-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_8683499-8898671

-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 GlimmerHMM_glimmerT_4311-T1
Valid prediction for GlimmerHMM_glimmerT_4307-T1
Valid prediction for GlimmerHMM_glimmerT_4314-T1
Valid prediction for GeneMark_model.6874_t
Valid prediction for GeneMark_model.6896_t
Valid prediction for Augustus_model.g2900.t1
Valid prediction for GlimmerHMM_glimmerT_4309-T1
Valid prediction for GlimmerHMM_glimmerT_4295-T1
Valid prediction for Augustus_model.g2896.t1
Valid prediction for Augustus_model.g2899.t1
Valid prediction for GeneMark_model.6877_t
Valid prediction for snap_scaffold_2-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_4313-T1
Valid prediction for Augustus_model.g2898.t1
Valid prediction for GeneMark_model.6889_t
Valid prediction for CodingQuarry_transcript_28579-T1
Valid prediction for GeneMark_model.6898_t
Valid prediction for GlimmerHMM_glimmerT_4312-T1
Valid prediction for snap_scaffold_2-snap.1762-T1
Valid prediction for Augustus_model.g2904.t1
Valid prediction for pasa_asmbl_24691.p2
Valid prediction for GeneMark_model.6884_t
Valid prediction for GeneMark_model.6892_t
Valid prediction for CodingQuarry_transcript_28580-T1
Valid prediction for CodingQuarry_transcript_28578-T1
Valid prediction for GeneMark_model.6900_t
Valid prediction for snap_scaffold_2-snap.1767-T1
Valid prediction for snap_scaffold_2-snap.1738-T1
Valid prediction for snap_scaffold_2-snap.1759-T1
Valid prediction for GlimmerHMM_glimmerT_4310-T1
Valid prediction for snap_scaffold_2-snap.1761-T1
Valid prediction for GeneMark_model.6908_t
Valid prediction for snap_scaffold_2-snap.1760-T1
Valid prediction for Augustus_model.g2887.t1
Valid prediction for GeneMark_model.6894_t
Valid prediction for pasa_asmbl_24685.p1
Valid prediction for GlimmerHMM_glimmerT_4297-T1
Valid prediction for GeneMark_model.6887_t
Valid prediction for GeneMark_model.6882_t
Valid prediction for snap_scaffold_2-snap.1736-T1
Valid prediction for Augustus_model.g2897.t1
Valid prediction for GlimmerHMM_glimmerT_4316-T1
Valid prediction for snap_scaffold_2-snap.1735-T1
Valid prediction for snap_scaffold_2-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_4292-T1
Valid prediction for snap_scaffold_2-snap.1745-T1
Valid prediction for GeneMark_model.6872_t
Valid prediction for snap_scaffold_2-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_4298-T1
Valid prediction for GlimmerHMM_glimmerT_4302-T1
Valid prediction for GeneMark_model.6901_t
Valid prediction for GeneMark_model.6879_t
Valid prediction for snap_scaffold_2-snap.1756-T1
Couldn't classify 173194, 173350
Couldn't classify 173689, 173815
Sorry, prediction pasa_asmbl_24679.p1 fails validation.
(ATG)	 GC	172656-172817	GT	AGG
(TAT)	 AG	172954-173077	GT	AGG
(GTT)	 AG	173194-173350	AT	AGA
(TTT)	 AC	173689-173815	TA	GGT
-recovered pasa_asmbl_24679.p1, initial, 172656, 172817
-recovered pasa_asmbl_24679.p1, terminal, 173194, 173350
-recovered pasa_asmbl_24679.p1, internal, 172954, 173077
Valid prediction for GeneMark_model.6906_t
Valid prediction for snap_scaffold_2-snap.1771-T1
Valid prediction for Augustus_model.g2902.t1
Valid prediction for snap_scaffold_2-snap.1743-T1
Valid prediction for GeneMark_model.6904_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 GlimmerHMM_glimmerT_4303-T1
Valid prediction for CodingQuarry_transcript_28576-T1
Couldn't classify 13658, 13817
Couldn't classify 17588, 17789
Sorry, prediction pasa_asmbl_23365.p1 fails validation.
(GAC)	 AG	13658-13817	GT	AGG
(ACT)	 AG	14023-14152	GT	TGG
(GTC)	 AG	15304-15438	GT	CTG
(ATT)	 AG	17588-17789	AC	CCA
-recovered pasa_asmbl_23365.p1, internal, 13658, 13817
-recovered pasa_asmbl_23365.p1, internal, 14023, 14152
-recovered pasa_asmbl_23365.p1, internal, 15304, 15438
Valid prediction for GeneMark_model.6881_t
Valid prediction for GlimmerHMM_glimmerT_4317-T1
Valid prediction for GlimmerHMM_glimmerT_4300-T1
Couldn't classify 29518, 31400
Sorry, prediction pasa_asmbl_24006.p1 fails validation.
(ATG)	 GA	25060-25851	GT	AGG
(ATG)	 AG	27699-27823	GT	AGG
(GGC)	 AG	29265-29344	GT	AGG
(ATA)	 AG	29518-31400	TC	CCT
-recovered pasa_asmbl_24006.p1, initial, 25060, 25851
-recovered pasa_asmbl_24006.p1, initial, 27699, 27823
add_exon() Sorry, pasa_asmbl_24006.p1 29265-29344-terminal-2 is invalid.
-recovered pasa_asmbl_24006.p1, terminal, 29265, 29344
-recovered pasa_asmbl_24006.p1, internal, 27699, 27823
-recovered pasa_asmbl_24006.p1, internal, 29265, 29344
Valid prediction for pasa_asmbl_23354.p1
Valid prediction for snap_scaffold_2-snap.1772-T1
Valid prediction for GeneMark_model.6893_t
Valid prediction for GeneMark_model.6903_t
Valid prediction for Augustus_model.g2905.t1
Valid prediction for GlimmerHMM_glimmerT_4299-T1
Valid prediction for snap_scaffold_2-snap.1746-T1
Valid prediction for GeneMark_model.6897_t
Valid prediction for HiQ_model.g2901.t1
Valid prediction for snap_scaffold_2-snap.1733-T1
Valid prediction for snap_scaffold_2-snap.1773-T1
Valid prediction for GeneMark_model.6890_t
Valid prediction for snap_scaffold_2-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_4305-T1
Valid prediction for GeneMark_model.6899_t
Valid prediction for CodingQuarry_transcript_28575-T1
Valid prediction for GlimmerHMM_glimmerT_4306-T1
