-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_9647775-9852752

-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.1922-T1
Valid prediction for snap_scaffold_2-snap.1934-T1
Valid prediction for pasa_asmbl_24687.p1
Valid prediction for snap_scaffold_2-snap.1926-T1
Valid prediction for snap_scaffold_2-snap.1911-T1
Valid prediction for GlimmerHMM_glimmerT_4354-T1
Valid prediction for GlimmerHMM_glimmerT_4346-T1
Valid prediction for Augustus_model.g2920.t1
Valid prediction for GlimmerHMM_glimmerT_4349-T1
Valid prediction for GlimmerHMM_glimmerT_4361-T1
Valid prediction for Augustus_model.g2914.t1
Couldn't classify 24255, 24307
Couldn't classify 24679, 24821
Sorry, prediction pasa_asmbl_25411.p1 fails validation.
(CAT)	 CT	24255-24307	GT	AAG
(GCC)	 AG	24390-24496	GT	AGG
(GGA)	 AG	24679-24821	GT	AGG
-recovered pasa_asmbl_25411.p1, internal, 24390, 24496
-recovered pasa_asmbl_25411.p1, internal, 24679, 24821
Valid prediction for snap_scaffold_2-snap.1932-T1
Valid prediction for GlimmerHMM_glimmerT_4347-T1
Valid prediction for Augustus_model.g2916.t1
Valid prediction for GlimmerHMM_glimmerT_4330-T1
Valid prediction for GlimmerHMM_glimmerT_4340-T1
Valid prediction for GlimmerHMM_glimmerT_4345-T1
Valid prediction for snap_scaffold_2-snap.1917-T1
Valid prediction for GlimmerHMM_glimmerT_4357-T1
Valid prediction for snap_scaffold_2-snap.1930-T1
Valid prediction for Augustus_model.g2926.t1
Valid prediction for GlimmerHMM_glimmerT_4331-T1
Valid prediction for GlimmerHMM_glimmerT_4358-T1
Valid prediction for snap_scaffold_2-snap.1946-T1
Valid prediction for GlimmerHMM_glimmerT_4350-T1
Valid prediction for snap_scaffold_2-snap.1933-T1
Valid prediction for snap_scaffold_2-snap.1928-T1
Valid prediction for GlimmerHMM_glimmerT_4338-T1
Valid prediction for Augustus_model.g2911.t1
Valid prediction for snap_scaffold_2-snap.1913-T1
Valid prediction for snap_scaffold_2-snap.1912-T1
Valid prediction for GlimmerHMM_glimmerT_4334-T1
Valid prediction for snap_scaffold_2-snap.1945-T1
Valid prediction for snap_scaffold_2-snap.1923-T1
Valid prediction for GlimmerHMM_glimmerT_4336-T1
Valid prediction for HiQ_model.g2922.t1
Valid prediction for GlimmerHMM_glimmerT_4343-T1
Valid prediction for snap_scaffold_2-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_4363-T1
Valid prediction for snap_scaffold_2-snap.1919-T1
Valid prediction for snap_scaffold_2-snap.1929-T1
Valid prediction for GlimmerHMM_glimmerT_4333-T1
Valid prediction for Augustus_model.g2918.t1
Valid prediction for snap_scaffold_2-snap.1909-T1
Valid prediction for snap_scaffold_2-snap.1920-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_4351-T1
Valid prediction for Augustus_model.g2910.t1
Valid prediction for Augustus_model.g2913.t1
Valid prediction for pasa_asmbl_23388.p1
Valid prediction for pasa_asmbl_23387.p1
Valid prediction for snap_scaffold_2-snap.1914-T1
Valid prediction for snap_scaffold_2-snap.1915-T1
Valid prediction for GlimmerHMM_glimmerT_4335-T1
Valid prediction for snap_scaffold_2-snap.1931-T1
Valid prediction for snap_scaffold_2-snap.1939-T1
Valid prediction for GlimmerHMM_glimmerT_4359-T1
Valid prediction for snap_scaffold_2-snap.1944-T1
Valid prediction for GlimmerHMM_glimmerT_4362-T1
Valid prediction for CodingQuarry_transcript_28651-T1
Valid prediction for snap_scaffold_2-snap.1936-T1
Valid prediction for pasa_asmbl_23390.p1
Valid prediction for GlimmerHMM_glimmerT_4341-T1
Valid prediction for Augustus_model.g2929.t1
Valid prediction for snap_scaffold_2-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_4356-T1
Valid prediction for GlimmerHMM_glimmerT_4355-T1
Valid prediction for Augustus_model.g2924.t1
Valid prediction for GlimmerHMM_glimmerT_4337-T1
Valid prediction for GlimmerHMM_glimmerT_4329-T1
Valid prediction for snap_scaffold_2-snap.1908-T1
Valid prediction for GlimmerHMM_glimmerT_4352-T1
Valid prediction for GlimmerHMM_glimmerT_4348-T1
Valid prediction for Augustus_model.g2917.t1
Valid prediction for snap_scaffold_2-snap.1924-T1
Valid prediction for HiQ_model.g2923.t1
Valid prediction for snap_scaffold_2-snap.1942-T1
Valid prediction for Augustus_model.g2925.t1
Valid prediction for GlimmerHMM_glimmerT_4353-T1
Valid prediction for CodingQuarry_transcript_28649-T1
Valid prediction for snap_scaffold_2-snap.1943-T1
Valid prediction for snap_scaffold_2-snap.1918-T1
Valid prediction for HiQ_model.g2927.t1
Valid prediction for snap_scaffold_2-snap.1910-T1
Couldn't classify 50126, 50201
Couldn't classify 51459, 51574
Sorry, prediction pasa_asmbl_23389.p1 fails validation.
(AGG)	 CA	50126-50201	GT	AGG
(TGT)	 AG	50624-50789	GT	AAG
(ATT)	 AG	51185-51324	GT	AGG
(ATG)	 AG	51459-51574	GC	AAG
add_exon() Sorry, pasa_asmbl_23389.p1 51459-51574-initial-1 is invalid.
-recovered pasa_asmbl_23389.p1, initial, 51459, 51574
-recovered pasa_asmbl_23389.p1, internal, 50624, 50789
