-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_11494692-11675505

-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 pasa_asmbl_21066.p1
Valid prediction for GlimmerHMM_glimmerT_43170-T1
Valid prediction for snap_scaffold_18-snap.2460-T1
Valid prediction for HiQ_model.g28759.t1
Valid prediction for snap_scaffold_18-snap.2478-T1
Valid prediction for snap_scaffold_18-snap.2458-T1
Valid prediction for snap_scaffold_18-snap.2472-T1
Valid prediction for snap_scaffold_18-snap.2463-T1
Valid prediction for GlimmerHMM_glimmerT_43153-T1
Valid prediction for GlimmerHMM_glimmerT_43163-T1
Valid prediction for snap_scaffold_18-snap.2481-T1
Valid prediction for Augustus_model.g28762.t1
Valid prediction for snap_scaffold_18-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_43157-T1
Valid prediction for snap_scaffold_18-snap.2483-T1
Valid prediction for pasa_asmbl_20946.p1
Valid prediction for GlimmerHMM_glimmerT_43158-T1
Valid prediction for GlimmerHMM_glimmerT_43168-T1
Valid prediction for GlimmerHMM_glimmerT_43152-T1
Valid prediction for snap_scaffold_18-snap.2470-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g28756.t1
Valid prediction for snap_scaffold_18-snap.2466-T1
Valid prediction for snap_scaffold_18-snap.2455-T1
Valid prediction for snap_scaffold_18-snap.2461-T1
Valid prediction for Augustus_model.g28757.t1
Valid prediction for snap_scaffold_18-snap.2475-T1
Valid prediction for snap_scaffold_18-snap.2448-T1
Valid prediction for Augustus_model.g28753.t1
Valid prediction for snap_scaffold_18-snap.2450-T1
Valid prediction for snap_scaffold_18-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_43169-T1
Valid prediction for snap_scaffold_18-snap.2486-T1
Valid prediction for CodingQuarry_transcript_23907-T1
Valid prediction for snap_scaffold_18-snap.2453-T1
Valid prediction for CodingQuarry_transcript_23909-T1
Valid prediction for CodingQuarry_transcript_23908-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 GlimmerHMM_glimmerT_43150-T1
Valid prediction for snap_scaffold_18-snap.2459-T1
Valid prediction for Augustus_model.g28752.t1
Valid prediction for GlimmerHMM_glimmerT_43162-T1
Valid prediction for GlimmerHMM_glimmerT_43167-T1
Valid prediction for GlimmerHMM_glimmerT_43154-T1
Valid prediction for GlimmerHMM_glimmerT_43149-T1
Valid prediction for snap_scaffold_18-snap.2473-T1
Valid prediction for snap_scaffold_18-snap.2482-T1
Valid prediction for snap_scaffold_18-snap.2452-T1
Valid prediction for snap_scaffold_18-snap.2447-T1
Valid prediction for Augustus_model.g28754.t1
Valid prediction for Augustus_model.g28761.t1
Valid prediction for GlimmerHMM_glimmerT_43161-T1
Valid prediction for GlimmerHMM_glimmerT_43164-T1
Valid prediction for snap_scaffold_18-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_43166-T1
Valid prediction for GlimmerHMM_glimmerT_43151-T1
Valid prediction for snap_scaffold_18-snap.2471-T1
Valid prediction for snap_scaffold_18-snap.2477-T1
Valid prediction for GlimmerHMM_glimmerT_43159-T1
Valid prediction for GlimmerHMM_glimmerT_43156-T1
Valid prediction for snap_scaffold_18-snap.2462-T1
Valid prediction for snap_scaffold_18-snap.2457-T1
Valid prediction for snap_scaffold_18-snap.2479-T1
Valid prediction for snap_scaffold_18-snap.2487-T1
Valid prediction for snap_scaffold_18-snap.2446-T1
Valid prediction for GlimmerHMM_glimmerT_43148-T1
Valid prediction for snap_scaffold_18-snap.2476-T1
Valid prediction for snap_scaffold_18-snap.2469-T1
Valid prediction for Augustus_model.g28755.t1
Valid prediction for Augustus_model.g28760.t1
Valid prediction for Augustus_model.g28750.t1
Valid prediction for snap_scaffold_18-snap.2468-T1
Valid prediction for snap_scaffold_18-snap.2449-T1
Valid prediction for GlimmerHMM_glimmerT_43160-T1
Valid prediction for snap_scaffold_18-snap.2454-T1
Couldn't classify 125158, 125217
Sorry, prediction pasa_asmbl_20137.p1 fails validation.
