-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_7274121-7427426

-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.34947_t
Valid prediction for GlimmerHMM_glimmerT_20443-T1
Valid prediction for GlimmerHMM_glimmerT_20430-T1
Valid prediction for pasa_asmbl_51970.p1
Valid prediction for GlimmerHMM_glimmerT_20420-T1
Valid prediction for GeneMark_model.34945_t
Valid prediction for snap_scaffold_8-snap.1416-T1
Valid prediction for GeneMark_model.34942_t
Valid prediction for CodingQuarry_transcript_59542-T1
Valid prediction for snap_scaffold_8-snap.1413-T1
Valid prediction for GeneMark_model.34944_t
Valid prediction for snap_scaffold_8-snap.1412-T1
Valid prediction for GeneMark_model.34929_t
Valid prediction for HiQ_model.g13668.t1
Valid prediction for GlimmerHMM_glimmerT_20435-T1
Valid prediction for snap_scaffold_8-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_20421-T1
Valid prediction for snap_scaffold_8-snap.1419-T1
Valid prediction for snap_scaffold_8-snap.1437-T1
Valid prediction for GeneMark_model.34938_t
Valid prediction for snap_scaffold_8-snap.1430-T1
Valid prediction for snap_scaffold_8-snap.1433-T1
Valid prediction for GlimmerHMM_glimmerT_20431-T1
Valid prediction for GeneMark_model.34922_t
Valid prediction for GlimmerHMM_glimmerT_20439-T1
Valid prediction for GeneMark_model.34936_t
Valid prediction for GeneMark_model.34935_t
Valid prediction for GeneMark_model.34932_t
Valid prediction for GlimmerHMM_glimmerT_20436-T1
Valid prediction for CodingQuarry_transcript_59543-T1
Valid prediction for Augustus_model.g13661.t1
Valid prediction for GeneMark_model.34934_t
Valid prediction for GeneMark_model.34940_t
Valid prediction for GlimmerHMM_glimmerT_20438-T1
Valid prediction for snap_scaffold_8-snap.1439-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 Augustus_model.g13664.t1
Valid prediction for Augustus_model.g13665.t1
Valid prediction for snap_scaffold_8-snap.1436-T1
Valid prediction for snap_scaffold_8-snap.1425-T1
Valid prediction for snap_scaffold_8-snap.1417-T1
Valid prediction for snap_scaffold_8-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_20441-T1
Valid prediction for GlimmerHMM_glimmerT_20426-T1
Valid prediction for snap_scaffold_8-snap.1426-T1
Valid prediction for snap_scaffold_8-snap.1438-T1
Valid prediction for Augustus_model.g13669.t1
Couldn't classify 29846, 29925
Sorry, prediction pasa_asmbl_52892.p1 fails validation.
(CTC)	 TC	29846-29925	GT	AGG
(CTC)	 AG	30060-30168	GT	AGG
(AAC)	 AG	30268-30426	GT	AGG
(GAC)	 AG	31508-31654	GT	AGG
(CTC)	 AG	31758-31865	GT	AGG
(GAC)	 AG	32070-32184	GT	GGG
(GGA)	 AG	32796-32920	GT	AGG
(GTT)	 AG	33153-33299	GG	GAG
-recovered pasa_asmbl_52892.p1, terminal, 33153, 33299
-recovered pasa_asmbl_52892.p1, internal, 30060, 30168
-recovered pasa_asmbl_52892.p1, internal, 30268, 30426
-recovered pasa_asmbl_52892.p1, internal, 31508, 31654
-recovered pasa_asmbl_52892.p1, internal, 31758, 31865
-recovered pasa_asmbl_52892.p1, internal, 32070, 32184
-recovered pasa_asmbl_52892.p1, internal, 32796, 32920
Valid prediction for GeneMark_model.34946_t
Valid prediction for GlimmerHMM_glimmerT_20444-T1
Couldn't classify 95659, 95754
Couldn't classify 98748, 98800
Sorry, prediction pasa_asmbl_53642.p1 fails validation.
(GAG)	 AG	95659-95754	GT	AGG
(GAC)	 AG	97584-97731	GT	AGG
(ACA)	 AG	98748-98800	GC	GTG
-recovered pasa_asmbl_53642.p1, internal, 95659, 95754
-recovered pasa_asmbl_53642.p1, internal, 97584, 97731
-recovered pasa_asmbl_53642.p1, internal, 98748, 98800
Valid prediction for GeneMark_model.34921_t
Valid prediction for snap_scaffold_8-snap.1427-T1
Valid prediction for GeneMark_model.34943_t
Valid prediction for GeneMark_model.34928_t
Valid prediction for GeneMark_model.34941_t
Valid prediction for GeneMark_model.34927_t
Valid prediction for snap_scaffold_8-snap.1440-T1
Valid prediction for snap_scaffold_8-snap.1435-T1
Valid prediction for snap_scaffold_8-snap.1422-T1
Valid prediction for GeneMark_model.34925_t
Valid prediction for Augustus_model.g13666.t1
Valid prediction for GlimmerHMM_glimmerT_20427-T1
Valid prediction for Augustus_model.g13662.t1
Valid prediction for GlimmerHMM_glimmerT_20428-T1
Valid prediction for GlimmerHMM_glimmerT_20429-T1
Valid prediction for snap_scaffold_8-snap.1424-T1
