-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_814528-1019058

-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_3-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_5955-T1
Valid prediction for Augustus_model.g3893.t1
Valid prediction for GlimmerHMM_glimmerT_5947-T1
Valid prediction for GlimmerHMM_glimmerT_5959-T1
Valid prediction for snap_scaffold_3-snap.222-T1
Valid prediction for snap_scaffold_3-snap.242-T1
Valid prediction for Augustus_model.g3889.t1
Valid prediction for snap_scaffold_3-snap.250-T1
Valid prediction for snap_scaffold_3-snap.210-T1
Valid prediction for Augustus_model.g3875.t1
Valid prediction for GlimmerHMM_glimmerT_5938-T1
Valid prediction for snap_scaffold_3-snap.241-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.227-T1
Valid prediction for Augustus_model.g3887.t1
Valid prediction for GlimmerHMM_glimmerT_5963-T1
Couldn't classify 119737, 120001
Sorry, prediction pasa_asmbl_39816.p1 fails validation.
(TCT)	 GT	119737-120001	GT	AGG
(GTT)	 AG	120155-120403	GT	AAG
(TGT)	 AG	120570-120850	GT	CGG
(ACT)	 AG	120966-121178	GT	GGG
(GCT)	 AG	121355-121457	GT	TGG
(AGG)	 AG	121691-122034	AA	AAA
-recovered pasa_asmbl_39816.p1, terminal, 121691, 122034
-recovered pasa_asmbl_39816.p1, internal, 120155, 120403
-recovered pasa_asmbl_39816.p1, internal, 120570, 120850
-recovered pasa_asmbl_39816.p1, internal, 120966, 121178
-recovered pasa_asmbl_39816.p1, internal, 121355, 121457
Valid prediction for snap_scaffold_3-snap.249-T1
Valid prediction for snap_scaffold_3-snap.226-T1
Valid prediction for Augustus_model.g3883.t1
Valid prediction for snap_scaffold_3-snap.253-T1
Valid prediction for snap_scaffold_3-snap.237-T1
Couldn't classify 124849, 124923
Sorry, prediction pasa_asmbl_39817.p1 fails validation.
(ATG)	 CA	124184-124355	GT	CGG
(GAT)	 AG	124571-124698	GT	AGG
(GGA)	 AG	124849-124923	GG	GAG
-recovered pasa_asmbl_39817.p1, initial, 124184, 124355
-recovered pasa_asmbl_39817.p1, internal, 124571, 124698
Valid prediction for Augustus_model.g3884.t1
Valid prediction for snap_scaffold_3-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_5957-T1
Couldn't classify 202378, 202413
Couldn't classify 203487, 203728
Sorry, prediction pasa_asmbl_39819.p1 fails validation.
(GAT)	 GG	202378-202413	GT	TGG
(GTG)	 AG	202634-202879	GT	AGG
(GTG)	 AG	203127-203292	GT	AGG
(GTA)	 AG	203487-203728	AC	ACA
-recovered pasa_asmbl_39819.p1, internal, 202634, 202879
-recovered pasa_asmbl_39819.p1, internal, 203127, 203292
Valid prediction for Augustus_model.g3891.t1
Valid prediction for snap_scaffold_3-snap.212-T1
Valid prediction for snap_scaffold_3-snap.224-T1
Valid prediction for snap_scaffold_3-snap.213-T1
Valid prediction for snap_scaffold_3-snap.219-T1
Valid prediction for GlimmerHMM_glimmerT_5941-T1
Valid prediction for GlimmerHMM_glimmerT_5956-T1
Valid prediction for snap_scaffold_3-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_5962-T1
Valid prediction for GlimmerHMM_glimmerT_5968-T1
Valid prediction for snap_scaffold_3-snap.221-T1
Valid prediction for snap_scaffold_3-snap.230-T1
Valid prediction for Augustus_model.g3872.t1
Valid prediction for snap_scaffold_3-snap.225-T1
Valid prediction for snap_scaffold_3-snap.251-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.229-T1
Valid prediction for snap_scaffold_3-snap.236-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_3-snap.247-T1
Valid prediction for snap_scaffold_3-snap.223-T1
Valid prediction for snap_scaffold_3-snap.208-T1
Valid prediction for GlimmerHMM_glimmerT_5954-T1
Couldn't classify 14112, 14339
Couldn't classify 16190, 16267
Sorry, prediction pasa_asmbl_38695.p1 fails validation.