(CAG)	 GC	125158-125217	GT	TGG
(GCT)	 AG	125340-125369	GT	GGG
(ATT)	 AG	126013-126086	GT	AGG
(CGA)	 AG	127394-127487	GT	AGG
(CTT)	 AG	128315-128389	GT	TGG
(CTT)	 AG	128807-128878	GT	AGG
(GAG)	 AG	130400-130501	AG	AGA
-recovered pasa_asmbl_20137.p1, terminal, 130400, 130501
-recovered pasa_asmbl_20137.p1, internal, 125340, 125369
-recovered pasa_asmbl_20137.p1, internal, 126013, 126086
-recovered pasa_asmbl_20137.p1, internal, 127394, 127487
-recovered pasa_asmbl_20137.p1, internal, 128315, 128389
-recovered pasa_asmbl_20137.p1, internal, 128807, 128878
Valid prediction for Augustus_model.g28751.t1
Valid prediction for GlimmerHMM_glimmerT_43171-T1
Valid prediction for snap_scaffold_18-snap.2467-T1
Valid prediction for GlimmerHMM_glimmerT_43155-T1
Valid prediction for snap_scaffold_18-snap.2451-T1
Valid prediction for GlimmerHMM_glimmerT_43165-T1
Couldn't classify 119158, 119362
Couldn't classify 120554, 120937
Sorry, prediction pasa_asmbl_20138.p1 fails validation.
(TTC)	 AT	119158-119362	GT	AGG
(ATA)	 AG	119593-119763	GT	AGG
(GAC)	 AG	120092-120198	GT	AGG
(GTG)	 AG	120554-120937	CT	CCC
-recovered pasa_asmbl_20138.p1, internal, 119593, 119763
-recovered pasa_asmbl_20138.p1, internal, 120092, 120198
Valid prediction for CodingQuarry_transcript_23906-T1
Valid prediction for snap_scaffold_18-snap.2465-T1
Valid prediction for Augustus_model.g28758.t1
Valid prediction for snap_scaffold_18-snap.2474-T1
Valid prediction for snap_scaffold_18-snap.2456-T1
Valid prediction for snap_scaffold_18-snap.2464-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 50317, rend_intergenic: 50314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15688, rend_intergenic: 12027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23949, rend_intergenic: 15743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47439, rend_intergenic: 46067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56654, rend_intergenic: 51253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61175, rend_intergenic: 58108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72130, rend_intergenic: 65315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76549, rend_intergenic: 72663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80858, rend_intergenic: 80091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87560, rend_intergenic: 81122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102675, rend_intergenic: 100258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127068, rend_intergenic: 124838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133902, rend_intergenic: 131165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147794, rend_intergenic: 143368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154608, rend_intergenic: 151587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160354, rend_intergenic: 156401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171950, rend_intergenic: 166832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180814
-exon list size: 269


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.5    
5.9    
6.3    
6.6    
7.0    
7.4    
7.7    
8.1    
8.5    
8.9    
9.2    
9.6    
10.0    
10.3    
10.7    
11.1    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.0    
14.4    
14.8    
15.1    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.5    
18.8    
19.2    
19.6    
19.9    
20.3    
20.7    
21.0    
21.4    
21.8    
22.1    
22.5    
22.9    
23.2    
23.6    
24.0    
24.4    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
26.9    
27.3    
27.7    
28.0    
28.4    
28.8    
29.2    
29.5    
29.9    
30.3    
30.6    
31.0    
31.4    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
33.9    
34.3    
34.7    
35.1    
35.4    
35.8    
36.2    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.7    
39.1    
39.5    
39.9    
40.2    
40.6    
41.0    
41.3    
41.7    
42.1    
42.4    
42.8    
43.2    
43.5    
43.9    
44.3    
44.6    
45.0    
45.4    
45.8    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.2    
54.6    
55.0    
55.4    
55.7    
56.1    
56.5    
56.8    
57.2    
57.6    
57.9    
58.3    
58.7    
59.0    
59.4    
59.8    
60.1    
60.5    
60.9    
61.3    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.8    
64.2    
64.6    
64.9    
65.3    
65.7    
66.1    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.6    
69.0    
69.4    
69.7    
70.1    
70.5    
70.8    
71.2    
71.6    
72.0    
72.3    
72.7    
73.1    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.6    
76.0    
76.4    
76.8    
77.1    
77.5    
77.9    
78.2    
78.6    
79.0    
79.3    
79.7    
80.1    
80.4    
80.8    
81.2    
81.5    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.9    
85.2    
85.6    
86.0    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
88.9    
89.3    
89.7    
90.0    
90.4    
90.8    
91.1    
91.5    
91.9    
92.3    
92.6    
93.0    
93.4    
93.7    
94.1    
94.5    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 25 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 50317, rend_intergenic: 50314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15688, rend_intergenic: 12027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23949, rend_intergenic: 15743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47439, rend_intergenic: 46067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56654, rend_intergenic: 51253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61175, rend_intergenic: 58108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72130, rend_intergenic: 65315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76549, rend_intergenic: 72663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80858, rend_intergenic: 80091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87560, rend_intergenic: 81122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102675, rend_intergenic: 100258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127068, rend_intergenic: 124838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133902, rend_intergenic: 131165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147794, rend_intergenic: 143368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154608, rend_intergenic: 151587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160354, rend_intergenic: 156401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171950, rend_intergenic: 166832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support