-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_9254798-9406906

-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_2-snap.1840-T1
Valid prediction for GlimmerHMM_glimmerT_4299-T1
Valid prediction for GlimmerHMM_glimmerT_4283-T1
Valid prediction for GlimmerHMM_glimmerT_4301-T1
Valid prediction for CodingQuarry_transcript_28646-T1
Valid prediction for GlimmerHMM_glimmerT_4297-T1
Valid prediction for Augustus_model.g2889.t1
Valid prediction for GlimmerHMM_glimmerT_4276-T1
Valid prediction for snap_scaffold_2-snap.1843-T1
Valid prediction for Augustus_model.g2893.t1
Valid prediction for snap_scaffold_2-snap.1829-T1
Valid prediction for CodingQuarry_transcript_28645-T1
Valid prediction for snap_scaffold_2-snap.1823-T1
Valid prediction for GlimmerHMM_glimmerT_4290-T1
Valid prediction for GlimmerHMM_glimmerT_4291-T1
Valid prediction for GlimmerHMM_glimmerT_4298-T1
Valid prediction for snap_scaffold_2-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_4289-T1
Valid prediction for snap_scaffold_2-snap.1822-T1
Valid prediction for Augustus_model.g2894.t1
Valid prediction for snap_scaffold_2-snap.1826-T1
Valid prediction for snap_scaffold_2-snap.1844-T1
Valid prediction for GlimmerHMM_glimmerT_4286-T1
Couldn't classify 41031, 41308
Sorry, prediction pasa_asmbl_24678.p1 fails validation.
(ATG)	 AA	40021-40248	GT	TGG
(GAT)	 AG	40380-40935	GT	CTG
(CTA)	 AG	41031-41308	AC	GCA
-recovered pasa_asmbl_24678.p1, initial, 40021, 40248
-recovered pasa_asmbl_24678.p1, internal, 40380, 40935
Valid prediction for snap_scaffold_2-snap.1837-T1
Valid prediction for snap_scaffold_2-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_4303-T1
Valid prediction for snap_scaffold_2-snap.1854-T1
Valid prediction for Augustus_model.g2882.t1
Valid prediction for snap_scaffold_2-snap.1820-T1
Valid prediction for Augustus_model.g2885.t1
Valid prediction for Augustus_model.g2891.t1
Valid prediction for GlimmerHMM_glimmerT_4287-T1
Valid prediction for GlimmerHMM_glimmerT_4279-T1
Valid prediction for Augustus_model.g2895.t1
Valid prediction for snap_scaffold_2-snap.1846-T1
Valid prediction for snap_scaffold_2-snap.1838-T1
Valid prediction for snap_scaffold_2-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_4295-T1
Valid prediction for snap_scaffold_2-snap.1832-T1
Couldn't classify 41636, 41677
Sorry, prediction pasa_asmbl_24681.p1 fails validation.
(CTG)	 AG	41636-41677	GT	TGG
(ATT)	 AG	41803-41887	GT	CGG
(GTG)	 AG	42022-42254	GC	AGG
(GCT)	 AG	42440-42634	GT	AGG
(GAC)	 AG	42718-42943	GT	GGG
(GCG)	 AG	43089-43627	GC	GAG
-recovered pasa_asmbl_24681.p1, terminal, 43089, 43627
-recovered pasa_asmbl_24681.p1, internal, 41636, 41677
-recovered pasa_asmbl_24681.p1, internal, 41803, 41887
-recovered pasa_asmbl_24681.p1, internal, 42022, 42254
-recovered pasa_asmbl_24681.p1, internal, 42440, 42634
-recovered pasa_asmbl_24681.p1, internal, 42718, 42943
-recovered pasa_asmbl_24681.p1, internal, 43089, 43627
Valid prediction for snap_scaffold_2-snap.1849-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_4300-T1
Valid prediction for snap_scaffold_2-snap.1845-T1
Valid prediction for pasa_asmbl_23376.p2
Valid prediction for GlimmerHMM_glimmerT_4293-T1
Valid prediction for pasa_asmbl_23372.p1
Valid prediction for CodingQuarry_transcript_28643-T1
Valid prediction for snap_scaffold_2-snap.1839-T1
Valid prediction for Augustus_model.g2884.t1
Valid prediction for snap_scaffold_2-snap.1817-T1
Valid prediction for snap_scaffold_2-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_4282-T1
Valid prediction for snap_scaffold_2-snap.1818-T1
Valid prediction for GlimmerHMM_glimmerT_4292-T1
Valid prediction for snap_scaffold_2-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_4302-T1
Valid prediction for GlimmerHMM_glimmerT_4285-T1
Valid prediction for snap_scaffold_2-snap.1828-T1
Valid prediction for GlimmerHMM_glimmerT_4278-T1
Valid prediction for CodingQuarry_transcript_28644-T1
Valid prediction for snap_scaffold_2-snap.1850-T1
Valid prediction for Augustus_model.g2879.t1
Valid prediction for Augustus_model.g2890.t1
Valid prediction for GlimmerHMM_glimmerT_4281-T1
Valid prediction for snap_scaffold_2-snap.1836-T1
Valid prediction for snap_scaffold_2-snap.1847-T1
Valid prediction for snap_scaffold_2-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_4280-T1
Valid prediction for snap_scaffold_2-snap.1842-T1
Valid prediction for Augustus_model.g2883.t1
Valid prediction for snap_scaffold_2-snap.1833-T1
Valid prediction for GlimmerHMM_glimmerT_4294-T1
