-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_18762455-18985695

-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 Augustus_model.g1831.t1
Valid prediction for Augustus_model.g1836.t1
Valid prediction for GlimmerHMM_glimmerT_2525-T1
Valid prediction for GlimmerHMM_glimmerT_2513-T1
Valid prediction for snap_scaffold_1-snap.3487-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g1833.t1
Valid prediction for snap_scaffold_1-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_2540-T1
Valid prediction for GlimmerHMM_glimmerT_2510-T1
Valid prediction for Augustus_model.g1835.t1
Valid prediction for snap_scaffold_1-snap.3484-T1
Valid prediction for GlimmerHMM_glimmerT_2511-T1
Valid prediction for snap_scaffold_1-snap.3455-T1
Valid prediction for snap_scaffold_1-snap.3486-T1
Valid prediction for GlimmerHMM_glimmerT_2526-T1
Valid prediction for snap_scaffold_1-snap.3474-T1
Valid prediction for GlimmerHMM_glimmerT_2531-T1
Valid prediction for Augustus_model.g1828.t1
Valid prediction for GlimmerHMM_glimmerT_2521-T1
Valid prediction for snap_scaffold_1-snap.3454-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3459-T1
Valid prediction for GlimmerHMM_glimmerT_2529-T1
Valid prediction for snap_scaffold_1-snap.3452-T1
Valid prediction for snap_scaffold_1-snap.3479-T1
Valid prediction for snap_scaffold_1-snap.3492-T1
Valid prediction for snap_scaffold_1-snap.3462-T1
Valid prediction for GlimmerHMM_glimmerT_2530-T1
Valid prediction for snap_scaffold_1-snap.3445-T1
Valid prediction for snap_scaffold_1-snap.3471-T1
Valid prediction for snap_scaffold_1-snap.3490-T1
Valid prediction for snap_scaffold_1-snap.3472-T1
Valid prediction for snap_scaffold_1-snap.3468-T1
Valid prediction for snap_scaffold_1-snap.3450-T1
Valid prediction for snap_scaffold_1-snap.3457-T1
Valid prediction for snap_scaffold_1-snap.3464-T1
Valid prediction for snap_scaffold_1-snap.3447-T1
Valid prediction for snap_scaffold_1-snap.3482-T1
Valid prediction for GlimmerHMM_glimmerT_2523-T1
Valid prediction for GlimmerHMM_glimmerT_2534-T1
Valid prediction for snap_scaffold_1-snap.3465-T1
Couldn't classify 232, 297
Couldn't classify 3677, 3779
Sorry, prediction pasa_asmbl_2571.p1 fails validation.
(CGA)	 AA	232-297	GT	ATG
(TTA)	 AG	695-809	GT	CGG
(ATA)	 AG	2757-2829	GT	AAG
(GTT)	 AG	3677-3779	GT	AGG
-recovered pasa_asmbl_2571.p1, terminal, 2757, 2829
-recovered pasa_asmbl_2571.p1, internal, 695, 809
-recovered pasa_asmbl_2571.p1, internal, 2757, 2829
-recovered pasa_asmbl_2571.p1, internal, 3677, 3779
Valid prediction for CodingQuarry_transcript_3003-T1
Valid prediction for Augustus_model.g1837.t1
Valid prediction for Augustus_model.g1834.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_2538-T1
Valid prediction for snap_scaffold_1-snap.3483-T1
Valid prediction for CodingQuarry_transcript_3005-T1
Valid prediction for snap_scaffold_1-snap.3461-T1
Valid prediction for snap_scaffold_1-snap.3451-T1
Valid prediction for GlimmerHMM_glimmerT_2544-T1
Valid prediction for GlimmerHMM_glimmerT_2535-T1
Valid prediction for Augustus_model.g1842.t1
Valid prediction for GlimmerHMM_glimmerT_2516-T1
Valid prediction for HiQ_model.g1844.t1
Couldn't classify 197442, 197522
Sorry, prediction pasa_asmbl_1131.p2 fails validation.
(GCG)	 AG	197442-197522	GT	TGG
(GCG)	 AG	197971-198235	GT	TGG
(GCT)	 AG	200473-200702	TG	GAT
-recovered pasa_asmbl_1131.p2, terminal, 200473, 200702
-recovered pasa_asmbl_1131.p2, internal, 197442, 197522
-recovered pasa_asmbl_1131.p2, internal, 197971, 198235
Valid prediction for GlimmerHMM_glimmerT_2518-T1
Valid prediction for Augustus_model.g1839.t1
Valid prediction for GlimmerHMM_glimmerT_2532-T1
Valid prediction for GlimmerHMM_glimmerT_2539-T1
Valid prediction for snap_scaffold_1-snap.3448-T1
Valid prediction for snap_scaffold_1-snap.3458-T1
Valid prediction for GlimmerHMM_glimmerT_2541-T1
Valid prediction for snap_scaffold_1-snap.3470-T1
Valid prediction for snap_scaffold_1-snap.3449-T1
Valid prediction for snap_scaffold_1-snap.3481-T1
Valid prediction for Augustus_model.g1832.t1
Valid prediction for GlimmerHMM_glimmerT_2517-T1
Valid prediction for GlimmerHMM_glimmerT_2514-T1
Valid prediction for CodingQuarry_transcript_3004-T1
Valid prediction for GlimmerHMM_glimmerT_2537-T1
Valid prediction for snap_scaffold_1-snap.3478-T1
Valid prediction for GlimmerHMM_glimmerT_2536-T1
Valid prediction for snap_scaffold_1-snap.3488-T1
Valid prediction for snap_scaffold_1-snap.3460-T1
Couldn't classify 13604, 14776
Sorry, prediction pasa_asmbl_1137.p1 fails validation.
