-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_10871886-11158786

-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_13-snap.2054-T1
Valid prediction for GlimmerHMM_glimmerT_33079-T1
Valid prediction for GeneMark_model.56414_t
Valid prediction for snap_scaffold_13-snap.2037-T1
Valid prediction for GeneMark_model.56430_t
Valid prediction for GeneMark_model.56428_t
Valid prediction for GlimmerHMM_glimmerT_33064-T1
Valid prediction for GeneMark_model.56419_t
Valid prediction for Augustus_model.g22223.t1
Valid prediction for snap_scaffold_13-snap.2017-T1
Valid prediction for snap_scaffold_13-snap.2029-T1
Valid prediction for CodingQuarry_transcript_13203-T1
Valid prediction for GeneMark_model.56406_t
Valid prediction for GeneMark_model.56410_t
Valid prediction for snap_scaffold_13-snap.2020-T1
Valid prediction for snap_scaffold_13-snap.2047-T1
Valid prediction for Augustus_model.g22220.t1
Valid prediction for snap_scaffold_13-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_33068-T1
Valid prediction for snap_scaffold_13-snap.2050-T1
Valid prediction for Augustus_model.g22210.t1
Valid prediction for snap_scaffold_13-snap.2022-T1
Valid prediction for Augustus_model.g22222.t1
Valid prediction for GeneMark_model.56429_t
Valid prediction for snap_scaffold_13-snap.2027-T1
Valid prediction for GlimmerHMM_glimmerT_33075-T1
Valid prediction for GeneMark_model.56432_t
Valid prediction for GlimmerHMM_glimmerT_33074-T1
Valid prediction for GlimmerHMM_glimmerT_33061-T1
Valid prediction for GeneMark_model.56412_t
Valid prediction for snap_scaffold_13-snap.2018-T1
Valid prediction for snap_scaffold_13-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_33073-T1
Valid prediction for snap_scaffold_13-snap.2051-T1
Valid prediction for GeneMark_model.56403_t
Valid prediction for snap_scaffold_13-snap.2025-T1
Valid prediction for snap_scaffold_13-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_33060-T1
Valid prediction for GeneMark_model.56427_t
Valid prediction for snap_scaffold_13-snap.2016-T1
Valid prediction for snap_scaffold_13-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_33062-T1
Valid prediction for snap_scaffold_13-snap.2039-T1
Valid prediction for snap_scaffold_13-snap.2024-T1
Valid prediction for GeneMark_model.56399_t
Valid prediction for snap_scaffold_13-snap.2026-T1
Valid prediction for snap_scaffold_13-snap.2046-T1
Valid prediction for snap_scaffold_13-snap.2049-T1
Valid prediction for snap_scaffold_13-snap.2028-T1
Valid prediction for snap_scaffold_13-snap.2048-T1
Valid prediction for snap_scaffold_13-snap.2038-T1
Valid prediction for GeneMark_model.56401_t
Valid prediction for GeneMark_model.56404_t
Valid prediction for Augustus_model.g22221.t1
Valid prediction for GlimmerHMM_glimmerT_33065-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 GlimmerHMM_glimmerT_33077-T1
Valid prediction for snap_scaffold_13-snap.2034-T1
Valid prediction for Augustus_model.g22212.t1
Couldn't classify 4567, 4746
Sorry, prediction pasa_asmbl_10031.p1 fails validation.