-recovered pasa_asmbl_23389.p1, internal, 51185, 51324
-recovered pasa_asmbl_23389.p1, internal, 51459, 51574
Valid prediction for snap_scaffold_2-snap.1940-T1
Valid prediction for Augustus_model.g2912.t1
Valid prediction for Augustus_model.g2919.t1
Valid prediction for snap_scaffold_2-snap.1937-T1
Valid prediction for GlimmerHMM_glimmerT_4344-T1
Valid prediction for snap_scaffold_2-snap.1916-T1
Valid prediction for CodingQuarry_transcript_28650-T1
Valid prediction for GlimmerHMM_glimmerT_4342-T1
Valid prediction for GlimmerHMM_glimmerT_4360-T1
Valid prediction for Augustus_model.g2928.t1
Valid prediction for GlimmerHMM_glimmerT_4339-T1
Valid prediction for snap_scaffold_2-snap.1925-T1
Valid prediction for HiQ_model.g2921.t1
Valid prediction for snap_scaffold_2-snap.1935-T1
Valid prediction for snap_scaffold_2-snap.1941-T1
Valid prediction for snap_scaffold_2-snap.1927-T1
Valid prediction for Augustus_model.g2915.t1
Valid prediction for GlimmerHMM_glimmerT_4332-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15474, rend_intergenic: 11975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24257, rend_intergenic: 15660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42641, rend_intergenic: 27115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57064, rend_intergenic: 53866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64082, rend_intergenic: 61987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82002, rend_intergenic: 70297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104233, rend_intergenic: 82652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116341, rend_intergenic: 109713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125214, rend_intergenic: 124714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131653, rend_intergenic: 126235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200524, rend_intergenic: 198225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204978
-exon list size: 404


building trellis

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0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
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3.4    
3.7    
3.9    
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4.4    
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5.2    
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5.9    
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6.7    
6.9    
7.1    
7.4    
7.6    
7.9    
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8.4    
8.6    
8.9    
9.1    
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9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
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    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
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61.6    
61.8    
62.1    
62.3    
62.6    
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63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
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65.3    
65.5    
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66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
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68.0    
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68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
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70.9    
71.2    
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72.9    
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73.4    
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73.9    
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74.4    
74.6    
74.9    
75.1    
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75.6    
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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    
94.8    
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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 15474, rend_intergenic: 11975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24257, rend_intergenic: 15660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42641, rend_intergenic: 27115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57064, rend_intergenic: 53866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64082, rend_intergenic: 61987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82002, rend_intergenic: 70297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104233, rend_intergenic: 82652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116341, rend_intergenic: 109713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125214, rend_intergenic: 124714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131653, rend_intergenic: 126235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200524, rend_intergenic: 198225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support