-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_7236373-7400016

-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_25-snap.1615-T1
Valid prediction for snap_scaffold_25-snap.1604-T1
Valid prediction for snap_scaffold_25-snap.1591-T1
Couldn't classify 85751, 85929
Couldn't classify 87735, 88848
Sorry, prediction CodingQuarry_transcript_38690-T1 fails validation.
(ATG)	 CC	85751-85929	CT	ACC
(CTA)	 AC	87735-88848	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_55786-T1
Valid prediction for GeneMark_model.97280_t
Valid prediction for snap_scaffold_25-snap.1587-T1
Valid prediction for GeneMark_model.97296_t
Valid prediction for GlimmerHMM_glimmerT_55792-T1
Valid prediction for CodingQuarry_transcript_38695-T1
Valid prediction for GeneMark_model.97276_t
Valid prediction for GlimmerHMM_glimmerT_55803-T1
Valid prediction for GeneMark_model.97277_t
Valid prediction for Augustus_model.g37215.t1
Valid prediction for GeneMark_model.97294_t
Valid prediction for CodingQuarry_transcript_38693-T1
Valid prediction for GlimmerHMM_glimmerT_55801-T1
Valid prediction for Augustus_model.g37225.t1
Valid prediction for GeneMark_model.97302_t
Valid prediction for GlimmerHMM_glimmerT_55811-T1
Valid prediction for snap_scaffold_25-snap.1588-T1
Valid prediction for GlimmerHMM_glimmerT_55798-T1
Valid prediction for HiQ_model.g37218.t1
Valid prediction for snap_scaffold_25-snap.1600-T1
Valid prediction for snap_scaffold_25-snap.1605-T1
Valid prediction for Augustus_model.g37216.t1
Valid prediction for snap_scaffold_25-snap.1598-T1
Valid prediction for snap_scaffold_25-snap.1593-T1
Couldn't classify 85751, 85791
Couldn't classify 87597, 88848
Sorry, prediction CodingQuarry_transcript_38692-T1 fails validation.
(ATG)	 CC	85751-85791	CT	ACC
(CTG)	 AC	87597-88848	TG	GAT
Valid prediction for GeneMark_model.97285_t
Valid prediction for GeneMark_model.97293_t
Valid prediction for Augustus_model.g37224.t1
Valid prediction for pasa_asmbl_33668.p1
Valid prediction for GeneMark_model.97304_t
Valid prediction for GlimmerHMM_glimmerT_55810-T1
Valid prediction for GeneMark_model.97292_t
Valid prediction for snap_scaffold_25-snap.1584-T1
Couldn't classify 85751, 86038
Couldn't classify 87844, 88848
Sorry, prediction CodingQuarry_transcript_38689-T1 fails validation.
(ATG)	 CC	85751-86038	CT	ACC
(CTC)	 AC	87844-88848	TG	GAT
Valid prediction for GeneMark_model.97282_t
Valid prediction for snap_scaffold_25-snap.1603-T1
Valid prediction for GlimmerHMM_glimmerT_55787-T1
Valid prediction for snap_scaffold_25-snap.1597-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.97290_t
Valid prediction for Augustus_model.g37219.t1
Valid prediction for GlimmerHMM_glimmerT_55797-T1
Valid prediction for snap_scaffold_25-snap.1602-T1
Valid prediction for GeneMark_model.97283_t
Valid prediction for GlimmerHMM_glimmerT_55808-T1
Valid prediction for snap_scaffold_25-snap.1599-T1
Valid prediction for GeneMark_model.97288_t
Valid prediction for GlimmerHMM_glimmerT_55799-T1
Valid prediction for snap_scaffold_25-snap.1582-T1
Valid prediction for snap_scaffold_25-snap.1578-T1
Valid prediction for GeneMark_model.97287_t
Valid prediction for GeneMark_model.97295_t
Valid prediction for GlimmerHMM_glimmerT_55800-T1
Valid prediction for CodingQuarry_transcript_38694-T1
Valid prediction for snap_scaffold_25-snap.1614-T1
Valid prediction for snap_scaffold_25-snap.1607-T1
Valid prediction for Augustus_model.g37209.t1
Valid prediction for Augustus_model.g37210.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 pasa_asmbl_34589.p1
Valid prediction for GeneMark_model.97300_t
Valid prediction for GlimmerHMM_glimmerT_55782-T1
Valid prediction for GlimmerHMM_glimmerT_55790-T1
Valid prediction for GlimmerHMM_glimmerT_55785-T1
Valid prediction for GlimmerHMM_glimmerT_55788-T1
Valid prediction for GeneMark_model.97281_t
Valid prediction for GlimmerHMM_glimmerT_55795-T1
Valid prediction for GlimmerHMM_glimmerT_55784-T1
Valid prediction for GeneMark_model.97291_t
Valid prediction for GlimmerHMM_glimmerT_55791-T1
Valid prediction for GeneMark_model.97284_t
Valid prediction for GlimmerHMM_glimmerT_55793-T1
Valid prediction for Augustus_model.g37222.t1
Valid prediction for HiQ_model.g37220.t1
Valid prediction for GlimmerHMM_glimmerT_55783-T1
Valid prediction for snap_scaffold_25-snap.1594-T1
Valid prediction for snap_scaffold_25-snap.1601-T1
Valid prediction for GeneMark_model.97303_t
Valid prediction for Augustus_model.g37214.t1
Valid prediction for snap_scaffold_25-snap.1609-T1
Valid prediction for snap_scaffold_25-snap.1589-T1
Valid prediction for GeneMark_model.97278_t
Valid prediction for snap_scaffold_25-snap.1580-T1
Couldn't classify 50936, 51006
Sorry, prediction pasa_asmbl_34373.p1 fails validation.
(GGG)	 TG	50936-51006	GT	AGG
(CAA)	 AG	51119-51208	GT	AGG
(ACC)	 AG	51333-51394	GT	ATG
(ATG)	 AG	51544-51710	GT	AGG