(CAG)	 AC	4567-4746	GT	AGG
(GTC)	 AG	5093-5203	GT	AGG
(GAG)	 AG	5850-5925	GT	GGG
(GAC)	 AG	6090-6268	AG	AGA
-recovered pasa_asmbl_10031.p1, terminal, 6090, 6268
-recovered pasa_asmbl_10031.p1, internal, 5093, 5203
-recovered pasa_asmbl_10031.p1, internal, 5850, 5925
Valid prediction for GeneMark_model.56423_t
Valid prediction for GeneMark_model.56411_t
Valid prediction for Augustus_model.g22214.t1
Valid prediction for snap_scaffold_13-snap.2032-T1
Valid prediction for GeneMark_model.56422_t
Valid prediction for GeneMark_model.56405_t
Valid prediction for Augustus_model.g22216.t1
Valid prediction for GeneMark_model.56420_t
Valid prediction for GeneMark_model.56433_t
Valid prediction for GeneMark_model.56416_t
Valid prediction for snap_scaffold_13-snap.2045-T1
Valid prediction for GeneMark_model.56425_t
Valid prediction for snap_scaffold_13-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_33070-T1
Valid prediction for snap_scaffold_13-snap.2023-T1
Valid prediction for GeneMark_model.56400_t
Valid prediction for GeneMark_model.56398_t
Valid prediction for GeneMark_model.56434_t
Valid prediction for GlimmerHMM_glimmerT_33080-T1
Valid prediction for GlimmerHMM_glimmerT_33067-T1
Valid prediction for GeneMark_model.56402_t
Valid prediction for GeneMark_model.56397_t
Valid prediction for Augustus_model.g22217.t1
Couldn't classify 240709, 240986
Sorry, prediction pasa_asmbl_10029.p1 fails validation.
(ACT)	 GT	240709-240986	GT	TGG
(CCC)	 AG	241302-241361	GT	TGG
(CTA)	 AG	241498-241595	GT	TGG
(TTA)	 AG	241772-241836	GT	CTG
(AAT)	 AG	241930-242049	GT	CGG
(GAG)	 AG	242202-242270	GT	AGG
(CAA)	 AG	242389-242448	GT	AGG
(GAA)	 AG	242661-242740	GT	AGG
(TAG)	 AG	243048-243105	GT	AGG
(GGT)	 AG	243234-243348	GT	AGG
(ATG)	 AG	243442-243577	GT	AGG
(CAT)	 AG	243777-243920	GT	AGG
(CTG)	 AG	244068-244176	GT	AGG
(GAG)	 AG	244487-244568	GT	AGG
(TGA)	 AG	244736-244852	GT	CGG
(ACC)	 AG	244978-245095	GT	GCG
(ATC)	 AG	245207-245331	GT	CGG
(GCA)	 AG	245599-245759	GT	GGG
(GAG)	 AG	245942-245986	GT	AGG
(GTG)	 AG	246230-246247	TG	GAT
add_exon() Sorry, pasa_asmbl_10029.p1 243442-243577-initial-1 is invalid.
-recovered pasa_asmbl_10029.p1, initial, 243442, 243577
add_exon() Sorry, pasa_asmbl_10029.p1 243442-243577-terminal-3 is invalid.
-recovered pasa_asmbl_10029.p1, terminal, 243442, 243577
-recovered pasa_asmbl_10029.p1, terminal, 246230, 246247
-recovered pasa_asmbl_10029.p1, internal, 241302, 241361
-recovered pasa_asmbl_10029.p1, internal, 241498, 241595
-recovered pasa_asmbl_10029.p1, internal, 241772, 241836
-recovered pasa_asmbl_10029.p1, internal, 241930, 242049
-recovered pasa_asmbl_10029.p1, internal, 242202, 242270
-recovered pasa_asmbl_10029.p1, internal, 242389, 242448
-recovered pasa_asmbl_10029.p1, internal, 242661, 242740
-recovered pasa_asmbl_10029.p1, internal, 243048, 243105
-recovered pasa_asmbl_10029.p1, internal, 243234, 243348
-recovered pasa_asmbl_10029.p1, internal, 243442, 243577
-recovered pasa_asmbl_10029.p1, internal, 243777, 243920
-recovered pasa_asmbl_10029.p1, internal, 244068, 244176
-recovered pasa_asmbl_10029.p1, internal, 244487, 244568
-recovered pasa_asmbl_10029.p1, internal, 244736, 244852
-recovered pasa_asmbl_10029.p1, internal, 244978, 245095
-recovered pasa_asmbl_10029.p1, internal, 245207, 245331
-recovered pasa_asmbl_10029.p1, internal, 245599, 245759
-recovered pasa_asmbl_10029.p1, internal, 245942, 245986
Couldn't classify 1395, 1444
Couldn't classify 3541, 3648
Sorry, prediction pasa_asmbl_10033.p1 fails validation.
