-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_8941148-9291510

-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_7-snap.1814-T1
Valid prediction for snap_scaffold_7-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_17846-T1
Valid prediction for GlimmerHMM_glimmerT_17856-T1
Valid prediction for GlimmerHMM_glimmerT_17861-T1
Valid prediction for snap_scaffold_7-snap.1773-T1
Valid prediction for snap_scaffold_7-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_17860-T1
Valid prediction for snap_scaffold_7-snap.1791-T1
Valid prediction for Augustus_model.g11987.t1
Valid prediction for snap_scaffold_7-snap.1796-T1
Valid prediction for snap_scaffold_7-snap.1788-T1
Valid prediction for Augustus_model.g11989.t1
Valid prediction for snap_scaffold_7-snap.1769-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g11988.t1
Valid prediction for GlimmerHMM_glimmerT_17858-T1
Valid prediction for snap_scaffold_7-snap.1802-T1
Valid prediction for Augustus_model.g11984.t1
Valid prediction for snap_scaffold_7-snap.1807-T1
Valid prediction for snap_scaffold_7-snap.1805-T1
Valid prediction for Augustus_model.g11983.t1
Couldn't classify 215730, 215883
Couldn't classify 219649, 219774
Sorry, prediction pasa_asmbl_50620.p1 fails validation.
(CCC)	 GT	215730-215883	GT	AGG
(GCT)	 AG	216957-217018	GT	CGG
(AAC)	 AG	219649-219774	TA	CCT
-recovered pasa_asmbl_50620.p1, internal, 216957, 217018
Valid prediction for snap_scaffold_7-snap.1790-T1
Couldn't classify 345244, 345319
Sorry, prediction pasa_asmbl_50073.p1 fails validation.
(CCC)	 AC	345244-345319	GT	TGG
(ATG)	 AG	345553-345648	GT	AGG
(AGA)	 AG	345761-345999	TT	AAT
add_exon() Sorry, pasa_asmbl_50073.p1 345553-345648-initial-1 is invalid.
-recovered pasa_asmbl_50073.p1, initial, 345553, 345648
-recovered pasa_asmbl_50073.p1, terminal, 345761, 345999
-recovered pasa_asmbl_50073.p1, internal, 345553, 345648
Valid prediction for snap_scaffold_7-snap.1806-T1
Valid prediction for GlimmerHMM_glimmerT_17864-T1
Valid prediction for HiQ_model.g11991.t1
Valid prediction for snap_scaffold_7-snap.1786-T1
Valid prediction for snap_scaffold_7-snap.1787-T1
Valid prediction for snap_scaffold_7-snap.1778-T1
Valid prediction for snap_scaffold_7-snap.1813-T1
Couldn't classify 345196, 345210
Sorry, prediction pasa_asmbl_50072.p1 fails validation.
(ATG)	 GG	337416-337616	GT	CTG
(GTG)	 AG	338869-339013	GT	AAG
(GCC)	 AG	339875-340026	GT	CTG
(GTT)	 AG	340531-340611	GT	TGG
(GTG)	 AG	341116-341265	GT	CTG
(GTG)	 AG	341538-341681	GT	AGG
(GTG)	 AG	341900-341998	GT	AGG
(ATC)	 AG	342726-342899	GT	TGG
(GGC)	 AG	343932-344192	GT	CGG
(TGG)	 AG	344506-344622	GT	GGG
(ATC)	 AG	344986-345075	GT	CAG
(GCT)	 AG	345196-345210	GA	AAG
-recovered pasa_asmbl_50072.p1, initial, 337416, 337616
-recovered pasa_asmbl_50072.p1, internal, 338869, 339013
-recovered pasa_asmbl_50072.p1, internal, 339875, 340026
-recovered pasa_asmbl_50072.p1, internal, 340531, 340611
-recovered pasa_asmbl_50072.p1, internal, 341116, 341265
-recovered pasa_asmbl_50072.p1, internal, 341538, 341681
-recovered pasa_asmbl_50072.p1, internal, 341900, 341998
-recovered pasa_asmbl_50072.p1, internal, 342726, 342899
-recovered pasa_asmbl_50072.p1, internal, 343932, 344192
-recovered pasa_asmbl_50072.p1, internal, 344506, 344622
-recovered pasa_asmbl_50072.p1, internal, 344986, 345075
Valid prediction for Augustus_model.g11985.t1
Valid prediction for snap_scaffold_7-snap.1779-T1
Valid prediction for snap_scaffold_7-snap.1771-T1
Valid prediction for GlimmerHMM_glimmerT_17852-T1
Valid prediction for GlimmerHMM_glimmerT_17849-T1
Valid prediction for snap_scaffold_7-snap.1760-T1
Valid prediction for snap_scaffold_7-snap.1803-T1
Valid prediction for snap_scaffold_7-snap.1775-T1
Valid prediction for Augustus_model.g11979.t1
Valid prediction for snap_scaffold_7-snap.1767-T1
Valid prediction for snap_scaffold_7-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_17857-T1
Valid prediction for snap_scaffold_7-snap.1798-T1
Valid prediction for GlimmerHMM_glimmerT_17870-T1
Valid prediction for snap_scaffold_7-snap.1799-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 snap_scaffold_7-snap.1809-T1
Valid prediction for snap_scaffold_7-snap.1783-T1
Valid prediction for snap_scaffold_7-snap.1774-T1
Valid prediction for snap_scaffold_7-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_17847-T1
Valid prediction for snap_scaffold_7-snap.1776-T1
Valid prediction for Augustus_model.g11981.t1
Valid prediction for GlimmerHMM_glimmerT_17840-T1
Valid prediction for snap_scaffold_7-snap.1793-T1
