-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_14756035-14990420

-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_13132-T1
Valid prediction for snap_scaffold_5-snap.2717-T1
Valid prediction for snap_scaffold_5-snap.2736-T1
Valid prediction for Augustus_model.g8742.t1
Valid prediction for snap_scaffold_5-snap.2719-T1
Valid prediction for snap_scaffold_5-snap.2710-T1
Valid prediction for GlimmerHMM_glimmerT_13130-T1
Valid prediction for snap_scaffold_5-snap.2733-T1
Valid prediction for snap_scaffold_5-snap.2729-T1
Valid prediction for Augustus_model.g8732.t1
Valid prediction for Augustus_model.g8731.t1
Valid prediction for GlimmerHMM_glimmerT_13140-T1
Valid prediction for Augustus_model.g8741.t1
Valid prediction for GlimmerHMM_glimmerT_13123-T1
Valid prediction for snap_scaffold_5-snap.2712-T1
Valid prediction for GlimmerHMM_glimmerT_13151-T1
Valid prediction for snap_scaffold_5-snap.2722-T1
Valid prediction for snap_scaffold_5-snap.2739-T1
Valid prediction for snap_scaffold_5-snap.2744-T1
Valid prediction for GlimmerHMM_glimmerT_13145-T1
Valid prediction for snap_scaffold_5-snap.2741-T1
Couldn't classify 54961, 55074
Couldn't classify 55163, 55345
Sorry, prediction pasa_asmbl_46400.p1 fails validation.
(GTA)	 CA	54961-55074	GT	AGG
(GTG)	 AG	55163-55345	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_13135-T1
Valid prediction for snap_scaffold_5-snap.2748-T1
Valid prediction for GlimmerHMM_glimmerT_13143-T1
Valid prediction for Augustus_model.g8737.t1
Valid prediction for GlimmerHMM_glimmerT_13129-T1
Valid prediction for GlimmerHMM_glimmerT_13148-T1
Valid prediction for Augustus_model.g8738.t1
Valid prediction for GlimmerHMM_glimmerT_13141-T1
Valid prediction for GlimmerHMM_glimmerT_13122-T1
Valid prediction for GlimmerHMM_glimmerT_13133-T1
Valid prediction for GlimmerHMM_glimmerT_13153-T1
Valid prediction for GlimmerHMM_glimmerT_13121-T1
Valid prediction for snap_scaffold_5-snap.2720-T1
Valid prediction for GlimmerHMM_glimmerT_13149-T1
Valid prediction for snap_scaffold_5-snap.2743-T1
Valid prediction for GlimmerHMM_glimmerT_13152-T1
Valid prediction for GlimmerHMM_glimmerT_13144-T1
Valid prediction for GlimmerHMM_glimmerT_13147-T1
Valid prediction for snap_scaffold_5-snap.2732-T1
Valid prediction for snap_scaffold_5-snap.2747-T1
Valid prediction for Augustus_model.g8736.t1
Valid prediction for snap_scaffold_5-snap.2708-T1
Valid prediction for snap_scaffold_5-snap.2746-T1
Valid prediction for Augustus_model.g8743.t1
Valid prediction for CodingQuarry_transcript_52364-T1
Valid prediction for snap_scaffold_5-snap.2738-T1
Valid prediction for GlimmerHMM_glimmerT_13150-T1
Valid prediction for pasa_asmbl_45969.p1
Valid prediction for GlimmerHMM_glimmerT_13124-T1
Valid prediction for snap_scaffold_5-snap.2730-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_5-snap.2713-T1
Valid prediction for snap_scaffold_5-snap.2723-T1
Valid prediction for HiQ_model.g8734.t1
Valid prediction for snap_scaffold_5-snap.2716-T1
Valid prediction for snap_scaffold_5-snap.2721-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2705-T1
Valid prediction for snap_scaffold_5-snap.2731-T1
Valid prediction for CodingQuarry_transcript_52361-T1
Valid prediction for CodingQuarry_transcript_52362-T1
Valid prediction for snap_scaffold_5-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_13127-T1
Valid prediction for pasa_asmbl_44625.p1
Valid prediction for snap_scaffold_5-snap.2711-T1
Valid prediction for GlimmerHMM_glimmerT_13131-T1
Valid prediction for Augustus_model.g8735.t1
Valid prediction for snap_scaffold_5-snap.2714-T1
Valid prediction for CodingQuarry_transcript_52363-T1
Valid prediction for CodingQuarry_transcript_52359-T1
Valid prediction for GlimmerHMM_glimmerT_13126-T1
Valid prediction for pasa_asmbl_44619.p1
Valid prediction for snap_scaffold_5-snap.2715-T1
Valid prediction for GlimmerHMM_glimmerT_13142-T1
Valid prediction for GlimmerHMM_glimmerT_13120-T1
Valid prediction for GlimmerHMM_glimmerT_13139-T1
Valid prediction for Augustus_model.g8744.t1
Valid prediction for snap_scaffold_5-snap.2724-T1
Valid prediction for snap_scaffold_5-snap.2740-T1
Valid prediction for snap_scaffold_5-snap.2707-T1
Valid prediction for snap_scaffold_5-snap.2718-T1
Valid prediction for snap_scaffold_5-snap.2706-T1
Valid prediction for HiQ_model.g8740.t1
Valid prediction for snap_scaffold_5-snap.2709-T1
Valid prediction for Augustus_model.g8739.t1
Valid prediction for GlimmerHMM_glimmerT_13136-T1
Valid prediction for snap_scaffold_5-snap.2734-T1
Couldn't classify 196211, 196471
Sorry, prediction pasa_asmbl_44622.p1 fails validation.
(ATG)	 TT	192557-192709	GT	CAG
(ATA)	 AG	193260-193357	GT	AAG
(AGA)	 AG	193495-193591	GT	AGG
(GTG)	 AG	193739-193888	GT	AGG
(CAC)	 AG	195340-195486	GT	AGG
(GGT)	 AG	195606-195644	GT	GGG
(GTC)	 AG	195738-195851	GT	AGG
(TTC)	 AG	196211-196471	GC	CCG
-recovered pasa_asmbl_44622.p1, initial, 192557, 192709
-recovered pasa_asmbl_44622.p1, internal, 193260, 193357
-recovered pasa_asmbl_44622.p1, internal, 193495, 193591
-recovered pasa_asmbl_44622.p1, internal, 193739, 193888
-recovered pasa_asmbl_44622.p1, internal, 195340, 195486
-recovered pasa_asmbl_44622.p1, internal, 195606, 195644
-recovered pasa_asmbl_44622.p1, internal, 195738, 195851
-recovered pasa_asmbl_44622.p1, internal, 196211, 196471
Valid prediction for GlimmerHMM_glimmerT_13146-T1
Valid prediction for GlimmerHMM_glimmerT_13125-T1
Valid prediction for snap_scaffold_5-snap.2735-T1
Valid prediction for snap_scaffold_5-snap.2725-T1
Couldn't classify 157235, 157834
Sorry, prediction pasa_asmbl_44626.p1 fails validation.
(CGA)	 CC	157235-157834	GA	GAG
Valid prediction for snap_scaffold_5-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_13137-T1
Valid prediction for snap_scaffold_5-snap.2745-T1
Valid prediction for CodingQuarry_transcript_52360-T1
Valid prediction for GlimmerHMM_glimmerT_13134-T1
Valid prediction for pasa_asmbl_44627.p2
Valid prediction for GlimmerHMM_glimmerT_13128-T1
Valid prediction for GlimmerHMM_glimmerT_13119-T1
Valid prediction for HiQ_model.g8730.t1
Valid prediction for snap_scaffold_5-snap.2726-T1
Valid prediction for GlimmerHMM_glimmerT_13138-T1
Valid prediction for snap_scaffold_5-snap.2742-T1
Valid prediction for Augustus_model.g8733.t1
Valid prediction for snap_scaffold_5-snap.2727-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14346, rend_intergenic: 11594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17771, rend_intergenic: 14902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24816, rend_intergenic: 20153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61088, rend_intergenic: 52559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66315, rend_intergenic: 63188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71614, rend_intergenic: 68686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73579, rend_intergenic: 72131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142873, rend_intergenic: 116388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150640, rend_intergenic: 146978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156830, rend_intergenic: 150691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157952, rend_intergenic: 156939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172271, rend_intergenic: 162167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176921, rend_intergenic: 173836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199442, rend_intergenic: 178541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210674, rend_intergenic: 202859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217673, rend_intergenic: 210886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224179, rend_intergenic: 218096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234386
-exon list size: 390


