-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_13668844-13845682

-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.2574_t
Valid prediction for Augustus_model.g1358.t1
Valid prediction for snap_scaffold_1-snap.2389-T1
Valid prediction for HiQ_model.g1376.t1
Valid prediction for GeneMark_model.2549_t
Valid prediction for snap_scaffold_1-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_1873-T1
Valid prediction for Augustus_model.g1357.t1
Valid prediction for snap_scaffold_1-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_1864-T1
Valid prediction for Augustus_model.g1365.t1
Valid prediction for GeneMark_model.2576_t
Valid prediction for GeneMark_model.2567_t
Valid prediction for Augustus_model.g1377.t1
Valid prediction for HiQ_model.g1362.t1
Valid prediction for snap_scaffold_1-snap.2386-T1
Valid prediction for snap_scaffold_1-snap.2396-T1
Valid prediction for GlimmerHMM_glimmerT_1847-T1
Valid prediction for GlimmerHMM_glimmerT_1863-T1
Valid prediction for CodingQuarry_transcript_2884-T1
Valid prediction for snap_scaffold_1-snap.2397-T1
Valid prediction for GeneMark_model.2559_t
Valid prediction for GeneMark_model.2564_t
Valid prediction for GlimmerHMM_glimmerT_1871-T1
Valid prediction for Augustus_model.g1370.t1
Valid prediction for snap_scaffold_1-snap.2373-T1
Valid prediction for pasa_asmbl_2301.p2
Valid prediction for CodingQuarry_transcript_2886-T1
Valid prediction for snap_scaffold_1-snap.2377-T1
Valid prediction for Augustus_model.g1364.t1
Valid prediction for GeneMark_model.2583_t
Valid prediction for GlimmerHMM_glimmerT_1867-T1
Valid prediction for snap_scaffold_1-snap.2395-T1
Valid prediction for GeneMark_model.2568_t
Valid prediction for snap_scaffold_1-snap.2371-T1
Valid prediction for snap_scaffold_1-snap.2393-T1
Valid prediction for snap_scaffold_1-snap.2380-T1
Valid prediction for Augustus_model.g1363.t1
Valid prediction for Augustus_model.g1374.t1
Valid prediction for snap_scaffold_1-snap.2387-T1
Valid prediction for CodingQuarry_transcript_2885-T1
Valid prediction for CodingQuarry_transcript_2887-T1
Valid prediction for snap_scaffold_1-snap.2382-T1
Valid prediction for GlimmerHMM_glimmerT_1866-T1
Valid prediction for Augustus_model.g1368.t1
Valid prediction for HiQ_model.g1378.t1
Valid prediction for GlimmerHMM_glimmerT_1869-T1
Valid prediction for snap_scaffold_1-snap.2391-T1
Valid prediction for GeneMark_model.2545_t
Valid prediction for snap_scaffold_1-snap.2400-T1
Valid prediction for GeneMark_model.2553_t
Valid prediction for GlimmerHMM_glimmerT_1860-T1
Valid prediction for GeneMark_model.2571_t
Valid prediction for snap_scaffold_1-snap.2372-T1
Valid prediction for GeneMark_model.2561_t
Valid prediction for GeneMark_model.2581_t
Valid prediction for snap_scaffold_1-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_1862-T1
Valid prediction for GlimmerHMM_glimmerT_1846-T1
Valid prediction for snap_scaffold_1-snap.2375-T1
Valid prediction for GeneMark_model.2566_t
Valid prediction for Augustus_model.g1373.t1
Valid prediction for GeneMark_model.2551_t
Valid prediction for snap_scaffold_1-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_1848-T1
Valid prediction for GeneMark_model.2554_t
Valid prediction for GeneMark_model.2579_t
Valid prediction for snap_scaffold_1-snap.2379-T1
Valid prediction for Augustus_model.g1359.t1
Valid prediction for Augustus_model.g1379.t1
Valid prediction for Augustus_model.g1366.t1
Couldn't classify 81453, 81540
Couldn't classify 84490, 84535
Sorry, prediction pasa_asmbl_2297.p1 fails validation.
(GGC)	 TG	81453-81540	GT	CGG
(GTT)	 AG	81691-81827	GT	TGG
(GAC)	 AG	82892-82997	GT	GGG
(GGC)	 AG	83118-83288	GT	GGG
(GCT)	 AG	83804-84020	GT	AGG
(CCA)	 AG	84490-84535	TA	AGT
-recovered pasa_asmbl_2297.p1, internal, 81691, 81827
-recovered pasa_asmbl_2297.p1, internal, 82892, 82997
-recovered pasa_asmbl_2297.p1, internal, 83118, 83288
-recovered pasa_asmbl_2297.p1, internal, 83804, 84020
Valid prediction for snap_scaffold_1-snap.2402-T1
Valid prediction for GlimmerHMM_glimmerT_1850-T1
Valid prediction for GeneMark_model.2578_t
Valid prediction for Augustus_model.g1371.t1
Valid prediction for GlimmerHMM_glimmerT_1856-T1
Valid prediction for GlimmerHMM_glimmerT_1857-T1
Valid prediction for pasa_asmbl_2299.p1
Valid prediction for snap_scaffold_1-snap.2401-T1
Valid prediction for GlimmerHMM_glimmerT_1853-T1
Valid prediction for GeneMark_model.2547_t
Valid prediction for GeneMark_model.2585_t
Valid prediction for GeneMark_model.2542_t
Valid prediction for GeneMark_model.2556_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 GeneMark_model.2570_t
Valid prediction for GeneMark_model.2555_t
Valid prediction for GlimmerHMM_glimmerT_1868-T1
Valid prediction for GeneMark_model.2562_t
Valid prediction for snap_scaffold_1-snap.2376-T1
Valid prediction for Augustus_model.g1360.t1
Valid prediction for GeneMark_model.2563_t
Valid prediction for snap_scaffold_1-snap.2381-T1
Valid prediction for GeneMark_model.2546_t
Valid prediction for GeneMark_model.2572_t
Valid prediction for snap_scaffold_1-snap.2384-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.2560_t
Valid prediction for GlimmerHMM_glimmerT_1849-T1
Valid prediction for GlimmerHMM_glimmerT_1852-T1
Valid prediction for GeneMark_model.2543_t
Valid prediction for Augustus_model.g1372.t1
Valid prediction for GlimmerHMM_glimmerT_1872-T1
Valid prediction for GeneMark_model.2557_t
Valid prediction for GeneMark_model.2586_t
Valid prediction for GeneMark_model.2552_t
Valid prediction for snap_scaffold_1-snap.2392-T1
Valid prediction for HiQ_model.g1375.t1
Valid prediction for GlimmerHMM_glimmerT_1861-T1
Valid prediction for GeneMark_model.2584_t
Valid prediction for GlimmerHMM_glimmerT_1855-T1
Valid prediction for GeneMark_model.2573_t
Valid prediction for GlimmerHMM_glimmerT_1865-T1
Valid prediction for Augustus_model.g1369.t1
Valid prediction for snap_scaffold_1-snap.2383-T1
Valid prediction for GeneMark_model.2558_t
Valid prediction for snap_scaffold_1-snap.2403-T1
Valid prediction for GlimmerHMM_glimmerT_1854-T1
Valid prediction for GlimmerHMM_glimmerT_1870-T1
Valid prediction for Augustus_model.g1380.t1
Valid prediction for GlimmerHMM_glimmerT_1851-T1
Valid prediction for GeneMark_model.2575_t
Valid prediction for GeneMark_model.2550_t
Valid prediction for CodingQuarry_transcript_2883-T1
Valid prediction for GlimmerHMM_glimmerT_1858-T1
Valid prediction for GeneMark_model.2544_t
Valid prediction for pasa_asmbl_844.p1
Valid prediction for GeneMark_model.2548_t
Valid prediction for snap_scaffold_1-snap.2390-T1
Valid prediction for snap_scaffold_1-snap.2370-T1
Valid prediction for GeneMark_model.2569_t
Valid prediction for snap_scaffold_1-snap.2369-T1
Valid prediction for Augustus_model.g1361.t1
Valid prediction for Augustus_model.g1367.t1
Valid prediction for GlimmerHMM_glimmerT_1859-T1
Valid prediction for GeneMark_model.2577_t
Valid prediction for snap_scaffold_1-snap.2385-T1
Valid prediction for GeneMark_model.2580_t
Valid prediction for snap_scaffold_1-snap.2398-T1
Valid prediction for GeneMark_model.2565_t
Valid prediction for snap_scaffold_1-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_1874-T1
Valid prediction for snap_scaffold_1-snap.2374-T1
Valid prediction for pasa_asmbl_850.p1
Valid prediction for snap_scaffold_1-snap.2394-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10596, rend_intergenic: 5980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30896, rend_intergenic: 10894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42483, rend_intergenic: 34354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47937, rend_intergenic: 42723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77821, rend_intergenic: 75672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84757, rend_intergenic: 79346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97663, rend_intergenic: 90287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120212, rend_intergenic: 113840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176839
-exon list size: 568


