-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_6717247-6917152

-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_2-snap.1487-T1
Valid prediction for GeneMark_model.6649_t
Valid prediction for snap_scaffold_2-snap.1501-T1
Valid prediction for Augustus_model.g2721.t1
Valid prediction for snap_scaffold_2-snap.1495-T1
Valid prediction for GlimmerHMM_glimmerT_4090-T1
Valid prediction for GlimmerHMM_glimmerT_4083-T1
Valid prediction for GlimmerHMM_glimmerT_4095-T1
Valid prediction for GlimmerHMM_glimmerT_4080-T1
Valid prediction for Augustus_model.g2711.t1
Valid prediction for snap_scaffold_2-snap.1513-T1
Valid prediction for snap_scaffold_2-snap.1509-T1
Valid prediction for Augustus_model.g2729.t1
Valid prediction for GlimmerHMM_glimmerT_4076-T1
Valid prediction for GeneMark_model.6651_t
Valid prediction for GeneMark_model.6657_t
Valid prediction for Augustus_model.g2735.t1
Valid prediction for Augustus_model.g2719.t1
Valid prediction for CodingQuarry_transcript_28538-T1
Valid prediction for GlimmerHMM_glimmerT_4097-T1
Valid prediction for GeneMark_model.6661_t
Valid prediction for snap_scaffold_2-snap.1479-T1
Valid prediction for snap_scaffold_2-snap.1507-T1
Valid prediction for Augustus_model.g2710.t1
Valid prediction for GlimmerHMM_glimmerT_4092-T1
Valid prediction for GlimmerHMM_glimmerT_4096-T1
Valid prediction for snap_scaffold_2-snap.1486-T1
Valid prediction for GlimmerHMM_glimmerT_4098-T1
Valid prediction for snap_scaffold_2-snap.1504-T1
Valid prediction for GeneMark_model.6641_t
Valid prediction for Augustus_model.g2730.t1
Valid prediction for GlimmerHMM_glimmerT_4075-T1
Valid prediction for Augustus_model.g2722.t1
Valid prediction for GlimmerHMM_glimmerT_4084-T1
Valid prediction for GlimmerHMM_glimmerT_4089-T1
Valid prediction for Augustus_model.g2725.t1
Valid prediction for GlimmerHMM_glimmerT_4093-T1
Valid prediction for pasa_asmbl_24517.p1
Valid prediction for GeneMark_model.6669_t
Couldn't classify 158524, 158619
Couldn't classify 162256, 162311
Sorry, prediction pasa_asmbl_25399.p1 fails validation.
(AGG)	 GC	158524-158619	GT	AAG
(GTG)	 AG	158823-158974	GT	CTG
(GTT)	 AG	160114-160168	GT	TTG
(GTT)	 AG	161722-161773	GT	GGG
(GCA)	 AG	162256-162311	GT	ATG
-recovered pasa_asmbl_25399.p1, internal, 158823, 158974
-recovered pasa_asmbl_25399.p1, internal, 160114, 160168
-recovered pasa_asmbl_25399.p1, internal, 161722, 161773
-recovered pasa_asmbl_25399.p1, internal, 162256, 162311
Valid prediction for GlimmerHMM_glimmerT_4087-T1
Valid prediction for Augustus_model.g2732.t1
Valid prediction for GlimmerHMM_glimmerT_4088-T1
Valid prediction for snap_scaffold_2-snap.1489-T1
Valid prediction for snap_scaffold_2-snap.1500-T1
Valid prediction for snap_scaffold_2-snap.1480-T1
Valid prediction for Augustus_model.g2733.t1
Valid prediction for snap_scaffold_2-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_4074-T1
Couldn't classify 166046, 166348
Sorry, prediction pasa_asmbl_24529.p2 fails validation.
(AAA)	 AC	166046-166348	CT	GAC
Valid prediction for GeneMark_model.6674_t
Valid prediction for GeneMark_model.6663_t
Valid prediction for snap_scaffold_2-snap.1498-T1
Valid prediction for snap_scaffold_2-snap.1493-T1
Valid prediction for snap_scaffold_2-snap.1494-T1
Valid prediction for snap_scaffold_2-snap.1499-T1
Valid prediction for snap_scaffold_2-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_4082-T1
Valid prediction for Augustus_model.g2728.t1
Valid prediction for Augustus_model.g2724.t1
Valid prediction for CodingQuarry_transcript_28540-T1
Valid prediction for CodingQuarry_transcript_28539-T1
Valid prediction for HiQ_model.g2726.t1
Valid prediction for GeneMark_model.6650_t
Valid prediction for GlimmerHMM_glimmerT_4079-T1
Couldn't classify 181837, 181920
Couldn't classify 186479, 186513
Sorry, prediction pasa_asmbl_24541.p1 fails validation.
(GCG)	 TA	181837-181920	GT	AGG
(GAC)	 AG	183046-183117	GT	AGG
(AAG)	 AG	183436-183513	GT	GGG
(GCT)	 AG	184305-184379	GT	TGG
(ATA)	 AG	184585-184786	GT	AGG
(AGG)	 AG	184863-184974	GT	AGG
(GTT)	 AG	185146-185203	GT	AGG
(TGT)	 AG	185778-185878	GT	CCG
(CAA)	 AG	185968-186110	GT	GCG
(ATT)	 AG	186479-186513	AT	TGA
add_exon() Sorry, pasa_asmbl_24541.p1 184585-184786-terminal-3 is invalid.