Valid prediction for snap_scaffold_2-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_4296-T1
Valid prediction for Augustus_model.g2888.t1
Valid prediction for snap_scaffold_2-snap.1857-T1
Valid prediction for pasa_asmbl_23374.p1
Valid prediction for snap_scaffold_2-snap.1841-T1
Valid prediction for GlimmerHMM_glimmerT_4288-T1
Valid prediction for GlimmerHMM_glimmerT_4277-T1
Valid prediction for HiQ_model.g2887.t1
Valid prediction for Augustus_model.g2892.t1
Valid prediction for snap_scaffold_2-snap.1834-T1
Valid prediction for CodingQuarry_transcript_28647-T1
Valid prediction for snap_scaffold_2-snap.1835-T1
Valid prediction for snap_scaffold_2-snap.1825-T1
Valid prediction for snap_scaffold_2-snap.1827-T1
Valid prediction for HiQ_model.g2886.t1
Valid prediction for Augustus_model.g2880.t1
Valid prediction for snap_scaffold_2-snap.1851-T1
Valid prediction for CodingQuarry_transcript_28648-T1
Valid prediction for snap_scaffold_2-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_4284-T1
Valid prediction for snap_scaffold_2-snap.1824-T1
Valid prediction for snap_scaffold_2-snap.1831-T1
Valid prediction for Augustus_model.g2881.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17744, rend_intergenic: 14240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26311, rend_intergenic: 19302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37946, rend_intergenic: 31444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73573, rend_intergenic: 62374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86244, rend_intergenic: 75532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99890, rend_intergenic: 95563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100544, rend_intergenic: 99926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104911, rend_intergenic: 103552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109000, rend_intergenic: 105034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114244, rend_intergenic: 111298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117494, rend_intergenic: 115019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120884, rend_intergenic: 117608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127230, rend_intergenic: 120988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128195, rend_intergenic: 127503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130366, rend_intergenic: 128733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135471, rend_intergenic: 131051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139457, rend_intergenic: 136535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141327, rend_intergenic: 139570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143681, rend_intergenic: 141654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152109
-exon list size: 348


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 17744, rend_intergenic: 14240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26311, rend_intergenic: 19302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37946, rend_intergenic: 31444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73573, rend_intergenic: 62374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86244, rend_intergenic: 75532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99890, rend_intergenic: 95563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100544, rend_intergenic: 99926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104911, rend_intergenic: 103552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109000, rend_intergenic: 105034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114244, rend_intergenic: 111298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117494, rend_intergenic: 115019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120884, rend_intergenic: 117608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127230, rend_intergenic: 120988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128195, rend_intergenic: 127503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130366, rend_intergenic: 128733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135471, rend_intergenic: 131051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139457, rend_intergenic: 136535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141327, rend_intergenic: 139570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143681, rend_intergenic: 141654  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