Valid prediction for GlimmerHMM_glimmerT_20422-T1
Valid prediction for snap_scaffold_8-snap.1414-T1
Valid prediction for Augustus_model.g13667.t1
Valid prediction for snap_scaffold_8-snap.1415-T1
Valid prediction for snap_scaffold_8-snap.1411-T1
Valid prediction for snap_scaffold_8-snap.1420-T1
Valid prediction for GeneMark_model.34930_t
Valid prediction for GeneMark_model.34939_t
Valid prediction for GlimmerHMM_glimmerT_20424-T1
Valid prediction for GlimmerHMM_glimmerT_20442-T1
Valid prediction for snap_scaffold_8-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_20434-T1
Valid prediction for GlimmerHMM_glimmerT_20440-T1
Valid prediction for GlimmerHMM_glimmerT_20432-T1
Valid prediction for GeneMark_model.34920_t
Valid prediction for GeneMark_model.34923_t
Valid prediction for snap_scaffold_8-snap.1429-T1
Valid prediction for snap_scaffold_8-snap.1432-T1
Couldn't classify 118142, 118225
Sorry, prediction pasa_asmbl_52887.p1 fails validation.
(TCT)	 AA	118142-118225	GT	TGG
(GAG)	 AG	118870-119172	GT	TGG
(GAC)	 AG	120037-120142	GT	AGG
(TCG)	 AG	122842-123224	GT	TGG
(GAG)	 AG	123403-123568	GT	AGG
(CGT)	 AG	123677-123818	GT	TGG
(TCT)	 AG	123985-124107	GT	ATG
(ACA)	 AG	124239-124330	GT	AGG
(ACC)	 AG	124416-124482	GT	AGG
(GTC)	 AG	124626-124758	GT	AGG
(GCG)	 AG	124956-125064	GT	CAG
(CTC)	 AG	125149-125267	GT	AAG
(GTC)	 AG	125690-125906	GT	CGG
(GAG)	 AG	126781-126965	AG	AGA
add_exon() Sorry, pasa_asmbl_52887.p1 123403-123568-terminal-3 is invalid.
-recovered pasa_asmbl_52887.p1, terminal, 123403, 123568
-recovered pasa_asmbl_52887.p1, terminal, 126781, 126965
-recovered pasa_asmbl_52887.p1, internal, 118870, 119172
-recovered pasa_asmbl_52887.p1, internal, 120037, 120142
-recovered pasa_asmbl_52887.p1, internal, 122842, 123224
-recovered pasa_asmbl_52887.p1, internal, 123403, 123568
-recovered pasa_asmbl_52887.p1, internal, 123677, 123818
-recovered pasa_asmbl_52887.p1, internal, 123985, 124107
-recovered pasa_asmbl_52887.p1, internal, 124239, 124330
-recovered pasa_asmbl_52887.p1, internal, 124416, 124482
-recovered pasa_asmbl_52887.p1, internal, 124626, 124758
-recovered pasa_asmbl_52887.p1, internal, 124956, 125064
-recovered pasa_asmbl_52887.p1, internal, 125149, 125267
-recovered pasa_asmbl_52887.p1, internal, 125690, 125906
Valid prediction for GlimmerHMM_glimmerT_20423-T1
Valid prediction for GeneMark_model.34931_t
Valid prediction for GlimmerHMM_glimmerT_20433-T1
Valid prediction for GeneMark_model.34933_t
Valid prediction for GeneMark_model.34937_t
Valid prediction for GeneMark_model.34924_t
Valid prediction for GlimmerHMM_glimmerT_20425-T1
Valid prediction for snap_scaffold_8-snap.1431-T1
Valid prediction for GlimmerHMM_glimmerT_20437-T1
Valid prediction for snap_scaffold_8-snap.1434-T1
Valid prediction for snap_scaffold_8-snap.1423-T1
Valid prediction for HiQ_model.g13663.t1
Valid prediction for Augustus_model.g13670.t1
Valid prediction for GeneMark_model.34926_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30305, rend_intergenic: 26342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54345, rend_intergenic: 52935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58690, rend_intergenic: 56731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135604, rend_intergenic: 133102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146888, rend_intergenic: 144580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153306
-exon list size: 372


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 30305, rend_intergenic: 26342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54345, rend_intergenic: 52935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58690, rend_intergenic: 56731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135604, rend_intergenic: 133102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146888, rend_intergenic: 144580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 137334 - 153306
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-found 2 predictions from path traversal
GOT 5prime partial gene.
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 143297 - 153306
-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 2 predictions from path traversal

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