-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_7487875-7686225

-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 GeneMark_model.39410_t
Valid prediction for GeneMark_model.39413_t
Valid prediction for GeneMark_model.39395_t
Valid prediction for GlimmerHMM_glimmerT_22987-T1
Valid prediction for snap_scaffold_9-snap.1618-T1
Valid prediction for snap_scaffold_9-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_22969-T1
Valid prediction for snap_scaffold_9-snap.1607-T1
Valid prediction for Augustus_model.g15377.t1
Valid prediction for GeneMark_model.39420_t
Valid prediction for GeneMark_model.39399_t
Valid prediction for snap_scaffold_9-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_22963-T1
Valid prediction for snap_scaffold_9-snap.1603-T1
Valid prediction for GlimmerHMM_glimmerT_22981-T1
Valid prediction for snap_scaffold_9-snap.1612-T1
Valid prediction for snap_scaffold_9-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_22965-T1
Valid prediction for GlimmerHMM_glimmerT_22974-T1
Valid prediction for Augustus_model.g15367.t1
Valid prediction for GlimmerHMM_glimmerT_22985-T1
Valid prediction for GlimmerHMM_glimmerT_22970-T1
Valid prediction for Augustus_model.g15378.t1
Valid prediction for GeneMark_model.39401_t
Valid prediction for GeneMark_model.39405_t
Valid prediction for snap_scaffold_9-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_22966-T1
Valid prediction for GeneMark_model.39400_t
Valid prediction for snap_scaffold_9-snap.1622-T1
Valid prediction for snap_scaffold_9-snap.1621-T1
Valid prediction for Augustus_model.g15376.t1
Valid prediction for snap_scaffold_9-snap.1584-T1
Valid prediction for Augustus_model.g15366.t1
Valid prediction for GlimmerHMM_glimmerT_22988-T1
Valid prediction for snap_scaffold_9-snap.1608-T1
Valid prediction for GeneMark_model.39383_t
Valid prediction for snap_scaffold_9-snap.1623-T1
Valid prediction for GlimmerHMM_glimmerT_22989-T1
Valid prediction for snap_scaffold_9-snap.1598-T1
Valid prediction for snap_scaffold_9-snap.1610-T1
Valid prediction for Augustus_model.g15379.t1
Valid prediction for GlimmerHMM_glimmerT_22978-T1
Valid prediction for GlimmerHMM_glimmerT_22990-T1
Valid prediction for GeneMark_model.39389_t
Valid prediction for snap_scaffold_9-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_22980-T1
Valid prediction for GeneMark_model.39419_t
Valid prediction for snap_scaffold_9-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_22973-T1
Valid prediction for GeneMark_model.39393_t
Valid prediction for GlimmerHMM_glimmerT_22967-T1
Valid prediction for GeneMark_model.39385_t
Valid prediction for snap_scaffold_9-snap.1599-T1
Valid prediction for GeneMark_model.39402_t
Valid prediction for GeneMark_model.39421_t
Valid prediction for GeneMark_model.39381_t
Valid prediction for GeneMark_model.39416_t
Valid prediction for GlimmerHMM_glimmerT_22977-T1
Valid prediction for GeneMark_model.39387_t
Valid prediction for GeneMark_model.39407_t
Valid prediction for GlimmerHMM_glimmerT_22961-T1
Valid prediction for GlimmerHMM_glimmerT_22983-T1
Valid prediction for GeneMark_model.39408_t
Valid prediction for GeneMark_model.39423_t
Valid prediction for GlimmerHMM_glimmerT_22972-T1
Valid prediction for snap_scaffold_9-snap.1624-T1
Valid prediction for GeneMark_model.39379_t
Valid prediction for GeneMark_model.39397_t
Valid prediction for Augustus_model.g15374.t1
Valid prediction for GeneMark_model.39391_t

