intergenic: 123910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143604, rend_intergenic: 137647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147209, rend_intergenic: 145184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159688, rend_intergenic: 156111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172670, rend_intergenic: 161166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174775, rend_intergenic: 172705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176829, rend_intergenic: 174953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support