(CTC)	 CT	14112-14339	GT	AGG
(TTG)	 AG	16190-16267	AT	AGA
Valid prediction for snap_scaffold_3-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_5937-T1
Valid prediction for GlimmerHMM_glimmerT_5948-T1
Valid prediction for snap_scaffold_3-snap.209-T1
Valid prediction for GlimmerHMM_glimmerT_5961-T1
Valid prediction for GlimmerHMM_glimmerT_5942-T1
Valid prediction for GlimmerHMM_glimmerT_5943-T1
Valid prediction for GlimmerHMM_glimmerT_5958-T1
Valid prediction for pasa_asmbl_38688.p1
Valid prediction for GlimmerHMM_glimmerT_5951-T1
Valid prediction for snap_scaffold_3-snap.234-T1
Valid prediction for GlimmerHMM_glimmerT_5944-T1
Valid prediction for GlimmerHMM_glimmerT_5953-T1
Valid prediction for GlimmerHMM_glimmerT_5967-T1
Valid prediction for snap_scaffold_3-snap.238-T1
Valid prediction for Augustus_model.g3874.t1
Valid prediction for Augustus_model.g3873.t1
Valid prediction for snap_scaffold_3-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_5966-T1
Valid prediction for GlimmerHMM_glimmerT_5940-T1
Valid prediction for pasa_asmbl_38692.p1
Valid prediction for Augustus_model.g3882.t1
Valid prediction for snap_scaffold_3-snap.233-T1
Valid prediction for GlimmerHMM_glimmerT_5952-T1
Couldn't classify 89479, 89697
Couldn't classify 90666, 90679
Sorry, prediction pasa_asmbl_38681.p1 fails validation.
(CTG)	 GC	89479-89697	GT	TGG
(GAG)	 AG	89962-90171	GT	AGG
(GCA)	 AG	90344-90446	GT	AGG
(AGC)	 AG	90666-90679	AT	GGA
-recovered pasa_asmbl_38681.p1, internal, 89962, 90171
-recovered pasa_asmbl_38681.p1, internal, 90344, 90446
Valid prediction for GlimmerHMM_glimmerT_5939-T1
Valid prediction for Augustus_model.g3880.t1
Couldn't classify 87807, 87932
Couldn't classify 88763, 88886
Sorry, prediction pasa_asmbl_39715.p1 fails validation.
(TTT)	 GA	87807-87932	GT	AGG
(GGC)	 AG	88479-88588	GT	CAG
(CTA)	 AG	88763-88886	TT	AGT
-recovered pasa_asmbl_39715.p1, internal, 88479, 88588
Valid prediction for Augustus_model.g3886.t1
Couldn't classify 16733, 16834
Couldn't classify 21844, 21998
Sorry, prediction pasa_asmbl_38694.p1 fails validation.
(ATC)	 CC	16733-16834	GT	CGG
(GTA)	 AG	19420-19665	GT	AGG
(TCG)	 AG	19871-20038	GT	GGG
(CTC)	 AG	21044-21123	GT	AGG
(GTA)	 AG	21460-21629	GT	AGG
(TCC)	 AG	21844-21998	AC	GCA
-recovered pasa_asmbl_38694.p1, internal, 19420, 19665
-recovered pasa_asmbl_38694.p1, internal, 19871, 20038
-recovered pasa_asmbl_38694.p1, internal, 21044, 21123
-recovered pasa_asmbl_38694.p1, internal, 21460, 21629
Valid prediction for snap_scaffold_3-snap.220-T1
Valid prediction for snap_scaffold_3-snap.228-T1
Valid prediction for snap_scaffold_3-snap.205-T1
Couldn't classify 147547, 147691
Sorry, prediction pasa_asmbl_39682.p1 fails validation.