(GCC)	 AG	13604-14776	AA	GCA
Valid prediction for snap_scaffold_1-snap.3473-T1
Valid prediction for GlimmerHMM_glimmerT_2527-T1
Valid prediction for GlimmerHMM_glimmerT_2542-T1
Valid prediction for snap_scaffold_1-snap.3453-T1
Valid prediction for snap_scaffold_1-snap.3491-T1
Valid prediction for snap_scaffold_1-snap.3469-T1
Valid prediction for snap_scaffold_1-snap.3456-T1
Valid prediction for GlimmerHMM_glimmerT_2528-T1
Valid prediction for GlimmerHMM_glimmerT_2515-T1
Valid prediction for snap_scaffold_1-snap.3489-T1
Valid prediction for GlimmerHMM_glimmerT_2520-T1
Valid prediction for Augustus_model.g1838.t1
Valid prediction for GlimmerHMM_glimmerT_2519-T1
Valid prediction for snap_scaffold_1-snap.3467-T1
Valid prediction for snap_scaffold_1-snap.3475-T1
Valid prediction for snap_scaffold_1-snap.3493-T1
Valid prediction for GlimmerHMM_glimmerT_2533-T1
Valid prediction for GlimmerHMM_glimmerT_2522-T1
Valid prediction for GlimmerHMM_glimmerT_2543-T1
Valid prediction for GlimmerHMM_glimmerT_2512-T1
Valid prediction for snap_scaffold_1-snap.3480-T1
Valid prediction for snap_scaffold_1-snap.3485-T1
Valid prediction for GlimmerHMM_glimmerT_2524-T1
Valid prediction for pasa_asmbl_1347.p1
Valid prediction for snap_scaffold_1-snap.3463-T1
Valid prediction for Augustus_model.g1829.t1
Valid prediction for Augustus_model.g1830.t1
Valid prediction for snap_scaffold_1-snap.3466-T1
Valid prediction for HiQ_model.g1843.t1
Valid prediction for HiQ_model.g1841.t1
Valid prediction for snap_scaffold_1-snap.3446-T1
Valid prediction for Augustus_model.g1840.t1
Valid prediction for snap_scaffold_1-snap.3477-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5767, rend_intergenic: 3203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7723, rend_intergenic: 6537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11659, rend_intergenic: 7803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15195, rend_intergenic: 14358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30860, rend_intergenic: 24544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38051, rend_intergenic: 35156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42839, rend_intergenic: 40282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46694, rend_intergenic: 43704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64396, rend_intergenic: 58249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70833, rend_intergenic: 69537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90252, rend_intergenic: 83856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120774, rend_intergenic: 102451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126176, rend_intergenic: 120968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133114, rend_intergenic: 128546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143857, rend_intergenic: 138088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153089, rend_intergenic: 147108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164589, rend_intergenic: 158487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179718, rend_intergenic: 168147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184688, rend_intergenic: 182838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194147, rend_intergenic: 184759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214683, rend_intergenic: 213396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217772, rend_intergenic: 215312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223241
-exon list size: 366


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
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2.4    
2.7    
3.0    
3.3    
3.5    
3.8    
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4.3    
4.6    
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5.7    
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6.8    
7.1    
7.3    
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8.2    
8.4    
8.7    
9.0    
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9.5    
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10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
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13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
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20.7    
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21.5    
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22.0    
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22.6    
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23.6    
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24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
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47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
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72.6    
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73.1    
73.4    
73.6    
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74.2    
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75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
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77.2    
77.4    
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78.0    
78.3    
78.5    
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79.1    
79.3    
79.6    
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80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
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82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
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84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 5767, rend_intergenic: 3203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7723, rend_intergenic: 6537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11659, rend_intergenic: 7803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15195, rend_intergenic: 14358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30860, rend_intergenic: 24544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38051, rend_intergenic: 35156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42839, rend_intergenic: 40282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46694, rend_intergenic: 43704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64396, rend_intergenic: 58249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70833, rend_intergenic: 69537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90252, rend_intergenic: 83856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120774, rend_intergenic: 102451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126176, rend_intergenic: 120968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133114, rend_intergenic: 128546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143857, rend_intergenic: 138088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153089, rend_intergenic: 147108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164589, rend_intergenic: 158487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179718, rend_intergenic: 168147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184688, rend_intergenic: 182838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194147, rend_intergenic: 184759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214683, rend_intergenic: 213396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217772, rend_intergenic: 215312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support