-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_12248424-12535557

-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.12601_t
Valid prediction for GeneMark_model.12594_t
Valid prediction for Augustus_model.g4992.t1
Valid prediction for snap_scaffold_3-snap.2430-T1
Valid prediction for snap_scaffold_3-snap.2435-T1
Valid prediction for snap_scaffold_3-snap.2429-T1
Valid prediction for GlimmerHMM_glimmerT_7626-T1
Valid prediction for GeneMark_model.12597_t
Valid prediction for snap_scaffold_3-snap.2424-T1
Valid prediction for snap_scaffold_3-snap.2423-T1
Valid prediction for GeneMark_model.12610_t
Valid prediction for GeneMark_model.12613_t
Valid prediction for Augustus_model.g5000.t1
Valid prediction for snap_scaffold_3-snap.2438-T1
Valid prediction for snap_scaffold_3-snap.2422-T1
Valid prediction for snap_scaffold_3-snap.2441-T1
Valid prediction for GlimmerHMM_glimmerT_7612-T1
Valid prediction for Augustus_model.g5002.t1
Valid prediction for snap_scaffold_3-snap.2440-T1
Valid prediction for Augustus_model.g4995.t1
Valid prediction for GlimmerHMM_glimmerT_7610-T1
Valid prediction for snap_scaffold_3-snap.2431-T1
Valid prediction for Augustus_model.g4993.t1
Valid prediction for snap_scaffold_3-snap.2427-T1
Couldn't classify 246801, 247391
Sorry, prediction pasa_asmbl_40362.p1 fails validation.
(CTT)	 CC	246801-247391	GT	AGG
(ATT)	 AG	247661-247765	CT	AAC
-recovered pasa_asmbl_40362.p1, terminal, 247661, 247765
Valid prediction for snap_scaffold_3-snap.2437-T1
Valid prediction for snap_scaffold_3-snap.2433-T1
Valid prediction for GlimmerHMM_glimmerT_7622-T1
Valid prediction for snap_scaffold_3-snap.2418-T1
Valid prediction for snap_scaffold_3-snap.2415-T1
Valid prediction for GeneMark_model.12612_t
Valid prediction for GlimmerHMM_glimmerT_7618-T1
Valid prediction for Augustus_model.g4999.t1
Valid prediction for GeneMark_model.12595_t
Valid prediction for GeneMark_model.12590_t
Valid prediction for snap_scaffold_3-snap.2436-T1
Valid prediction for snap_scaffold_3-snap.2421-T1
Valid prediction for GeneMark_model.12591_t
Valid prediction for GlimmerHMM_glimmerT_7623-T1
Valid prediction for Augustus_model.g4998.t1
Valid prediction for GeneMark_model.12602_t
Valid prediction for Augustus_model.g4990.t1
Valid prediction for GlimmerHMM_glimmerT_7615-T1
Valid prediction for GeneMark_model.12609_t
Valid prediction for GeneMark_model.12599_t
Valid prediction for snap_scaffold_3-snap.2425-T1
Valid prediction for GeneMark_model.12600_t
Valid prediction for GeneMark_model.12614_t
Valid prediction for GlimmerHMM_glimmerT_7617-T1
Couldn't classify 245681, 246497
Sorry, prediction pasa_asmbl_40361.p1 fails validation.
(ATG)	 TG	244991-245018	GT	GAG
(TGA)	 AG	245311-245452	GT	GTG
(TAA)	 AG	245681-246497	AC	CCA
-recovered pasa_asmbl_40361.p1, initial, 244991, 245018
-recovered pasa_asmbl_40361.p1, internal, 245311, 245452
Valid prediction for GeneMark_model.12618_t
Valid prediction for snap_scaffold_3-snap.2426-T1
Valid prediction for Augustus_model.g5001.t1
Valid prediction for GeneMark_model.12606_t
Valid prediction for GeneMark_model.12615_t
Valid prediction for snap_scaffold_3-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_7620-T1
Valid prediction for snap_scaffold_3-snap.2414-T1
Valid prediction for snap_scaffold_3-snap.2439-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 GeneMark_model.12604_t
Valid prediction for snap_scaffold_3-snap.2428-T1
Valid prediction for GeneMark_model.12588_t
Valid prediction for Augustus_model.g4991.t1
Valid prediction for GlimmerHMM_glimmerT_7613-T1
Valid prediction for GlimmerHMM_glimmerT_7614-T1
Valid prediction for GlimmerHMM_glimmerT_7619-T1
Valid prediction for GeneMark_model.12593_t
Valid prediction for GlimmerHMM_glimmerT_7616-T1
Valid prediction for Augustus_model.g4989.t1
Valid prediction for GeneMark_model.12603_t
Valid prediction for GeneMark_model.12611_t
Valid prediction for Augustus_model.g4994.t1
Valid prediction for GlimmerHMM_glimmerT_7606-T1
Valid prediction for GlimmerHMM_glimmerT_7611-T1
Valid prediction for GlimmerHMM_glimmerT_7605-T1
Valid prediction for pasa_asmbl_39163.p1
Valid prediction for GeneMark_model.12616_t
Valid prediction for GeneMark_model.12608_t
Valid prediction for GlimmerHMM_glimmerT_7608-T1
Valid prediction for GeneMark_model.12596_t
Valid prediction for GeneMark_model.12617_t
Valid prediction for GeneMark_model.12598_t
Valid prediction for GlimmerHMM_glimmerT_7607-T1
Valid prediction for snap_scaffold_3-snap.2420-T1
Valid prediction for snap_scaffold_3-snap.2416-T1
Valid prediction for CodingQuarry_transcript_46194-T1
Valid prediction for GlimmerHMM_glimmerT_7621-T1
Valid prediction for snap_scaffold_3-snap.2432-T1
Couldn't classify 141554, 141973
Sorry, prediction pasa_asmbl_40352.p1 fails validation.
(ATG)	 CA	141554-141973	TG	CCT
Valid prediction for GeneMark_model.12607_t
Valid prediction for HiQ_model.g4997.t1
Valid prediction for HiQ_model.g4996.t1
Valid prediction for Augustus_model.g4988.t1
Valid prediction for GlimmerHMM_glimmerT_7625-T1
Valid prediction for snap_scaffold_3-snap.2434-T1
Valid prediction for GeneMark_model.12605_t
Valid prediction for GeneMark_model.12589_t
Valid prediction for GlimmerHMM_glimmerT_7609-T1
Valid prediction for snap_scaffold_3-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_7624-T1
Valid prediction for CodingQuarry_transcript_46193-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 166553, rend_intergenic: 163875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206583, rend_intergenic: 205083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287134
-exon list size: 334


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 166553, rend_intergenic: 163875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206583, rend_intergenic: 205083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18937
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 - 17530
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 2964 - 17530
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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