-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_30

-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: +)Couldn't classify 17103, 17540
Sorry, prediction pasa_asmbl_40847.p1 fails validation.
(GCG)	 AC	17103-17540	GA	ATG
Valid prediction for GeneMark_model.106135_t
Valid prediction for GeneMark_model.106131_t
Valid prediction for Augustus_model.g40538.t1
Valid prediction for Augustus_model.g40540.t1
Valid prediction for snap_scaffold_30-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_60932-T1
Valid prediction for snap_scaffold_30-snap.7-T1
Valid prediction for GeneMark_model.106129_t
Valid prediction for Augustus_model.g40541.t1
Valid prediction for GeneMark_model.106132_t
Valid prediction for snap_scaffold_30-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_60933-T1
Valid prediction for snap_scaffold_30-snap.13-T1
Valid prediction for Augustus_model.g40544.t1
Valid prediction for Augustus_model.g40537.t1
Valid prediction for GeneMark_model.106133_t
Valid prediction for GeneMark_model.106137_t
Valid prediction for GlimmerHMM_glimmerT_60937-T1
Valid prediction for GlimmerHMM_glimmerT_60930-T1
Couldn't classify 51130, 51176
Sorry, prediction GlimmerHMM_glimmerT_60940-T1 fails validation.
(ATG)	 AC	47382-47580	GT	AGG
(GTT)	 AG	47864-47889	GT	AGG
(CGT)	 AG	48627-48777	GT	AGG
(TGT)	 AG	51130-51176	GT	ATG
-recovered GlimmerHMM_glimmerT_60940-T1, initial, 47382, 47580
-recovered GlimmerHMM_glimmerT_60940-T1, internal, 47864, 47889
-recovered GlimmerHMM_glimmerT_60940-T1, internal, 48627, 48777
-recovered GlimmerHMM_glimmerT_60940-T1, internal, 51130, 51176
Valid prediction for GeneMark_model.106134_t
Couldn't classify 1166, 1268
Sorry, prediction snap_scaffold_30-snap.1-T1 fails validation.
(CCG)	 AG	1166-1268	GT	AGG
(CAT)	 AG	4430-4470	GT	TGG
(GTC)	 AG	4648-4723	GG	GAG
-recovered snap_scaffold_30-snap.1-T1, terminal, 4648, 4723
-recovered snap_scaffold_30-snap.1-T1, internal, 1166, 1268
-recovered snap_scaffold_30-snap.1-T1, internal, 4430, 4470

-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.106136_t
Valid prediction for Augustus_model.g40542.t1
Valid prediction for GlimmerHMM_glimmerT_60929-T1
Valid prediction for GeneMark_model.106138_t
Valid prediction for GlimmerHMM_glimmerT_60931-T1
Valid prediction for snap_scaffold_30-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_60936-T1
Valid prediction for snap_scaffold_30-snap.6-T1
Valid prediction for GeneMark_model.106127_t
Valid prediction for GlimmerHMM_glimmerT_60939-T1
Valid prediction for snap_scaffold_30-snap.12-T1
Valid prediction for snap_scaffold_30-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_60934-T1
Valid prediction for snap_scaffold_30-snap.9-T1
Valid prediction for snap_scaffold_30-snap.2-T1
Valid prediction for snap_scaffold_30-snap.4-T1
Valid prediction for Augustus_model.g40543.t1
Valid prediction for Augustus_model.g40539.t1
Valid prediction for GeneMark_model.106128_t
Valid prediction for GlimmerHMM_glimmerT_60935-T1
Couldn't classify 758, 781
Sorry, prediction GeneMark_model.106140_t fails validation.
(AGA)	 AG	758-781	GT	GAG
(GAG)	 AG	811-837	GT	GAG
(GAG)	 AG	865-921	GT	TGG
(TAA)	 AG	1837-1879	TC	AAT
-recovered GeneMark_model.106140_t, terminal, 758, 781
add_exon() Sorry, GeneMark_model.106140_t 811-837-terminal-1 is invalid.
-recovered GeneMark_model.106140_t, terminal, 811, 837
-recovered GeneMark_model.106140_t, terminal, 1837, 1879
-recovered GeneMark_model.106140_t, internal, 758, 781
-recovered GeneMark_model.106140_t, internal, 811, 837
-recovered GeneMark_model.106140_t, internal, 865, 921
Valid prediction for GlimmerHMM_glimmerT_60938-T1
Valid prediction for snap_scaffold_30-snap.8-T1
Valid prediction for Augustus_model.g40536.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4723, rend_intergenic: 3134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10380, rend_intergenic: 7892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14386, rend_intergenic: 11376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17566, rend_intergenic: 14878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36702, rend_intergenic: 34333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40809, rend_intergenic: 37440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 52216
-exon list size: 171


building trellis

0.6    
1.2    
1.7    
2.3    
2.9    
3.5    
4.0    
4.6    
5.2    
5.8    
6.4    
6.9    
7.5    
8.1    
8.7    
9.2    
9.8    
10.4    
11.0    
11.6    
12.1    
12.7    
13.3    
13.9    
14.5    
15.0    
15.6    
16.2    
16.8    
17.3    
17.9    
18.5    
19.1    
19.7    
20.2    
20.8    
21.4    
22.0    
22.5    
23.1    
23.7    
24.3    
24.9    
25.4    
26.0    
26.6    
27.2    
27.7    
28.3    
28.9    
29.5    
30.1    
30.6    
31.2    
31.8    
32.4    
32.9    
33.5    
34.1    
34.7    
35.3    
35.8    
36.4    
37.0    
37.6    
38.2    
38.7    
39.3    
39.9    
40.5    
41.0    
41.6    
42.2    
42.8    
43.4    
43.9    
44.5    
45.1    
45.7    
46.2    
46.8    
47.4    
48.0    
48.6    
49.1    
49.7    
50.3    
50.9    
51.4    
52.0    
52.6    
53.2    
53.8    
54.3    
54.9    
55.5    
56.1    
56.6    
57.2    
57.8    
58.4    
59.0    
59.5    
60.1    
60.7    
61.3    
61.8    
62.4    
63.0    
63.6    
64.2    
64.7    
65.3    
65.9    
66.5    
67.1    
67.6    
68.2    
68.8    
69.4    
69.9    
70.5    
71.1    
71.7    
72.3    
72.8    
73.4    
74.0    
74.6    
75.1    
75.7    
76.3    
76.9    
77.5    
78.0    
78.6    
79.2    
79.8    
80.3    
80.9    
81.5    
82.1    
82.7    
83.2    
83.8    
84.4    
85.0    
85.5    
86.1    
86.7    
87.3    
87.9    
88.4    
89.0    
89.6    
90.2    
90.8    
91.3    
91.9    
92.5    
93.1    
93.6    
94.2    
94.8    
95.4    
96.0    
96.5    
97.1    
97.7    
98.3    
98.8    
99.4    
-found 13 predictions from path traversal
Error with prediction: snap lend_intergenic: 4723, rend_intergenic: 3134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10380, rend_intergenic: 7892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14386, rend_intergenic: 11376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17566, rend_intergenic: 14878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36702, rend_intergenic: 34333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40809, rend_intergenic: 37440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support