(ATG)	 AA	146996-147109	GT	TTG
(GTG)	 AG	147263-147315	GT	GCG
(GAT)	 AG	147547-147691	GG	GGG
-recovered pasa_asmbl_39682.p1, initial, 146996, 147109
-recovered pasa_asmbl_39682.p1, internal, 147263, 147315
Valid prediction for snap_scaffold_3-snap.246-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g3888.t1
Valid prediction for Augustus_model.g3878.t1
Valid prediction for snap_scaffold_3-snap.239-T1
Valid prediction for snap_scaffold_3-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_5949-T1
Valid prediction for Augustus_model.g3877.t1
Valid prediction for snap_scaffold_3-snap.206-T1
Valid prediction for snap_scaffold_3-snap.252-T1
Valid prediction for Augustus_model.g3879.t1
Valid prediction for snap_scaffold_3-snap.211-T1
Valid prediction for snap_scaffold_3-snap.240-T1
Valid prediction for snap_scaffold_3-snap.232-T1
Valid prediction for HiQ_model.g3892.t1
Valid prediction for snap_scaffold_3-snap.245-T1
Valid prediction for snap_scaffold_3-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_5945-T1
Valid prediction for snap_scaffold_3-snap.218-T1
Valid prediction for snap_scaffold_3-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_5950-T1
Valid prediction for GlimmerHMM_glimmerT_5960-T1
Valid prediction for Augustus_model.g3881.t1
Valid prediction for Augustus_model.g3876.t1
Valid prediction for snap_scaffold_3-snap.217-T1
Valid prediction for GlimmerHMM_glimmerT_5946-T1
Valid prediction for snap_scaffold_3-snap.214-T1
Valid prediction for Augustus_model.g3890.t1
Valid prediction for GlimmerHMM_glimmerT_5965-T1
Valid prediction for GlimmerHMM_glimmerT_5964-T1
Valid prediction for HiQ_model.g3885.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17693, rend_intergenic: 14389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19568, rend_intergenic: 17901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30208, rend_intergenic: 27490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36820, rend_intergenic: 31510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38195, rend_intergenic: 36923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45377, rend_intergenic: 41673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54593, rend_intergenic: 45468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66879, rend_intergenic: 59481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73374, rend_intergenic: 66954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88230, rend_intergenic: 75293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103684, rend_intergenic: 90642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106066, rend_intergenic: 105050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192688, rend_intergenic: 181185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204531
-exon list size: 404


building trellis

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2.5    
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3.7    
3.9    
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4.9    
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10.6    
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14.5    
14.8    
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15.3    
15.5    
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16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
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59.4    
59.6    
59.9    
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60.3    
60.6    
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67.2    
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68.0    
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68.5    
68.7    
69.0    
69.2    
69.5    
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70.0    
70.2    
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70.7    
70.9    
71.2    
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71.9    
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73.2    
73.4    
73.6    
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74.1    
74.4    
74.6    
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75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
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78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
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95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 17693, rend_intergenic: 14389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19568, rend_intergenic: 17901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30208, rend_intergenic: 27490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36820, rend_intergenic: 31510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38195, rend_intergenic: 36923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45377, rend_intergenic: 41673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54593, rend_intergenic: 45468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66879, rend_intergenic: 59481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73374, rend_intergenic: 66954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88230, rend_intergenic: 75293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103684, rend_intergenic: 90642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106066, rend_intergenic: 105050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192688, rend_intergenic: 181185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support