-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_1090943-1297478

-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 GlimmerHMM_glimmerT_36329-T1
Valid prediction for snap_scaffold_15-snap.256-T1
Valid prediction for GlimmerHMM_glimmerT_36339-T1
Valid prediction for GlimmerHMM_glimmerT_36334-T1
Valid prediction for GlimmerHMM_glimmerT_36327-T1
Valid prediction for GlimmerHMM_glimmerT_36336-T1
Valid prediction for GeneMark_model.62474_t
Valid prediction for GeneMark_model.62475_t
Valid prediction for GlimmerHMM_glimmerT_36340-T1
Valid prediction for snap_scaffold_15-snap.258-T1
Valid prediction for snap_scaffold_15-snap.266-T1
Valid prediction for GlimmerHMM_glimmerT_36338-T1
Valid prediction for GeneMark_model.62486_t
Valid prediction for GlimmerHMM_glimmerT_36321-T1
Valid prediction for snap_scaffold_15-snap.260-T1
Valid prediction for GeneMark_model.62492_t
Valid prediction for GlimmerHMM_glimmerT_36325-T1
Valid prediction for GeneMark_model.62483_t
Valid prediction for snap_scaffold_15-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_36330-T1
Valid prediction for GeneMark_model.62499_t
Couldn't classify 174210, 174216
Couldn't classify 175614, 175811
Sorry, prediction pasa_asmbl_13940.p1 fails validation.
(CAC)	 TG	174210-174216	GT	CGG
(GCA)	 AG	174508-174638	GT	GGG
(TAC)	 AG	174899-174980	GT	AGG
(GTT)	 AG	175275-175384	GT	AGG
(GTA)	 AG	175614-175811	GA	GGG
-recovered pasa_asmbl_13940.p1, internal, 174508, 174638
-recovered pasa_asmbl_13940.p1, internal, 174899, 174980
-recovered pasa_asmbl_13940.p1, internal, 175275, 175384
Valid prediction for GeneMark_model.62473_t
Valid prediction for snap_scaffold_15-snap.251-T1
Valid prediction for GeneMark_model.62482_t
Valid prediction for Augustus_model.g24418.t1
Valid prediction for snap_scaffold_15-snap.243-T1
Valid prediction for snap_scaffold_15-snap.246-T1
Valid prediction for GeneMark_model.62496_t
Valid prediction for snap_scaffold_15-snap.263-T1
Valid prediction for GeneMark_model.62488_t
Valid prediction for GeneMark_model.62491_t
Couldn't classify 174088, 174125
Sorry, prediction pasa_asmbl_13936.p1 fails validation.
(ATG)	 CA	170633-170719	GT	AGG
(GTG)	 AG	171072-171182	GT	AGG
(CTG)	 AG	171305-171370	GT	CAG
(GTC)	 AG	171510-171555	GT	TGG
(TGC)	 AG	172013-172151	GT	AAG
(CCT)	 AG	172890-173014	GC	AGG
(GCA)	 AG	174088-174125	GG	GGG
-recovered pasa_asmbl_13936.p1, initial, 170633, 170719
-recovered pasa_asmbl_13936.p1, internal, 171072, 171182
-recovered pasa_asmbl_13936.p1, internal, 171305, 171370
-recovered pasa_asmbl_13936.p1, internal, 171510, 171555
-recovered pasa_asmbl_13936.p1, internal, 172013, 172151
-recovered pasa_asmbl_13936.p1, internal, 172890, 173014
Valid prediction for snap_scaffold_15-snap.242-T1
Valid prediction for snap_scaffold_15-snap.250-T1
Valid prediction for snap_scaffold_15-snap.264-T1
Valid prediction for GeneMark_model.62485_t
Valid prediction for snap_scaffold_15-snap.255-T1
Valid prediction for GlimmerHMM_glimmerT_36324-T1
Valid prediction for CodingQuarry_transcript_17859-T1
Valid prediction for GeneMark_model.62490_t
Couldn't classify 180413, 180577
Sorry, prediction pasa_asmbl_13941.p1 fails validation.
(GCC)	 TT	180413-180577	GT	AGG
(GGG)	 AG	181313-181412	GT	AGG
(ATA)	 AG	182314-182375	GT	AGG
(CCT)	 AG	183888-184003	GT	AAG
(GAA)	 AG	184571-184751	TG	GAT
-recovered pasa_asmbl_13941.p1, terminal, 184571, 184751
-recovered pasa_asmbl_13941.p1, internal, 181313, 181412
-recovered pasa_asmbl_13941.p1, internal, 182314, 182375
-recovered pasa_asmbl_13941.p1, internal, 183888, 184003
Valid prediction for CodingQuarry_transcript_17858-T1
Valid prediction for Augustus_model.g24421.t1
Valid prediction for GeneMark_model.62494_t
Valid prediction for Augustus_model.g24419.t1
Valid prediction for Augustus_model.g24422.t1
Valid prediction for GeneMark_model.62478_t
Valid prediction for GeneMark_model.62487_t
Valid prediction for snap_scaffold_15-snap.245-T1
Valid prediction for Augustus_model.g24423.t1
Valid prediction for snap_scaffold_15-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_36332-T1
Valid prediction for GeneMark_model.62472_t
Valid prediction for snap_scaffold_15-snap.261-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.62476_t
Valid prediction for GeneMark_model.62497_t
Valid prediction for GeneMark_model.62480_t
Valid prediction for GeneMark_model.62477_t
Valid prediction for GlimmerHMM_glimmerT_36331-T1
Valid prediction for snap_scaffold_15-snap.257-T1
Valid prediction for GeneMark_model.62471_t
Valid prediction for snap_scaffold_15-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_36326-T1
Valid prediction for GlimmerHMM_glimmerT_36322-T1
Valid prediction for GlimmerHMM_glimmerT_36337-T1
Valid prediction for snap_scaffold_15-snap.244-T1
Valid prediction for Augustus_model.g24420.t1
Valid prediction for snap_scaffold_15-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_36341-T1
Valid prediction for GlimmerHMM_glimmerT_36320-T1
Valid prediction for GeneMark_model.62493_t
Valid prediction for GlimmerHMM_glimmerT_36333-T1
Valid prediction for GlimmerHMM_glimmerT_36328-T1
Valid prediction for GeneMark_model.62489_t
Valid prediction for GeneMark_model.62484_t
Valid prediction for GeneMark_model.62470_t
Valid prediction for GlimmerHMM_glimmerT_36323-T1
Valid prediction for snap_scaffold_15-snap.254-T1
Valid prediction for snap_scaffold_15-snap.247-T1
Valid prediction for GeneMark_model.62479_t
Valid prediction for snap_scaffold_15-snap.259-T1
Valid prediction for snap_scaffold_15-snap.252-T1
Valid prediction for GeneMark_model.62495_t
Valid prediction for snap_scaffold_15-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_36335-T1
Valid prediction for GeneMark_model.62481_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11223, rend_intergenic: 10953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14486, rend_intergenic: 11364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95572, rend_intergenic: 92896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186609, rend_intergenic: 177601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206536
-exon list size: 315


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 11223, rend_intergenic: 10953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14486, rend_intergenic: 11364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95572, rend_intergenic: 92896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186609, rend_intergenic: 177601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support