(CAG)	 CC	1395-1444	GT	AGG
(GTA)	 AG	1833-1902	GT	AGG
(GTC)	 AG	2177-2356	GT	AGG
(CTG)	 AG	2535-2642	GT	CAG
(TCA)	 AG	2909-2971	GT	AGG
(GAC)	 AG	3541-3648	CC	GGC
-recovered pasa_asmbl_10033.p1, internal, 1833, 1902
-recovered pasa_asmbl_10033.p1, internal, 2177, 2356
-recovered pasa_asmbl_10033.p1, internal, 2535, 2642
-recovered pasa_asmbl_10033.p1, internal, 2909, 2971
Valid prediction for Augustus_model.g22219.t1
Valid prediction for snap_scaffold_13-snap.2033-T1
Valid prediction for GeneMark_model.56426_t
Valid prediction for Augustus_model.g22207.t1
Valid prediction for GeneMark_model.56415_t
Valid prediction for GlimmerHMM_glimmerT_33072-T1
Valid prediction for Augustus_model.g22213.t1
Valid prediction for GlimmerHMM_glimmerT_33078-T1
Valid prediction for GlimmerHMM_glimmerT_33063-T1
Valid prediction for GeneMark_model.56417_t
Valid prediction for Augustus_model.g22215.t1
Valid prediction for snap_scaffold_13-snap.2052-T1
Valid prediction for Augustus_model.g22211.t1
Valid prediction for GeneMark_model.56431_t
Valid prediction for GlimmerHMM_glimmerT_33071-T1
Valid prediction for snap_scaffold_13-snap.2042-T1
Valid prediction for HiQ_model.g22209.t1
Valid prediction for snap_scaffold_13-snap.2031-T1
Valid prediction for GlimmerHMM_glimmerT_33076-T1
Valid prediction for GlimmerHMM_glimmerT_33066-T1
Valid prediction for Augustus_model.g22218.t1
Valid prediction for snap_scaffold_13-snap.2043-T1
Valid prediction for GeneMark_model.56409_t
Valid prediction for GeneMark_model.56395_t
Valid prediction for GlimmerHMM_glimmerT_33069-T1
Valid prediction for CodingQuarry_transcript_13202-T1
Valid prediction for GeneMark_model.56424_t
Valid prediction for GeneMark_model.56407_t
Valid prediction for snap_scaffold_13-snap.2044-T1
Valid prediction for snap_scaffold_13-snap.2040-T1
Valid prediction for snap_scaffold_13-snap.2019-T1
Valid prediction for GeneMark_model.56421_t
Valid prediction for GeneMark_model.56418_t
Valid prediction for snap_scaffold_13-snap.2035-T1
Valid prediction for GeneMark_model.56396_t
Valid prediction for snap_scaffold_13-snap.2036-T1
Valid prediction for Augustus_model.g22208.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27536, rend_intergenic: 24771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108253, rend_intergenic: 107475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 270654, rend_intergenic: 268841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 286901
-exon list size: 482


building trellis

0.2    
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0.6    
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1.0    
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1.7    
1.9    
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2.5    
2.7    
2.9    
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3.7    
3.9    
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6.8    
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8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
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10.1    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
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15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
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    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
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    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
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    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
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    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
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    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
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    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
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    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
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    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
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    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 27536, rend_intergenic: 24771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108253, rend_intergenic: 107475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 270654, rend_intergenic: 268841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support