-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_19628949-19756009

-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_4-snap.4036-T1
Valid prediction for snap_scaffold_4-snap.4043-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11552-T1
Valid prediction for GeneMark_model.19157_t
Valid prediction for snap_scaffold_4-snap.4040-T1
Valid prediction for GlimmerHMM_glimmerT_11543-T1
Valid prediction for CodingQuarry_transcript_49307-T1
Valid prediction for GeneMark_model.19140_t
Valid prediction for snap_scaffold_4-snap.4049-T1
Valid prediction for snap_scaffold_4-snap.4057-T1
Valid prediction for GeneMark_model.19149_t
Valid prediction for GlimmerHMM_glimmerT_11538-T1
Valid prediction for snap_scaffold_4-snap.4050-T1
Valid prediction for snap_scaffold_4-snap.4031-T1
Valid prediction for GeneMark_model.19169_t
Valid prediction for GlimmerHMM_glimmerT_11548-T1
Valid prediction for GeneMark_model.19151_t
Valid prediction for GlimmerHMM_glimmerT_11550-T1
Valid prediction for GlimmerHMM_glimmerT_11544-T1
Valid prediction for GeneMark_model.19152_t
Valid prediction for GeneMark_model.19161_t
Valid prediction for GeneMark_model.19144_t
Valid prediction for snap_scaffold_4-snap.4045-T1
Valid prediction for GlimmerHMM_glimmerT_11547-T1
Valid prediction for GeneMark_model.19147_t
Valid prediction for GeneMark_model.19165_t
Valid prediction for snap_scaffold_4-snap.4038-T1
Valid prediction for GeneMark_model.19176_t
Valid prediction for GlimmerHMM_glimmerT_11546-T1
Valid prediction for pasa_asmbl_43506.p1
Valid prediction for GeneMark_model.19173_t
Couldn't classify 49929, 49930
Sorry, prediction CodingQuarry_transcript_49306-T1 fails validation.
(ATG)	 CT	49929-49930	GT	ATG
(GAT)	 AG	50746-50917	GT	TGG
(GTG)	 AG	51025-51162	GT	AGG
(GTG)	 AG	51252-51419	GT	TGG
(GTC)	 AG	51792-52526	TA	GAT
-recovered CodingQuarry_transcript_49306-T1, terminal, 51792, 52526
-recovered CodingQuarry_transcript_49306-T1, internal, 50746, 50917
-recovered CodingQuarry_transcript_49306-T1, internal, 51025, 51162
-recovered CodingQuarry_transcript_49306-T1, internal, 51252, 51419
Valid prediction for snap_scaffold_4-snap.4035-T1
Valid prediction for snap_scaffold_4-snap.4046-T1
Valid prediction for snap_scaffold_4-snap.4044-T1
Valid prediction for GeneMark_model.19156_t
Valid prediction for GeneMark_model.19164_t
Valid prediction for GeneMark_model.19154_t
Valid prediction for GeneMark_model.19159_t
Valid prediction for pasa_asmbl_43503.p1
Valid prediction for GeneMark_model.19175_t
Valid prediction for GeneMark_model.19146_t
Valid prediction for snap_scaffold_4-snap.4052-T1
Valid prediction for CodingQuarry_transcript_49311-T1
Valid prediction for snap_scaffold_4-snap.4042-T1
Valid prediction for GeneMark_model.19167_t
Valid prediction for GlimmerHMM_glimmerT_11553-T1
Valid prediction for GlimmerHMM_glimmerT_11542-T1
Valid prediction for GeneMark_model.19172_t
Valid prediction for GlimmerHMM_glimmerT_11545-T1
Valid prediction for snap_scaffold_4-snap.4034-T1
Valid prediction for CodingQuarry_transcript_49309-T1
Couldn't classify 50250, 50341
Sorry, prediction pasa_asmbl_43500.p1 fails validation.
