-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_7034444-7150967

-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 Augustus_model.g6416.t1
Valid prediction for snap_scaffold_4-snap.1509-T1
Valid prediction for GeneMark_model.15937_t
Valid prediction for GeneMark_model.15949_t
Valid prediction for GlimmerHMM_glimmerT_9807-T1
Couldn't classify 27463, 27607
Sorry, prediction pasa_asmbl_42790.p1 fails validation.
(ACC)	 AG	27463-27607	GT	CGG
(GTG)	 AG	28345-28502	GT	AGG
(GTA)	 AG	28641-28821	GT	AGG
(CGG)	 AG	29025-29188	AC	GAA
-recovered pasa_asmbl_42790.p1, terminal, 29025, 29188
-recovered pasa_asmbl_42790.p1, internal, 27463, 27607
-recovered pasa_asmbl_42790.p1, internal, 28345, 28502
-recovered pasa_asmbl_42790.p1, internal, 28641, 28821
Valid prediction for GlimmerHMM_glimmerT_9801-T1
Couldn't classify 33448, 33655
Sorry, prediction pasa_asmbl_42791.p1 fails validation.
(ATG)	 AG	31451-31880	GT	AGG
(GCC)	 AG	32951-33158	GT	AGG
(CCC)	 AG	33448-33655	GT	AGG
-recovered pasa_asmbl_42791.p1, initial, 31451, 31880
-recovered pasa_asmbl_42791.p1, internal, 31451, 31880
-recovered pasa_asmbl_42791.p1, internal, 32951, 33158
-recovered pasa_asmbl_42791.p1, internal, 33448, 33655
Valid prediction for pasa_asmbl_42796.p1
Valid prediction for GeneMark_model.15932_t
Valid prediction for Augustus_model.g6410.t1
Valid prediction for GeneMark_model.15952_t
Valid prediction for GeneMark_model.15938_t
Valid prediction for pasa_asmbl_42787.p1
Valid prediction for GeneMark_model.15928_t
Valid prediction for GlimmerHMM_glimmerT_9799-T1
Valid prediction for GeneMark_model.15943_t
Valid prediction for CodingQuarry_transcript_48934-T1
Valid prediction for GlimmerHMM_glimmerT_9811-T1
Valid prediction for GlimmerHMM_glimmerT_9804-T1
Couldn't classify 40059, 40170
Sorry, prediction pasa_asmbl_42792.p1 fails validation.
(GTG)	 AG	40059-40170	GT	GGG
(GAC)	 AG	40430-40521	GT	AGG
(GAA)	 AG	41455-41656	GT	TGG
(GCG)	 AG	43688-43848	CA	AGC
-recovered pasa_asmbl_42792.p1, terminal, 43688, 43848
-recovered pasa_asmbl_42792.p1, internal, 40059, 40170
-recovered pasa_asmbl_42792.p1, internal, 40430, 40521
-recovered pasa_asmbl_42792.p1, internal, 41455, 41656
Valid prediction for Augustus_model.g6412.t1
Valid prediction for GlimmerHMM_glimmerT_9806-T1
Valid prediction for snap_scaffold_4-snap.1512-T1
Valid prediction for snap_scaffold_4-snap.1501-T1
Valid prediction for snap_scaffold_4-snap.1496-T1
Valid prediction for Augustus_model.g6415.t1
Valid prediction for CodingQuarry_transcript_48933-T1
Valid prediction for snap_scaffold_4-snap.1506-T1
Valid prediction for GeneMark_model.15934_t
Valid prediction for snap_scaffold_4-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_9808-T1
Valid prediction for GeneMark_model.15947_t
Valid prediction for snap_scaffold_4-snap.1511-T1
Valid prediction for snap_scaffold_4-snap.1514-T1
Valid prediction for GlimmerHMM_glimmerT_9803-T1
Valid prediction for GeneMark_model.15936_t
Valid prediction for GeneMark_model.15946_t
Valid prediction for GeneMark_model.15927_t
Valid prediction for GeneMark_model.15942_t
Valid prediction for CodingQuarry_transcript_48932-T1
Valid prediction for Augustus_model.g6411.t1
Valid prediction for CodingQuarry_transcript_48930-T1
Valid prediction for snap_scaffold_4-snap.1505-T1
Valid prediction for snap_scaffold_4-snap.1500-T1
Valid prediction for Augustus_model.g6413.t1
Valid prediction for snap_scaffold_4-snap.1513-T1
Valid prediction for snap_scaffold_4-snap.1493-T1
Valid prediction for HiQ_model.g6414.t1
Valid prediction for GeneMark_model.15931_t
Valid prediction for snap_scaffold_4-snap.1503-T1
Valid prediction for GeneMark_model.15939_t
Valid prediction for GlimmerHMM_glimmerT_9809-T1
Valid prediction for snap_scaffold_4-snap.1498-T1
Valid prediction for CodingQuarry_transcript_48929-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 snap_scaffold_4-snap.1507-T1
Valid prediction for GeneMark_model.15933_t
Valid prediction for GlimmerHMM_glimmerT_9810-T1
Valid prediction for snap_scaffold_4-snap.1510-T1
Valid prediction for snap_scaffold_4-snap.1495-T1
Valid prediction for Augustus_model.g6417.t1
Valid prediction for snap_scaffold_4-snap.1494-T1
Valid prediction for snap_scaffold_4-snap.1502-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_48928-T1
Valid prediction for snap_scaffold_4-snap.1499-T1
Valid prediction for GeneMark_model.15945_t
Valid prediction for snap_scaffold_4-snap.1497-T1
Valid prediction for GeneMark_model.15935_t
Valid prediction for GeneMark_model.15929_t
Valid prediction for GeneMark_model.15948_t
Valid prediction for GeneMark_model.15930_t
Valid prediction for GeneMark_model.15951_t
Valid prediction for GlimmerHMM_glimmerT_9800-T1
Valid prediction for snap_scaffold_4-snap.1508-T1
Valid prediction for GeneMark_model.15940_t
Valid prediction for GlimmerHMM_glimmerT_9805-T1
Valid prediction for GeneMark_model.15944_t
Valid prediction for Augustus_model.g6409.t1
Valid prediction for GlimmerHMM_glimmerT_9802-T1
Valid prediction for GeneMark_model.15950_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9910, rend_intergenic: 6927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18257, rend_intergenic: 15130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24688, rend_intergenic: 22992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29188, rend_intergenic: 25141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43402, rend_intergenic: 41392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90659, rend_intergenic: 79055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 116524
-exon list size: 316


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 9910, rend_intergenic: 6927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18257, rend_intergenic: 15130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24688, rend_intergenic: 22992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29188, rend_intergenic: 25141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43402, rend_intergenic: 41392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90659, rend_intergenic: 79055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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