-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.g15371.t1
Couldn't classify 74940, 75116
Sorry, prediction pasa_asmbl_55073.p1 fails validation.
(TTG)	 GG	74940-75116	GT	AGG
(GTG)	 AG	76157-76324	GT	GGG
(GCC)	 AG	76415-76515	GT	AAG
(ACA)	 AG	76631-76976	GC	AGG
-recovered pasa_asmbl_55073.p1, terminal, 76631, 76976
-recovered pasa_asmbl_55073.p1, internal, 76157, 76324
-recovered pasa_asmbl_55073.p1, internal, 76415, 76515
-recovered pasa_asmbl_55073.p1, internal, 76631, 76976
Valid prediction for snap_scaffold_9-snap.1594-T1
Valid prediction for Augustus_model.g15363.t1
Valid prediction for GlimmerHMM_glimmerT_22968-T1
Valid prediction for snap_scaffold_9-snap.1605-T1
Valid prediction for snap_scaffold_9-snap.1613-T1
Valid prediction for Augustus_model.g15365.t1
Valid prediction for snap_scaffold_9-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_22960-T1
Valid prediction for Augustus_model.g15370.t1
Valid prediction for snap_scaffold_9-snap.1617-T1
Valid prediction for snap_scaffold_9-snap.1586-T1
Valid prediction for GeneMark_model.39403_t
Valid prediction for GlimmerHMM_glimmerT_22962-T1
Valid prediction for snap_scaffold_9-snap.1593-T1
Valid prediction for snap_scaffold_9-snap.1595-T1
Valid prediction for Augustus_model.g15372.t1
Valid prediction for snap_scaffold_9-snap.1615-T1
Valid prediction for snap_scaffold_9-snap.1590-T1
Valid prediction for GeneMark_model.39417_t
Valid prediction for Augustus_model.g15362.t1
Valid prediction for GeneMark_model.39398_t
Valid prediction for GeneMark_model.39392_t
Valid prediction for snap_scaffold_9-snap.1588-T1
Valid prediction for GeneMark_model.39390_t
Valid prediction for GeneMark_model.39388_t
Valid prediction for GlimmerHMM_glimmerT_22959-T1
Valid prediction for GlimmerHMM_glimmerT_22971-T1
Valid prediction for GeneMark_model.39415_t
Valid prediction for Augustus_model.g15373.t1
Valid prediction for GlimmerHMM_glimmerT_22964-T1
Valid prediction for snap_scaffold_9-snap.1587-T1
Valid prediction for GeneMark_model.39414_t
Valid prediction for snap_scaffold_9-snap.1625-T1
Valid prediction for snap_scaffold_9-snap.1592-T1
Valid prediction for snap_scaffold_9-snap.1611-T1
Couldn't classify 69944, 70122
Sorry, prediction pasa_asmbl_55074.p1 fails validation.
(ATG)	 TT	60493-60613	GT	AGG
(AAC)	 AG	63222-63352	GT	TGG
(TTC)	 AG	65391-65505	GT	AGG
(TGT)	 AG	66792-66903	GT	CGG
(GCT)	 AG	66992-67107	GT	GAG
(TGA)	 AG	69944-70122	TG	AGT
-recovered pasa_asmbl_55074.p1, initial, 60493, 60613
add_exon() Sorry, pasa_asmbl_55074.p1 66992-67107-terminal-2 is invalid.
-recovered pasa_asmbl_55074.p1, terminal, 66992, 67107
-recovered pasa_asmbl_55074.p1, internal, 63222, 63352
-recovered pasa_asmbl_55074.p1, internal, 65391, 65505
-recovered pasa_asmbl_55074.p1, internal, 66792, 66903
-recovered pasa_asmbl_55074.p1, internal, 66992, 67107
Valid prediction for GlimmerHMM_glimmerT_22957-T1
Valid prediction for GlimmerHMM_glimmerT_22958-T1
Valid prediction for GeneMark_model.39394_t
Valid prediction for GlimmerHMM_glimmerT_22976-T1
Valid prediction for GeneMark_model.39412_t
Valid prediction for snap_scaffold_9-snap.1614-T1
Valid prediction for GlimmerHMM_glimmerT_22986-T1
Valid prediction for GeneMark_model.39418_t
Valid prediction for snap_scaffold_9-snap.1600-T1
Valid prediction for Augustus_model.g15375.t1
Valid prediction for GeneMark_model.39406_t
Valid prediction for snap_scaffold_9-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_22991-T1
Valid prediction for GeneMark_model.39382_t
Valid prediction for GeneMark_model.39380_t
Valid prediction for GeneMark_model.39422_t
Valid prediction for snap_scaffold_9-snap.1582-T1
Valid prediction for GlimmerHMM_glimmerT_22984-T1
Valid prediction for GlimmerHMM_glimmerT_22975-T1
Valid prediction for snap_scaffold_9-snap.1619-T1
Valid prediction for GeneMark_model.39411_t
Valid prediction for snap_scaffold_9-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_22982-T1
Valid prediction for GeneMark_model.39396_t
Valid prediction for Augustus_model.g15364.t1
Valid prediction for GeneMark_model.39386_t
Couldn't classify 74940, 75116
Couldn't classify 78480, 78808
Sorry, prediction pasa_asmbl_55072.p1 fails validation.
(TTG)	 GG	74940-75116	GT	AGG
(GTG)	 AG	76157-76324	GT	GGG
(GCC)	 AG	76415-76515	GT	AAG
(ACA)	 AG	76631-76863	GT	ATG
(CTC)	 AG	78480-78808	TT	ACT
-recovered pasa_asmbl_55072.p1, internal, 76157, 76324
-recovered pasa_asmbl_55072.p1, internal, 76415, 76515
-recovered pasa_asmbl_55072.p1, internal, 76631, 76863
Valid prediction for Augustus_model.g15369.t1
Valid prediction for snap_scaffold_9-snap.1609-T1
Valid prediction for snap_scaffold_9-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_22979-T1
Valid prediction for GeneMark_model.39409_t
Valid prediction for snap_scaffold_9-snap.1591-T1
Valid prediction for snap_scaffold_9-snap.1585-T1
Valid prediction for GeneMark_model.39384_t
Valid prediction for Augustus_model.g15368.t1
Valid prediction for GeneMark_model.39378_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 25006, rend_intergenic: 25003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13622, rend_intergenic: 11166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58487, rend_intergenic: 50248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96622, rend_intergenic: 92145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101630, rend_intergenic: 97416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111234, rend_intergenic: 107981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128391, rend_intergenic: 126042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130912, rend_intergenic: 128559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198351
-exon list size: 595