(CTT)	 AA	50250-50341	GT	AGG
(GAT)	 AG	50746-50917	GT	TGG
(GTG)	 AG	51025-51162	GT	AGG
(GTG)	 AG	51252-51419	GT	TGG
(GTC)	 AG	51792-52526	TA	GAT
-recovered pasa_asmbl_43500.p1, terminal, 51792, 52526
-recovered pasa_asmbl_43500.p1, internal, 50746, 50917
-recovered pasa_asmbl_43500.p1, internal, 51025, 51162
-recovered pasa_asmbl_43500.p1, internal, 51252, 51419
Valid prediction for snap_scaffold_4-snap.4039-T1
Valid prediction for snap_scaffold_4-snap.4053-T1
Valid prediction for GeneMark_model.19142_t
Valid prediction for snap_scaffold_4-snap.4056-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_11537-T1
Valid prediction for snap_scaffold_4-snap.4055-T1
Valid prediction for GeneMark_model.19171_t
Valid prediction for snap_scaffold_4-snap.4032-T1
Valid prediction for GlimmerHMM_glimmerT_11541-T1
Valid prediction for GeneMark_model.19145_t
Valid prediction for snap_scaffold_4-snap.4048-T1
Valid prediction for GeneMark_model.19166_t
Valid prediction for GeneMark_model.19160_t
Valid prediction for snap_scaffold_4-snap.4037-T1
Valid prediction for GeneMark_model.19168_t
Valid prediction for GeneMark_model.19150_t
Valid prediction for snap_scaffold_4-snap.4054-T1
Valid prediction for GeneMark_model.19143_t
Valid prediction for GeneMark_model.19158_t
Valid prediction for GlimmerHMM_glimmerT_11539-T1
Valid prediction for GeneMark_model.19141_t
Valid prediction for CodingQuarry_transcript_49308-T1
Valid prediction for GeneMark_model.19148_t
Valid prediction for snap_scaffold_4-snap.4047-T1
Valid prediction for snap_scaffold_4-snap.4041-T1
Couldn't classify 31184, 31349
Sorry, prediction pasa_asmbl_42241.p1 fails validation.
(ATG)	 GC	28894-29032	GT	TGG
(ATG)	 AG	29363-29531	GT	GGG
(GTG)	 AG	31184-31349	GG	GAG
-recovered pasa_asmbl_42241.p1, initial, 28894, 29032
add_exon() Sorry, pasa_asmbl_42241.p1 29363-29531-initial-1 is invalid.
-recovered pasa_asmbl_42241.p1, initial, 29363, 29531
-recovered pasa_asmbl_42241.p1, internal, 29363, 29531
Valid prediction for GlimmerHMM_glimmerT_11551-T1
Valid prediction for snap_scaffold_4-snap.4033-T1
Valid prediction for GlimmerHMM_glimmerT_11540-T1
Valid prediction for GeneMark_model.19170_t
Valid prediction for snap_scaffold_4-snap.4051-T1
Valid prediction for GeneMark_model.19163_t
Valid prediction for CodingQuarry_transcript_49305-T1
Valid prediction for GlimmerHMM_glimmerT_11549-T1
Valid prediction for GeneMark_model.19155_t
Valid prediction for GeneMark_model.19153_t
Valid prediction for GeneMark_model.19174_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14010, rend_intergenic: 4504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41679, rend_intergenic: 15571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49393, rend_intergenic: 42739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52526, rend_intergenic: 51753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64308, rend_intergenic: 52997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68850, rend_intergenic: 65991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82185, rend_intergenic: 71962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93165, rend_intergenic: 85973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115187, rend_intergenic: 94283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 127061
-exon list size: 417


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.5    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.2    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.8    
9.1    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 14010, rend_intergenic: 4504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41679, rend_intergenic: 15571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49393, rend_intergenic: 42739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52526, rend_intergenic: 51753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64308, rend_intergenic: 52997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68850, rend_intergenic: 65991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82185, rend_intergenic: 71962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93165, rend_intergenic: 85973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115187, rend_intergenic: 94283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support