-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_8963045-9301900

-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_16-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_38778-T1
Valid prediction for snap_scaffold_16-snap.1672-T1
Valid prediction for snap_scaffold_16-snap.1658-T1
Valid prediction for snap_scaffold_16-snap.1696-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1699-T1
Valid prediction for snap_scaffold_16-snap.1677-T1
Valid prediction for snap_scaffold_16-snap.1683-T1
Valid prediction for CodingQuarry_transcript_20048-T1
Valid prediction for snap_scaffold_16-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_38766-T1
Valid prediction for GlimmerHMM_glimmerT_38760-T1
Valid prediction for snap_scaffold_16-snap.1700-T1
Valid prediction for snap_scaffold_16-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_38769-T1
Couldn't classify 189981, 190063
Sorry, prediction pasa_asmbl_16471.p1 fails validation.
(CTG)	 AG	189981-190063	GT	ATG
(GTA)	 AG	190236-190339	GT	AGG
(ACA)	 AG	190504-190658	GT	AGG
(TAC)	 AG	190809-190910	GT	AGG
(GCT)	 AG	191049-191216	TG	GAT
-recovered pasa_asmbl_16471.p1, terminal, 191049, 191216
-recovered pasa_asmbl_16471.p1, internal, 189981, 190063
-recovered pasa_asmbl_16471.p1, internal, 190236, 190339
-recovered pasa_asmbl_16471.p1, internal, 190504, 190658
-recovered pasa_asmbl_16471.p1, internal, 190809, 190910
Valid prediction for CodingQuarry_transcript_20046-T1
Valid prediction for HiQ_model.g25883.t1
Valid prediction for GlimmerHMM_glimmerT_38777-T1
Valid prediction for GlimmerHMM_glimmerT_38759-T1
Valid prediction for snap_scaffold_16-snap.1704-T1
Valid prediction for snap_scaffold_16-snap.1695-T1
Couldn't classify 308062, 308601
Sorry, prediction pasa_asmbl_16475.p2 fails validation.
(ATG)	 TA	308062-308601	GG	GGG
Valid prediction for snap_scaffold_16-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_38774-T1
Valid prediction for HiQ_model.g25889.t1
Valid prediction for GlimmerHMM_glimmerT_38761-T1
Valid prediction for GlimmerHMM_glimmerT_38780-T1
Valid prediction for GlimmerHMM_glimmerT_38775-T1
Valid prediction for GlimmerHMM_glimmerT_38757-T1
Valid prediction for Augustus_model.g25882.t1
Valid prediction for HiQ_model.g25890.t1
Valid prediction for GlimmerHMM_glimmerT_38768-T1
Valid prediction for CodingQuarry_transcript_20049-T1
Valid prediction for snap_scaffold_16-snap.1678-T1
Valid prediction for snap_scaffold_16-snap.1657-T1
Valid prediction for pasa_asmbl_16467.p1
Valid prediction for snap_scaffold_16-snap.1679-T1
Valid prediction for pasa_asmbl_16455.p1
Valid prediction for snap_scaffold_16-snap.1680-T1
Valid prediction for CodingQuarry_transcript_20047-T1
Valid prediction for snap_scaffold_16-snap.1674-T1
Valid prediction for snap_scaffold_16-snap.1669-T1
Valid prediction for snap_scaffold_16-snap.1662-T1
Valid prediction for CodingQuarry_transcript_20045-T1
Valid prediction for snap_scaffold_16-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_38763-T1
Valid prediction for GlimmerHMM_glimmerT_38779-T1
Valid prediction for Augustus_model.g25894.t1
Valid prediction for snap_scaffold_16-snap.1692-T1
Valid prediction for snap_scaffold_16-snap.1655-T1
Valid prediction for snap_scaffold_16-snap.1661-T1
Valid prediction for Augustus_model.g25895.t1
Valid prediction for CodingQuarry_transcript_20050-T1
Valid prediction for pasa_asmbl_16459.p1
Valid prediction for GlimmerHMM_glimmerT_38765-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.g25887.t1
Valid prediction for snap_scaffold_16-snap.1698-T1
Couldn't classify 163675, 163781
Sorry, prediction pasa_asmbl_17265.p1 fails validation.
(ATC)	 AT	163675-163781	GT	GGG
(GAT)	 AG	163970-164121	GT	AGG
(GAA)	 AG	164236-164354	AC	AGA
-recovered pasa_asmbl_17265.p1, terminal, 164236, 164354
-recovered pasa_asmbl_17265.p1, internal, 163970, 164121
Valid prediction for snap_scaffold_16-snap.1670-T1
Valid prediction for snap_scaffold_16-snap.1664-T1
Valid prediction for snap_scaffold_16-snap.1666-T1
Valid prediction for snap_scaffold_16-snap.1663-T1
Valid prediction for Augustus_model.g25892.t1
Couldn't classify 95498, 95621
Sorry, prediction pasa_asmbl_17271.p1 fails validation.
