-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_19530772-19817920

-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_2638-T1
Valid prediction for snap_scaffold_1-snap.3606-T1
Valid prediction for snap_scaffold_1-snap.3642-T1
Valid prediction for GlimmerHMM_glimmerT_2635-T1
Valid prediction for snap_scaffold_1-snap.3615-T1
Valid prediction for snap_scaffold_1-snap.3650-T1
Valid prediction for GlimmerHMM_glimmerT_2648-T1
Valid prediction for GlimmerHMM_glimmerT_2651-T1
Valid prediction for GlimmerHMM_glimmerT_2627-T1
Valid prediction for snap_scaffold_1-snap.3618-T1
Valid prediction for GlimmerHMM_glimmerT_2631-T1
Valid prediction for Augustus_model.g1894.t1
Valid prediction for snap_scaffold_1-snap.3643-T1
Valid prediction for snap_scaffold_1-snap.3607-T1
Valid prediction for GlimmerHMM_glimmerT_2645-T1
Valid prediction for snap_scaffold_1-snap.3637-T1
Valid prediction for snap_scaffold_1-snap.3648-T1
Valid prediction for snap_scaffold_1-snap.3629-T1
Valid prediction for Augustus_model.g1900.t1
Valid prediction for Augustus_model.g1899.t1
Valid prediction for snap_scaffold_1-snap.3647-T1
Valid prediction for GlimmerHMM_glimmerT_2640-T1
Valid prediction for snap_scaffold_1-snap.3628-T1
Valid prediction for GlimmerHMM_glimmerT_2649-T1
Valid prediction for snap_scaffold_1-snap.3640-T1
Valid prediction for snap_scaffold_1-snap.3608-T1
Valid prediction for snap_scaffold_1-snap.3612-T1
Valid prediction for Augustus_model.g1901.t1
Valid prediction for snap_scaffold_1-snap.3632-T1
Valid prediction for snap_scaffold_1-snap.3633-T1
Valid prediction for GlimmerHMM_glimmerT_2626-T1
Valid prediction for snap_scaffold_1-snap.3622-T1
Valid prediction for snap_scaffold_1-snap.3649-T1
Valid prediction for GlimmerHMM_glimmerT_2622-T1
Valid prediction for GlimmerHMM_glimmerT_2647-T1
Valid prediction for snap_scaffold_1-snap.3619-T1
Valid prediction for GlimmerHMM_glimmerT_2632-T1
Valid prediction for snap_scaffold_1-snap.3611-T1
Valid prediction for snap_scaffold_1-snap.3641-T1
Valid prediction for Augustus_model.g1898.t1
Valid prediction for snap_scaffold_1-snap.3616-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2636-T1
Valid prediction for Augustus_model.g1892.t1
Valid prediction for snap_scaffold_1-snap.3626-T1
Valid prediction for GlimmerHMM_glimmerT_2652-T1
Valid prediction for GlimmerHMM_glimmerT_2634-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.g1891.t1
Valid prediction for GlimmerHMM_glimmerT_2639-T1
Valid prediction for GlimmerHMM_glimmerT_2633-T1
Valid prediction for snap_scaffold_1-snap.3625-T1
Valid prediction for GlimmerHMM_glimmerT_2654-T1
Valid prediction for GlimmerHMM_glimmerT_2623-T1
Valid prediction for snap_scaffold_1-snap.3635-T1
Valid prediction for GlimmerHMM_glimmerT_2643-T1
Valid prediction for GlimmerHMM_glimmerT_2621-T1
Valid prediction for GlimmerHMM_glimmerT_2637-T1
Valid prediction for snap_scaffold_1-snap.3623-T1
Valid prediction for Augustus_model.g1907.t1
Couldn't classify 230261, 230641
Sorry, prediction pasa_asmbl_1149.p4 fails validation.
(ATG)	 GA	230261-230641	TC	TCT
Valid prediction for GlimmerHMM_glimmerT_2625-T1
Valid prediction for snap_scaffold_1-snap.3610-T1
Valid prediction for snap_scaffold_1-snap.3617-T1
Valid prediction for Augustus_model.g1890.t1
Valid prediction for snap_scaffold_1-snap.3630-T1
Valid prediction for snap_scaffold_1-snap.3646-T1
Valid prediction for GlimmerHMM_glimmerT_2655-T1
Valid prediction for snap_scaffold_1-snap.3609-T1
Valid prediction for CodingQuarry_transcript_3017-T1
Valid prediction for GlimmerHMM_glimmerT_2624-T1
Valid prediction for snap_scaffold_1-snap.3614-T1
Valid prediction for HiQ_model.g1895.t1
Valid prediction for GlimmerHMM_glimmerT_2629-T1
Valid prediction for snap_scaffold_1-snap.3624-T1
Valid prediction for Augustus_model.g1893.t1
Couldn't classify 203124, 203182
Sorry, prediction pasa_asmbl_1150.p1 fails validation.
