-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_17107198-17337134

-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.g15780.t1
Valid prediction for GlimmerHMM_glimmerT_23699-T1
Valid prediction for GlimmerHMM_glimmerT_23713-T1
Valid prediction for GlimmerHMM_glimmerT_23711-T1
Valid prediction for GlimmerHMM_glimmerT_23706-T1
Valid prediction for GlimmerHMM_glimmerT_23703-T1
Valid prediction for GlimmerHMM_glimmerT_23704-T1
Valid prediction for snap_scaffold_9-snap.3469-T1
Valid prediction for snap_scaffold_9-snap.3476-T1
Valid prediction for snap_scaffold_9-snap.3464-T1
Valid prediction for snap_scaffold_9-snap.3465-T1
Valid prediction for snap_scaffold_9-snap.3462-T1
Valid prediction for GlimmerHMM_glimmerT_23718-T1
Valid prediction for snap_scaffold_9-snap.3467-T1
Valid prediction for GlimmerHMM_glimmerT_23700-T1
Valid prediction for GlimmerHMM_glimmerT_23708-T1
Valid prediction for snap_scaffold_9-snap.3456-T1
Valid prediction for snap_scaffold_9-snap.3457-T1
Valid prediction for snap_scaffold_9-snap.3472-T1
Valid prediction for GlimmerHMM_glimmerT_23716-T1
Valid prediction for snap_scaffold_9-snap.3481-T1
Valid prediction for snap_scaffold_9-snap.3473-T1
Valid prediction for GlimmerHMM_glimmerT_23715-T1
Valid prediction for GlimmerHMM_glimmerT_23705-T1
Valid prediction for GlimmerHMM_glimmerT_23712-T1
Valid prediction for GlimmerHMM_glimmerT_23719-T1
Valid prediction for GlimmerHMM_glimmerT_23709-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_23707-T1
Valid prediction for snap_scaffold_9-snap.3475-T1
Valid prediction for snap_scaffold_9-snap.3477-T1
Valid prediction for snap_scaffold_9-snap.3471-T1
Valid prediction for Augustus_model.g15781.t1
Valid prediction for GlimmerHMM_glimmerT_23720-T1
Valid prediction for snap_scaffold_9-snap.3478-T1
Valid prediction for snap_scaffold_9-snap.3458-T1
Valid prediction for GlimmerHMM_glimmerT_23714-T1
Valid prediction for GlimmerHMM_glimmerT_23710-T1
Valid prediction for snap_scaffold_9-snap.3463-T1
Valid prediction for snap_scaffold_9-snap.3460-T1
Valid prediction for GlimmerHMM_glimmerT_23717-T1
Valid prediction for snap_scaffold_9-snap.3461-T1
Valid prediction for snap_scaffold_9-snap.3474-T1
Valid prediction for snap_scaffold_9-snap.3482-T1
Valid prediction for GlimmerHMM_glimmerT_23702-T1
Valid prediction for snap_scaffold_9-snap.3455-T1
Valid prediction for snap_scaffold_9-snap.3479-T1
Valid prediction for snap_scaffold_9-snap.3459-T1
Valid prediction for snap_scaffold_9-snap.3468-T1
Couldn't classify 32511, 32630
Sorry, prediction pasa_asmbl_55636.p1 fails validation.
(GGC)	 CA	32511-32630	GT	AGG
(GTG)	 AG	32919-33134	AA	GAA
-recovered pasa_asmbl_55636.p1, terminal, 32919, 33134
Valid prediction for GlimmerHMM_glimmerT_23701-T1
Valid prediction for snap_scaffold_9-snap.3480-T1
Valid prediction for Augustus_model.g15782.t1
Valid prediction for snap_scaffold_9-snap.3470-T1
Couldn't classify 25724, 25844
Couldn't classify 28985, 29244
Sorry, prediction pasa_asmbl_55637.p1 fails validation.
(GAT)	 CA	25724-25844	GT	AGG
(ATC)	 AG	26418-26618	GT	AGG
(AAG)	 AG	26942-27022	GT	CAG
(GCT)	 AG	27301-27546	GT	AGG
(GTA)	 AG	28985-29244	GG	CAG
-recovered pasa_asmbl_55637.p1, internal, 26418, 26618
-recovered pasa_asmbl_55637.p1, internal, 26942, 27022
-recovered pasa_asmbl_55637.p1, internal, 27301, 27546
Valid prediction for snap_scaffold_9-snap.3466-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 221477, rend_intergenic: 221474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159214, rend_intergenic: 156780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166198, rend_intergenic: 159989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175469, rend_intergenic: 171216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224707, rend_intergenic: 223682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229937
-exon list size: 167


building trellis

0.6    
1.2    
1.8    
2.4    
3.0    
3.6    
4.1    
4.7    
5.3    
5.9    
6.5    
7.1    
7.7    
8.3    
8.9    
9.5    
10.1    
10.7    
11.2    
11.8    
12.4    
13.0    
13.6    
14.2    
14.8    
15.4    
16.0    
16.6    
17.2    
17.8    
18.3    
18.9    
19.5    
20.1    
20.7    
21.3    
21.9    
22.5    
23.1    
23.7    
24.3    
24.9    
25.4    
26.0    
26.6    
27.2    
27.8    
28.4    
29.0    
29.6    
30.2    
30.8    
31.4    
32.0    
32.5    
33.1    
33.7    
34.3    
34.9    
35.5    
36.1    
36.7    
37.3    
37.9    
38.5    
39.1    
39.6    
40.2    
40.8    
41.4    
42.0    
42.6    
43.2    
43.8    
44.4    
45.0    
45.6    
46.2    
46.7    
47.3    
47.9    
48.5    
49.1    
49.7    
50.3    
50.9    
51.5    
52.1    
52.7    
53.3    
53.8    
54.4    
55.0    
55.6    
56.2    
56.8    
57.4    
58.0    
58.6    
59.2    
59.8    
60.4    
60.9    
61.5    
62.1    
62.7    
63.3    
63.9    
64.5    
65.1    
65.7    
66.3    
66.9    
67.5    
68.0    
68.6    
69.2    
69.8    
70.4    
71.0    
71.6    
72.2    
72.8    
73.4    
74.0    
74.6    
75.1    
75.7    
76.3    
76.9    
77.5    
78.1    
78.7    
79.3    
79.9    
80.5    
81.1    
81.7    
82.2    
82.8    
83.4    
84.0    
84.6    
85.2    
85.8    
86.4    
87.0    
87.6    
88.2    
88.8    
89.3    
89.9    
90.5    
91.1    
91.7    
92.3    
92.9    
93.5    
94.1    
94.7    
95.3    
95.9    
96.4    
97.0    
97.6    
98.2    
98.8    
99.4    
-found 14 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 221477, rend_intergenic: 221474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159214, rend_intergenic: 156780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166198, rend_intergenic: 159989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175469, rend_intergenic: 171216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224707, rend_intergenic: 223682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 50351
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10388
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support