(GAA)	 CA	95498-95621	GT	GCG
(GAG)	 AG	95897-96024	GT	AGG
(GCC)	 AG	96138-96314	GT	TGG
(CCA)	 AG	96679-96786	GT	ACG
(GTC)	 AG	96906-96980	GT	TGG
(GAG)	 AG	97100-97199	GT	GAG
(GTG)	 AG	97285-97413	GT	TAG
(ACA)	 AG	97533-97615	AG	GAA
-recovered pasa_asmbl_17271.p1, terminal, 97533, 97615
-recovered pasa_asmbl_17271.p1, internal, 95897, 96024
-recovered pasa_asmbl_17271.p1, internal, 96138, 96314
-recovered pasa_asmbl_17271.p1, internal, 96679, 96786
-recovered pasa_asmbl_17271.p1, internal, 96906, 96980
-recovered pasa_asmbl_17271.p1, internal, 97100, 97199
-recovered pasa_asmbl_17271.p1, internal, 97285, 97413
Valid prediction for snap_scaffold_16-snap.1668-T1
Valid prediction for snap_scaffold_16-snap.1703-T1
Valid prediction for Augustus_model.g25896.t1
Valid prediction for GlimmerHMM_glimmerT_38781-T1
Valid prediction for snap_scaffold_16-snap.1665-T1
Valid prediction for snap_scaffold_16-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_38767-T1
Valid prediction for snap_scaffold_16-snap.1688-T1
Valid prediction for Augustus_model.g25884.t1
Valid prediction for GlimmerHMM_glimmerT_38762-T1
Valid prediction for GlimmerHMM_glimmerT_38758-T1
Valid prediction for snap_scaffold_16-snap.1682-T1
Valid prediction for Augustus_model.g25891.t1
Valid prediction for HiQ_model.g25893.t1
Valid prediction for snap_scaffold_16-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_38771-T1
Valid prediction for snap_scaffold_16-snap.1673-T1
Valid prediction for Augustus_model.g25886.t1
Valid prediction for GlimmerHMM_glimmerT_38776-T1
Valid prediction for Augustus_model.g25885.t1
Valid prediction for GlimmerHMM_glimmerT_38770-T1
Valid prediction for GlimmerHMM_glimmerT_38773-T1
Valid prediction for snap_scaffold_16-snap.1659-T1
Valid prediction for snap_scaffold_16-snap.1653-T1
Valid prediction for snap_scaffold_16-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_38764-T1
Valid prediction for GlimmerHMM_glimmerT_38772-T1
Valid prediction for snap_scaffold_16-snap.1676-T1
Valid prediction for snap_scaffold_16-snap.1681-T1
Valid prediction for snap_scaffold_16-snap.1687-T1
Valid prediction for snap_scaffold_16-snap.1684-T1
Valid prediction for Augustus_model.g25888.t1
Valid prediction for snap_scaffold_16-snap.1690-T1
Valid prediction for snap_scaffold_16-snap.1693-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1686-T1
Valid prediction for GlimmerHMM_glimmerT_38756-T1
Valid prediction for snap_scaffold_16-snap.1691-T1
Valid prediction for snap_scaffold_16-snap.1702-T1
Valid prediction for snap_scaffold_16-snap.1697-T1
Couldn't classify 163461, 163568
Sorry, prediction pasa_asmbl_17266.p1 fails validation.
(ATG)	 CG	162186-162260	GT	AGG
(ATG)	 AG	162556-162689	GT	AGG
(TTT)	 AG	162862-162966	GT	AGG
(GTT)	 AG	163295-163340	GT	AGG
(ATC)	 AG	163461-163568	GG	AAG
-recovered pasa_asmbl_17266.p1, initial, 162186, 162260
-recovered pasa_asmbl_17266.p1, initial, 162556, 162689
-recovered pasa_asmbl_17266.p1, internal, 162556, 162689
-recovered pasa_asmbl_17266.p1, internal, 162862, 162966
-recovered pasa_asmbl_17266.p1, internal, 163295, 163340
Valid prediction for snap_scaffold_16-snap.1667-T1
Valid prediction for snap_scaffold_16-snap.1701-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 147402, rend_intergenic: 144441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149924, rend_intergenic: 147789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209977, rend_intergenic: 196741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226602, rend_intergenic: 219042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235232, rend_intergenic: 229885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260097, rend_intergenic: 246493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 274625, rend_intergenic: 268199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306885, rend_intergenic: 293027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 321116, rend_intergenic: 309527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 331196, rend_intergenic: 322657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 336070, rend_intergenic: 332827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 338856
-exon list size: 363


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
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7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
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21.4    
21.6    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.6    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.9    
30.1    
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    
36.2    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.8    
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    
69.9    
70.1    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.4    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 147402, rend_intergenic: 144441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149924, rend_intergenic: 147789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209977, rend_intergenic: 196741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226602, rend_intergenic: 219042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235232, rend_intergenic: 229885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260097, rend_intergenic: 246493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 274625, rend_intergenic: 268199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306885, rend_intergenic: 293027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 321116, rend_intergenic: 309527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 331196, rend_intergenic: 322657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 336070, rend_intergenic: 332827  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