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.8    
2.0    
2.2    
2.3    
2.5    
2.7    
2.8    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.0    
4.2    
4.4    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.5    
6.7    
6.9    
7.0    
7.2    
7.4    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.5    
8.7    
8.9    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.2    
11.4    
11.6    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.7    
12.9    
13.1    
13.2    
13.4    
13.6    
13.7    
13.9    
14.1    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.2    
16.4    
16.6    
16.8    
16.9    
17.1    
17.3    
17.4    
17.6    
17.8    
17.9    
18.1    
18.3    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
19.9    
20.1    
20.3    
20.4    
20.6    
20.8    
20.9    
21.1    
21.3    
21.4    
21.6    
21.8    
21.9    
22.1    
22.3    
22.4    
22.6    
22.8    
22.9    
23.1    
23.3    
23.5    
23.6    
23.8    
24.0    
24.1    
24.3    
24.5    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.5    
40.7    
40.9    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.4    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 25006, rend_intergenic: 25003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13622, rend_intergenic: 11166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58487, rend_intergenic: 50248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96622, rend_intergenic: 92145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101630, rend_intergenic: 97416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111234, rend_intergenic: 107981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128391, rend_intergenic: 126042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130912, rend_intergenic: 128559  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

-building DP trellis

-building trellis in range 170795 - 198351
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 170795 - 183017
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 170795 - 181744
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 170795 - 181466
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 183031 - 198351
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support