(ATC)	 AG	51992-52192	GG	AGG
add_exon() Sorry, pasa_asmbl_34373.p1 51544-51710-initial-1 is invalid.
-recovered pasa_asmbl_34373.p1, initial, 51544, 51710
-recovered pasa_asmbl_34373.p1, terminal, 51992, 52192
-recovered pasa_asmbl_34373.p1, internal, 51119, 51208
-recovered pasa_asmbl_34373.p1, internal, 51333, 51394
-recovered pasa_asmbl_34373.p1, internal, 51544, 51710
Valid prediction for HiQ_model.g37221.t1
Valid prediction for snap_scaffold_25-snap.1612-T1
Valid prediction for snap_scaffold_25-snap.1585-T1
Valid prediction for Augustus_model.g37208.t1
Valid prediction for Augustus_model.g37212.t1
Couldn't classify 40269, 40275
Sorry, prediction pasa_asmbl_34374.p2 fails validation.
(GAC)	 CC	40269-40275	GT	AAG
(GGT)	 AG	40430-40596	GT	AGG
(GTC)	 AG	40820-40978	GA	AAG
-recovered pasa_asmbl_34374.p2, terminal, 40820, 40978
-recovered pasa_asmbl_34374.p2, internal, 40430, 40596
Valid prediction for GeneMark_model.97289_t
Valid prediction for CodingQuarry_transcript_38698-T1
Valid prediction for snap_scaffold_25-snap.1611-T1
Valid prediction for GeneMark_model.97299_t
Valid prediction for GlimmerHMM_glimmerT_55796-T1
Valid prediction for GlimmerHMM_glimmerT_55807-T1
Valid prediction for GlimmerHMM_glimmerT_55806-T1
Valid prediction for snap_scaffold_25-snap.1610-T1
Valid prediction for snap_scaffold_25-snap.1590-T1
Valid prediction for GlimmerHMM_glimmerT_55781-T1
Valid prediction for GlimmerHMM_glimmerT_55794-T1
Valid prediction for GlimmerHMM_glimmerT_55809-T1
Valid prediction for GeneMark_model.97298_t
Valid prediction for GeneMark_model.97305_t
Valid prediction for Augustus_model.g37213.t1
Valid prediction for snap_scaffold_25-snap.1579-T1
Valid prediction for Augustus_model.g37223.t1
Valid prediction for snap_scaffold_25-snap.1613-T1
Valid prediction for Augustus_model.g37211.t1
Valid prediction for snap_scaffold_25-snap.1595-T1
Valid prediction for GeneMark_model.97286_t
Valid prediction for GlimmerHMM_glimmerT_55802-T1
Valid prediction for snap_scaffold_25-snap.1596-T1
Valid prediction for snap_scaffold_25-snap.1581-T1
Valid prediction for CodingQuarry_transcript_38697-T1
Valid prediction for snap_scaffold_25-snap.1592-T1
Valid prediction for GeneMark_model.97306_t
Valid prediction for GeneMark_model.97279_t
Valid prediction for snap_scaffold_25-snap.1606-T1
Valid prediction for snap_scaffold_25-snap.1608-T1
Valid prediction for snap_scaffold_25-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_55804-T1
Valid prediction for GlimmerHMM_glimmerT_55805-T1
Valid prediction for snap_scaffold_25-snap.1586-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_38696-T1
Valid prediction for Augustus_model.g37217.t1
Valid prediction for GlimmerHMM_glimmerT_55789-T1
Valid prediction for GeneMark_model.97301_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35435, rend_intergenic: 33289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43448, rend_intergenic: 38407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47509, rend_intergenic: 44054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80703, rend_intergenic: 78512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98943, rend_intergenic: 97052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 67403, rend_intergenic: 67400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163644
-exon list size: 462


building trellis

0.2    
0.4    
0.6    
0.9    
1.1    
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1.7    
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2.2    
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2.6    
2.8    
3.0    
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3.4    
3.7    
3.9    
4.1    
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4.5    
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5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.5    
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17.9    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 35435, rend_intergenic: 33289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43448, rend_intergenic: 38407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47509, rend_intergenic: 44054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80703, rend_intergenic: 78512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98943, rend_intergenic: 97052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 67403, rend_intergenic: 67400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 139759 - 163644
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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 139759 - 153623
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 142759 - 153623
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 142759 - 153181
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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