-recovered pasa_asmbl_24541.p1, terminal, 184585, 184786
-recovered pasa_asmbl_24541.p1, internal, 183046, 183117
-recovered pasa_asmbl_24541.p1, internal, 183436, 183513
-recovered pasa_asmbl_24541.p1, internal, 184305, 184379
-recovered pasa_asmbl_24541.p1, internal, 184585, 184786
-recovered pasa_asmbl_24541.p1, internal, 184863, 184974
-recovered pasa_asmbl_24541.p1, internal, 185146, 185203
-recovered pasa_asmbl_24541.p1, internal, 185778, 185878
-recovered pasa_asmbl_24541.p1, internal, 185968, 186110
Valid prediction for Augustus_model.g2731.t1
Valid prediction for CodingQuarry_transcript_28537-T1
Valid prediction for snap_scaffold_2-snap.1481-T1
Valid prediction for Augustus_model.g2723.t1
Valid prediction for snap_scaffold_2-snap.1502-T1
Valid prediction for CodingQuarry_transcript_28535-T1
Valid prediction for GeneMark_model.6670_t
Valid prediction for snap_scaffold_2-snap.1510-T1
Valid prediction for GeneMark_model.6666_t
Valid prediction for snap_scaffold_2-snap.1508-T1
Valid prediction for GeneMark_model.6648_t
Valid prediction for snap_scaffold_2-snap.1511-T1
Valid prediction for pasa_asmbl_24548.p1
Valid prediction for GeneMark_model.6665_t
Couldn't classify 152960, 153313
Sorry, prediction pasa_asmbl_24528.p1 fails validation.
(ATG)	 AG	151075-151179	GT	AAG
(CTC)	 AG	152960-153313	GT	ATG
-recovered pasa_asmbl_24528.p1, initial, 151075, 151179
-recovered pasa_asmbl_24528.p1, internal, 151075, 151179
-recovered pasa_asmbl_24528.p1, internal, 152960, 153313
Valid prediction for Augustus_model.g2712.t1
Valid prediction for GeneMark_model.6640_t
Valid prediction for HiQ_model.g2718.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.g2716.t1
Valid prediction for Augustus_model.g2713.t1
Valid prediction for Augustus_model.g2714.t1
Valid prediction for HiQ_model.g2717.t1
Valid prediction for snap_scaffold_2-snap.1483-T1
Valid prediction for snap_scaffold_2-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_4081-T1
Valid prediction for snap_scaffold_2-snap.1497-T1
Valid prediction for snap_scaffold_2-snap.1506-T1
Valid prediction for GeneMark_model.6656_t
Valid prediction for Augustus_model.g2734.t1
Valid prediction for CodingQuarry_transcript_28533-T1
Valid prediction for Augustus_model.g2715.t1
Valid prediction for GeneMark_model.6654_t
Valid prediction for GeneMark_model.6664_t
Valid prediction for snap_scaffold_2-snap.1512-T1
Valid prediction for GeneMark_model.6646_t
Valid prediction for GeneMark_model.6673_t
Valid prediction for snap_scaffold_2-snap.1488-T1
Valid prediction for GeneMark_model.6671_t
Valid prediction for snap_scaffold_2-snap.1485-T1
Valid prediction for GlimmerHMM_glimmerT_4077-T1
Valid prediction for GeneMark_model.6645_t
Valid prediction for Augustus_model.g2720.t1
Valid prediction for GeneMark_model.6652_t
Valid prediction for GlimmerHMM_glimmerT_4100-T1
Valid prediction for snap_scaffold_2-snap.1482-T1
Valid prediction for GeneMark_model.6647_t
Valid prediction for GeneMark_model.6653_t
Valid prediction for snap_scaffold_2-snap.1505-T1
Valid prediction for snap_scaffold_2-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_4091-T1
Valid prediction for Augustus_model.g2727.t1
Valid prediction for GeneMark_model.6660_t
Valid prediction for GeneMark_model.6643_t
Valid prediction for GlimmerHMM_glimmerT_4085-T1
Valid prediction for GeneMark_model.6655_t
Valid prediction for CodingQuarry_transcript_28534-T1
Valid prediction for GeneMark_model.6659_t
Valid prediction for GlimmerHMM_glimmerT_4099-T1
Valid prediction for GlimmerHMM_glimmerT_4078-T1
Valid prediction for GeneMark_model.6658_t
Valid prediction for GeneMark_model.6644_t
Valid prediction for GlimmerHMM_glimmerT_4094-T1
Valid prediction for snap_scaffold_2-snap.1484-T1
Valid prediction for GeneMark_model.6662_t
Valid prediction for GeneMark_model.6672_t
Valid prediction for snap_scaffold_2-snap.1491-T1
Valid prediction for GeneMark_model.6667_t
Valid prediction for GlimmerHMM_glimmerT_4086-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65853, rend_intergenic: 62568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95269, rend_intergenic: 92880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134543, rend_intergenic: 129997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199906
-exon list size: 400


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 65853, rend_intergenic: 62568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95269, rend_intergenic: 92880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134543, rend_intergenic: 129997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support