Valid prediction for HiQ_model.g2893.t1
Valid prediction for Augustus_model.g2895.t1
Valid prediction for Augustus_model.g2886.t1
Valid prediction for snap_scaffold_2-snap.1754-T1
Valid prediction for snap_scaffold_2-snap.1732-T1
Valid prediction for Augustus_model.g2889.t1
Valid prediction for GlimmerHMM_glimmerT_4308-T1
Valid prediction for snap_scaffold_2-snap.1753-T1
Valid prediction for GeneMark_model.6880_t
Valid prediction for snap_scaffold_2-snap.1744-T1
Valid prediction for GeneMark_model.6875_t
Valid prediction for snap_scaffold_2-snap.1765-T1
Valid prediction for snap_scaffold_2-snap.1741-T1
Valid prediction for GlimmerHMM_glimmerT_4318-T1
Valid prediction for snap_scaffold_2-snap.1755-T1
Valid prediction for snap_scaffold_2-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_4315-T1
Valid prediction for GeneMark_model.6909_t
Valid prediction for GlimmerHMM_glimmerT_4294-T1
Valid prediction for snap_scaffold_2-snap.1742-T1
Valid prediction for GeneMark_model.6895_t
Valid prediction for Augustus_model.g2892.t1
Valid prediction for snap_scaffold_2-snap.1740-T1
Valid prediction for GeneMark_model.6902_t
Valid prediction for GeneMark_model.6905_t
Valid prediction for GlimmerHMM_glimmerT_4304-T1
Valid prediction for Augustus_model.g2903.t1
Valid prediction for snap_scaffold_2-snap.1739-T1
Valid prediction for snap_scaffold_2-snap.1747-T1
Valid prediction for GeneMark_model.6888_t
Valid prediction for snap_scaffold_2-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_4293-T1
Valid prediction for snap_scaffold_2-snap.1763-T1
Valid prediction for snap_scaffold_2-snap.1766-T1
Valid prediction for GeneMark_model.6883_t
Valid prediction for snap_scaffold_2-snap.1737-T1
Valid prediction for GeneMark_model.6907_t
Valid prediction for GeneMark_model.6886_t
Couldn't classify 118325, 118513
Sorry, prediction pasa_asmbl_23351.p1 fails validation.
(GCA)	 CT	118325-118513	GT	TGG
(TCG)	 AG	120635-120658	GT	TGG
(AAT)	 AG	122182-122308	GT	TGG
(ACT)	 AG	122470-122593	GT	GTG
(GGG)	 AG	122806-123142	AG	AGA
-recovered pasa_asmbl_23351.p1, terminal, 122806, 123142
-recovered pasa_asmbl_23351.p1, internal, 120635, 120658
-recovered pasa_asmbl_23351.p1, internal, 122182, 122308
-recovered pasa_asmbl_23351.p1, internal, 122470, 122593
Valid prediction for GeneMark_model.6873_t
Valid prediction for GeneMark_model.6876_t
Valid prediction for GeneMark_model.6891_t
Valid prediction for snap_scaffold_2-snap.1750-T1
Valid prediction for GlimmerHMM_glimmerT_4301-T1
Valid prediction for snap_scaffold_2-snap.1757-T1
Valid prediction for snap_scaffold_2-snap.1764-T1
Valid prediction for Augustus_model.g2894.t1
Valid prediction for GeneMark_model.6878_t
Valid prediction for Augustus_model.g2890.t1
Valid prediction for snap_scaffold_2-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_4296-T1
Valid prediction for GeneMark_model.6885_t
Valid prediction for snap_scaffold_2-snap.1751-T1
Valid prediction for Augustus_model.g2891.t1
Valid prediction for Augustus_model.g2888.t1
Valid prediction for snap_scaffold_2-snap.1769-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 73725, rend_intergenic: 72178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80000, rend_intergenic: 75717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137745, rend_intergenic: 136177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181270, rend_intergenic: 179989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199553, rend_intergenic: 197052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207822, rend_intergenic: 204483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211805, rend_intergenic: 209054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215173
-exon list size: 502


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
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1.4    
1.6    
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2.0    
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2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
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4.6    
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5.8    
6.0    
6.2    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
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16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 73725, rend_intergenic: 72178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80000, rend_intergenic: 75717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137745, rend_intergenic: 136177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181270, rend_intergenic: 179989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199553, rend_intergenic: 197052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207822, rend_intergenic: 204483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211805, rend_intergenic: 209054  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

-building DP trellis

-building trellis in range 1 - 29880
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 1 - 17287
-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 17328 - 29880
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 17726 - 29880
-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