building trellis

0.2    
0.4    
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0.9    
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2.8    
3.0    
3.2    
3.3    
3.5    
3.7    
3.9    
4.0    
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4.6    
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4.9    
5.1    
5.3    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.7    
6.8    
7.0    
7.2    
7.4    
7.5    
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7.9    
8.1    
8.2    
8.4    
8.6    
8.8    
8.9    
9.1    
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9.5    
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10.0    
10.2    
10.4    
10.5    
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10.9    
11.1    
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11.9    
12.1    
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13.5    
13.7    
13.9    
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14.9    
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15.6    
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18.6    
18.8    
18.9    
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20.7    
20.9    
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22.3    
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22.6    
22.8    
23.0    
23.2    
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23.5    
23.7    
23.9    
24.0    
24.2    
24.4    
24.6    
24.7    
24.9    
25.1    
25.3    
25.4    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.7    
26.8    
27.0    
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27.4    
27.5    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.8    
28.9    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.2    
40.4    
40.5    
40.7    
40.9    
41.1    
41.2    
41.4    
41.6    
41.8    
41.9    
42.1    
42.3    
42.5    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.3    
45.4    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.5    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.5    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.4    
57.5    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.8    
58.9    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 10596, rend_intergenic: 5980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30896, rend_intergenic: 10894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42483, rend_intergenic: 34354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47937, rend_intergenic: 42723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77821, rend_intergenic: 75672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84757, rend_intergenic: 79346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97663, rend_intergenic: 90287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120212, rend_intergenic: 113840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 166308 - 176839
-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

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

-building DP trellis

-building trellis in range 166380 - 176839
-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 166751 - 176839
-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