-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_7252071-7334642

-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_18076-T1
Valid prediction for GlimmerHMM_glimmerT_18066-T1
Valid prediction for GlimmerHMM_glimmerT_18070-T1
Valid prediction for snap_scaffold_7-snap.1497-T1
Couldn't classify 40424, 40558
Sorry, prediction pasa_asmbl_50801.p1 fails validation.
(GTG)	 AG	40424-40558	GT	AGG
(CGT)	 AG	41705-41884	GC	GAG
-recovered pasa_asmbl_50801.p1, terminal, 41705, 41884
-recovered pasa_asmbl_50801.p1, internal, 40424, 40558
-recovered pasa_asmbl_50801.p1, internal, 41705, 41884
Valid prediction for snap_scaffold_7-snap.1496-T1
Valid prediction for GeneMark_model.30306_t
Valid prediction for snap_scaffold_7-snap.1498-T1
Valid prediction for snap_scaffold_7-snap.1491-T1
Valid prediction for GeneMark_model.30293_t
Valid prediction for GeneMark_model.30304_t
Valid prediction for snap_scaffold_7-snap.1500-T1
Valid prediction for CodingQuarry_transcript_57392-T1
Couldn't classify 28848, 29009
Couldn't classify 31124, 31183
Sorry, prediction pasa_asmbl_51488.p1 fails validation.
(GTT)	 AG	28848-29009	GT	AGG
(GTG)	 AG	29825-29902	GT	AGG
(GTA)	 AG	31124-31183	TA	GCT
-recovered pasa_asmbl_51488.p1, internal, 28848, 29009
-recovered pasa_asmbl_51488.p1, internal, 29825, 29902
Valid prediction for Augustus_model.g12137.t1
Valid prediction for snap_scaffold_7-snap.1495-T1
Valid prediction for snap_scaffold_7-snap.1493-T1
Valid prediction for Augustus_model.g12135.t1
Valid prediction for GlimmerHMM_glimmerT_18063-T1
Valid prediction for snap_scaffold_7-snap.1488-T1
Valid prediction for GeneMark_model.30297_t
Valid prediction for GeneMark_model.30316_t
Valid prediction for snap_scaffold_7-snap.1489-T1
Valid prediction for Augustus_model.g12139.t1
Valid prediction for GeneMark_model.30311_t
Valid prediction for GlimmerHMM_glimmerT_18073-T1
Valid prediction for HiQ_model.g12138.t1
Valid prediction for GlimmerHMM_glimmerT_18071-T1
Valid prediction for Augustus_model.g12140.t1
Valid prediction for GlimmerHMM_glimmerT_18064-T1
Valid prediction for snap_scaffold_7-snap.1490-T1
Valid prediction for GeneMark_model.30320_t
Valid prediction for Augustus_model.g12142.t1
Valid prediction for snap_scaffold_7-snap.1502-T1
Valid prediction for GeneMark_model.30299_t
Valid prediction for GeneMark_model.30319_t
Couldn't classify 19584, 19816
Couldn't classify 25549, 25766
Sorry, prediction pasa_asmbl_51465.p1 fails validation.
(GTT)	 CA	19584-19816	GT	AGG
(GTC)	 AG	21873-22018	GT	GGG
(AGA)	 AG	24408-24518	GT	TGG
(ACA)	 AG	25549-25766	GT	AGG
-recovered pasa_asmbl_51465.p1, internal, 21873, 22018
-recovered pasa_asmbl_51465.p1, internal, 24408, 24518
-recovered pasa_asmbl_51465.p1, internal, 25549, 25766
Valid prediction for GlimmerHMM_glimmerT_18074-T1
Valid prediction for GeneMark_model.30310_t
Valid prediction for GeneMark_model.30308_t

-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_18059-T1
Valid prediction for GeneMark_model.30300_t
Valid prediction for GlimmerHMM_glimmerT_18056-T1
Valid prediction for GlimmerHMM_glimmerT_18060-T1
Valid prediction for GlimmerHMM_glimmerT_18065-T1
Valid prediction for Augustus_model.g12136.t1
Valid prediction for GlimmerHMM_glimmerT_18058-T1
Valid prediction for GlimmerHMM_glimmerT_18077-T1
Valid prediction for GlimmerHMM_glimmerT_18057-T1
Valid prediction for GeneMark_model.30296_t
Valid prediction for GeneMark_model.30298_t
Valid prediction for GeneMark_model.30321_t
Valid prediction for GeneMark_model.30315_t
Valid prediction for GeneMark_model.30295_t
Valid prediction for snap_scaffold_7-snap.1487-T1
Valid prediction for snap_scaffold_7-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_18067-T1
Valid prediction for GeneMark_model.30317_t
Valid prediction for GeneMark_model.30303_t
Valid prediction for GeneMark_model.30292_t
Valid prediction for GlimmerHMM_glimmerT_18062-T1
Valid prediction for GeneMark_model.30318_t
Valid prediction for Augustus_model.g12131.t1
Valid prediction for GlimmerHMM_glimmerT_18072-T1
Valid prediction for GeneMark_model.30312_t
Valid prediction for GeneMark_model.30307_t
Valid prediction for GlimmerHMM_glimmerT_18075-T1
Valid prediction for GeneMark_model.30309_t
Valid prediction for Augustus_model.g12141.t1
Valid prediction for Augustus_model.g12132.t1
Valid prediction for GeneMark_model.30305_t
Valid prediction for Augustus_model.g12143.t1
Valid prediction for GlimmerHMM_glimmerT_18061-T1
Valid prediction for GlimmerHMM_glimmerT_18068-T1
Valid prediction for Augustus_model.g12133.t1
Valid prediction for GeneMark_model.30301_t
Valid prediction for GeneMark_model.30314_t
Valid prediction for snap_scaffold_7-snap.1494-T1
Valid prediction for Augustus_model.g12134.t1
Valid prediction for snap_scaffold_7-snap.1499-T1
Valid prediction for snap_scaffold_7-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_18069-T1
Valid prediction for GeneMark_model.30294_t
Valid prediction for GeneMark_model.30313_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22690, rend_intergenic: 21840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25759, rend_intergenic: 22746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41374, rend_intergenic: 31788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66477, rend_intergenic: 64451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68185, rend_intergenic: 67012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73758, rend_intergenic: 68328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 31186, rend_intergenic: 31183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 82572
-exon list size: 353


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.4    
19.7    
20.0    
20.3    
20.6    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
40.0    
40.3    
40.6    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.4    
59.7    
60.0    
60.3    
60.6    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.4    
79.7    
80.0    
80.3    
80.6    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 22690, rend_intergenic: 21840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25759, rend_intergenic: 22746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41374, rend_intergenic: 31788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66477, rend_intergenic: 64451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68185, rend_intergenic: 67012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73758, rend_intergenic: 68328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 31186, rend_intergenic: 31183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support