building trellis

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1.0    
1.3    
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2.0    
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5.9    
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6.4    
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7.9    
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8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
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21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
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24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
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54.3    
54.6    
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55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
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60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
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65.3    
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71.9    
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73.0    
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73.7    
74.0    
74.2    
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75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
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77.6    
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78.1    
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78.6    
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79.6    
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80.4    
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81.1    
81.4    
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82.4    
82.7    
82.9    
83.2    
83.4    
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84.2    
84.4    
84.7    
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85.2    
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86.0    
86.2    
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87.0    
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88.5    
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89.3    
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90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
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93.4    
93.6    
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94.1    
94.4    
94.6    
94.9    
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95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 14346, rend_intergenic: 11594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17771, rend_intergenic: 14902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24816, rend_intergenic: 20153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61088, rend_intergenic: 52559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66315, rend_intergenic: 63188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71614, rend_intergenic: 68686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73579, rend_intergenic: 72131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142873, rend_intergenic: 116388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150640, rend_intergenic: 146978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156830, rend_intergenic: 150691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157952, rend_intergenic: 156939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172271, rend_intergenic: 162167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176921, rend_intergenic: 173836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199442, rend_intergenic: 178541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210674, rend_intergenic: 202859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217673, rend_intergenic: 210886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224179, rend_intergenic: 218096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support