Valid prediction for snap_scaffold_7-snap.1770-T1
Valid prediction for snap_scaffold_7-snap.1780-T1
Valid prediction for snap_scaffold_7-snap.1800-T1
Valid prediction for CodingQuarry_transcript_57584-T1
Valid prediction for snap_scaffold_7-snap.1782-T1
Valid prediction for snap_scaffold_7-snap.1797-T1
Valid prediction for snap_scaffold_7-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_17848-T1
Valid prediction for snap_scaffold_7-snap.1785-T1
Valid prediction for snap_scaffold_7-snap.1765-T1
Valid prediction for snap_scaffold_7-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_17865-T1
Valid prediction for snap_scaffold_7-snap.1808-T1
Valid prediction for snap_scaffold_7-snap.1761-T1
Valid prediction for GlimmerHMM_glimmerT_17863-T1
Valid prediction for GlimmerHMM_glimmerT_17867-T1
Valid prediction for snap_scaffold_7-snap.1766-T1
Valid prediction for snap_scaffold_7-snap.1810-T1
Valid prediction for snap_scaffold_7-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_17868-T1
Valid prediction for GlimmerHMM_glimmerT_17843-T1
Valid prediction for GlimmerHMM_glimmerT_17842-T1
Valid prediction for GlimmerHMM_glimmerT_17853-T1
Valid prediction for snap_scaffold_7-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_17845-T1
Valid prediction for snap_scaffold_7-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_17854-T1
Valid prediction for GlimmerHMM_glimmerT_17866-T1
Valid prediction for GlimmerHMM_glimmerT_17862-T1
Valid prediction for snap_scaffold_7-snap.1777-T1
Valid prediction for snap_scaffold_7-snap.1789-T1
Valid prediction for Augustus_model.g11982.t1
Valid prediction for GlimmerHMM_glimmerT_17869-T1
Valid prediction for Augustus_model.g11980.t1
Valid prediction for snap_scaffold_7-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_17850-T1
Valid prediction for snap_scaffold_7-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_17841-T1
Valid prediction for Augustus_model.g11990.t1
Valid prediction for Augustus_model.g11986.t1
Valid prediction for snap_scaffold_7-snap.1812-T1
Valid prediction for snap_scaffold_7-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_17859-T1
Valid prediction for GlimmerHMM_glimmerT_17844-T1
Valid prediction for GlimmerHMM_glimmerT_17851-T1
Valid prediction for pasa_asmbl_51043.p1
Valid prediction for GlimmerHMM_glimmerT_17855-T1
Valid prediction for snap_scaffold_7-snap.1784-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8088, rend_intergenic: 7890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10343, rend_intergenic: 9592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14742, rend_intergenic: 13728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62870, rend_intergenic: 58884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69444, rend_intergenic: 65208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81305, rend_intergenic: 69742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101077, rend_intergenic: 95476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113426, rend_intergenic: 102297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151053, rend_intergenic: 141902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167554, rend_intergenic: 165167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185978, rend_intergenic: 183453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195314, rend_intergenic: 189159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 350363
-exon list size: 351


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 8088, rend_intergenic: 7890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10343, rend_intergenic: 9592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14742, rend_intergenic: 13728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62870, rend_intergenic: 58884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69444, rend_intergenic: 65208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81305, rend_intergenic: 69742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101077, rend_intergenic: 95476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113426, rend_intergenic: 102297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151053, rend_intergenic: 141902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167554, rend_intergenic: 165167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185978, rend_intergenic: 183453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195314, rend_intergenic: 189159  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