(GTG)	 AG	203124-203182	GT	GTG
(GTA)	 AG	203271-203382	GT	AGG
(TAC)	 AG	203571-203600	GT	GGG
(GAC)	 AG	203862-203909	GT	AGG
(ATT)	 AG	204452-204566	GT	AGG
(TGG)	 AG	205208-205279	GT	CCG
(ATA)	 AG	206099-206178	GT	AGG
(GCC)	 AG	206606-206684	GT	AGG
(CGG)	 AG	207270-207443	GT	GAG
(GGT)	 AG	207861-207928	GT	GAG
-recovered pasa_asmbl_1150.p1, terminal, 206606, 206684
-recovered pasa_asmbl_1150.p1, terminal, 207861, 207928
-recovered pasa_asmbl_1150.p1, internal, 203124, 203182
-recovered pasa_asmbl_1150.p1, internal, 203271, 203382
-recovered pasa_asmbl_1150.p1, internal, 203571, 203600
-recovered pasa_asmbl_1150.p1, internal, 203862, 203909
-recovered pasa_asmbl_1150.p1, internal, 204452, 204566
-recovered pasa_asmbl_1150.p1, internal, 205208, 205279
-recovered pasa_asmbl_1150.p1, internal, 206099, 206178
-recovered pasa_asmbl_1150.p1, internal, 206606, 206684
-recovered pasa_asmbl_1150.p1, internal, 207270, 207443
-recovered pasa_asmbl_1150.p1, internal, 207861, 207928
Valid prediction for GlimmerHMM_glimmerT_2641-T1
Valid prediction for Augustus_model.g1896.t1
Valid prediction for snap_scaffold_1-snap.3636-T1
Valid prediction for snap_scaffold_1-snap.3634-T1
Valid prediction for snap_scaffold_1-snap.3631-T1
Valid prediction for snap_scaffold_1-snap.3639-T1
Valid prediction for GlimmerHMM_glimmerT_2620-T1
Valid prediction for snap_scaffold_1-snap.3627-T1
Valid prediction for GlimmerHMM_glimmerT_2628-T1
Valid prediction for GlimmerHMM_glimmerT_2653-T1
Valid prediction for Augustus_model.g1904.t1
Valid prediction for Augustus_model.g1902.t1
Valid prediction for Augustus_model.g1903.t1
Couldn't classify 119489, 119582
Sorry, prediction pasa_asmbl_1153.p1 fails validation.
(GTC)	 CA	119489-119582	GT	AGG
(AGT)	 AG	119866-119973	GT	AGG
(GGA)	 AG	120596-120652	GT	CAG
(GAT)	 AG	121361-121402	GT	TAG
(TTG)	 AG	121500-121548	GT	GGG
(CTC)	 AG	122697-122765	GT	AGG
(GAA)	 AG	122892-122946	CC	GAC
-recovered pasa_asmbl_1153.p1, terminal, 122892, 122946
-recovered pasa_asmbl_1153.p1, internal, 119866, 119973
-recovered pasa_asmbl_1153.p1, internal, 120596, 120652
-recovered pasa_asmbl_1153.p1, internal, 121361, 121402
-recovered pasa_asmbl_1153.p1, internal, 121500, 121548
-recovered pasa_asmbl_1153.p1, internal, 122697, 122765
Valid prediction for CodingQuarry_transcript_3016-T1
Valid prediction for snap_scaffold_1-snap.3645-T1
Valid prediction for HiQ_model.g1897.t1
Valid prediction for GlimmerHMM_glimmerT_2644-T1
Valid prediction for snap_scaffold_1-snap.3620-T1
Valid prediction for GlimmerHMM_glimmerT_2650-T1
Valid prediction for GlimmerHMM_glimmerT_2646-T1
Valid prediction for Augustus_model.g1905.t1
Valid prediction for GlimmerHMM_glimmerT_2642-T1
Valid prediction for snap_scaffold_1-snap.3621-T1
Valid prediction for snap_scaffold_1-snap.3638-T1
Valid prediction for snap_scaffold_1-snap.3644-T1
Valid prediction for Augustus_model.g1906.t1
Valid prediction for snap_scaffold_1-snap.3613-T1
Valid prediction for GlimmerHMM_glimmerT_2630-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 218977, rend_intergenic: 218974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37189, rend_intergenic: 17340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51211, rend_intergenic: 48135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75413, rend_intergenic: 57973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85037, rend_intergenic: 79222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95103, rend_intergenic: 86637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112030, rend_intergenic: 106831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124807, rend_intergenic: 112849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126947, rend_intergenic: 126397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137646, rend_intergenic: 127078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140243, rend_intergenic: 138141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150428, rend_intergenic: 142146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156699, rend_intergenic: 151872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185125, rend_intergenic: 177677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189167, rend_intergenic: 185179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216892, rend_intergenic: 189936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249490, rend_intergenic: 218988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283486, rend_intergenic: 249888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287149
-exon list size: 509


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
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1.4    
1.6    
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2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
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5.9    
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7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
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11.0    
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11.9    
12.1    
12.3    
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12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 218977, rend_intergenic: 218974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37189, rend_intergenic: 17340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51211, rend_intergenic: 48135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75413, rend_intergenic: 57973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85037, rend_intergenic: 79222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95103, rend_intergenic: 86637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112030, rend_intergenic: 106831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124807, rend_intergenic: 112849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126947, rend_intergenic: 126397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137646, rend_intergenic: 127078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140243, rend_intergenic: 138141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150428, rend_intergenic: 142146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156699, rend_intergenic: 151872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185125, rend_intergenic: 177677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189167, rend_intergenic: 185179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216892, rend_intergenic: 189936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249490, rend_intergenic: 218988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283486, rend_intergenic: 249888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support