-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_14855830-15044497

-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_7804-T1
Valid prediction for GlimmerHMM_glimmerT_7803-T1
Couldn't classify 55338, 55494
Sorry, prediction pasa_asmbl_40833.p1 fails validation.
(TCC)	 GT	55338-55494	GT	AGG
(GTG)	 AG	55706-55887	GC	GAG
-recovered pasa_asmbl_40833.p1, terminal, 55706, 55887
-recovered pasa_asmbl_40833.p1, internal, 55706, 55887
Valid prediction for snap_scaffold_3-snap.2834-T1
Valid prediction for snap_scaffold_3-snap.2843-T1
Valid prediction for Augustus_model.g5152.t1
Valid prediction for snap_scaffold_3-snap.2846-T1
Valid prediction for Augustus_model.g5155.t1
Valid prediction for snap_scaffold_3-snap.2842-T1
Valid prediction for Augustus_model.g5154.t1
Valid prediction for snap_scaffold_3-snap.2827-T1
Valid prediction for Augustus_model.g5149.t1
Valid prediction for snap_scaffold_3-snap.2824-T1
Valid prediction for snap_scaffold_3-snap.2829-T1
Valid prediction for snap_scaffold_3-snap.2826-T1
Valid prediction for snap_scaffold_3-snap.2833-T1
Valid prediction for GlimmerHMM_glimmerT_7798-T1
Valid prediction for snap_scaffold_3-snap.2818-T1
Valid prediction for Augustus_model.g5148.t1
Valid prediction for GlimmerHMM_glimmerT_7808-T1
Valid prediction for Augustus_model.g5156.t1
Valid prediction for snap_scaffold_3-snap.2837-T1
Valid prediction for GlimmerHMM_glimmerT_7800-T1
Valid prediction for Augustus_model.g5153.t1
Valid prediction for snap_scaffold_3-snap.2840-T1
Couldn't classify 177113, 177213
Sorry, prediction pasa_asmbl_40856.p1 fails validation.
(ATG)	 CC	176329-176430	GT	AGG
(GAG)	 AG	176669-176804	GT	ACG
(CGA)	 AG	177113-177213	CA	GCC
-recovered pasa_asmbl_40856.p1, initial, 176329, 176430
-recovered pasa_asmbl_40856.p1, internal, 176669, 176804
Valid prediction for snap_scaffold_3-snap.2822-T1
Valid prediction for snap_scaffold_3-snap.2839-T1
Valid prediction for GlimmerHMM_glimmerT_7802-T1
Valid prediction for snap_scaffold_3-snap.2819-T1
Valid prediction for GlimmerHMM_glimmerT_7791-T1
Valid prediction for snap_scaffold_3-snap.2838-T1
Valid prediction for Augustus_model.g5150.t1
Valid prediction for GlimmerHMM_glimmerT_7807-T1
Valid prediction for GlimmerHMM_glimmerT_7797-T1
Valid prediction for GlimmerHMM_glimmerT_7793-T1
Valid prediction for snap_scaffold_3-snap.2823-T1
Valid prediction for snap_scaffold_3-snap.2844-T1
Valid prediction for GlimmerHMM_glimmerT_7809-T1
Valid prediction for GlimmerHMM_glimmerT_7806-T1
Valid prediction for snap_scaffold_3-snap.2836-T1
Valid prediction for snap_scaffold_3-snap.2831-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_7795-T1
Valid prediction for GlimmerHMM_glimmerT_7794-T1
Valid prediction for GlimmerHMM_glimmerT_7792-T1
Valid prediction for snap_scaffold_3-snap.2848-T1
Valid prediction for snap_scaffold_3-snap.2828-T1
Valid prediction for snap_scaffold_3-snap.2820-T1
Valid prediction for snap_scaffold_3-snap.2845-T1
Valid prediction for GlimmerHMM_glimmerT_7796-T1
Valid prediction for Augustus_model.g5157.t1
Valid prediction for GlimmerHMM_glimmerT_7805-T1
Valid prediction for snap_scaffold_3-snap.2825-T1
Valid prediction for snap_scaffold_3-snap.2835-T1
Valid prediction for snap_scaffold_3-snap.2850-T1
Valid prediction for pasa_asmbl_39432.p1
Valid prediction for HiQ_model.g5151.t1
Valid prediction for CodingQuarry_transcript_46377-T1
Valid prediction for snap_scaffold_3-snap.2849-T1
Valid prediction for snap_scaffold_3-snap.2847-T1
Valid prediction for snap_scaffold_3-snap.2821-T1
Valid prediction for snap_scaffold_3-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_7801-T1
Valid prediction for snap_scaffold_3-snap.2830-T1
Valid prediction for GlimmerHMM_glimmerT_7799-T1
Valid prediction for snap_scaffold_3-snap.2832-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16696, rend_intergenic: 10444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21927, rend_intergenic: 17048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41774, rend_intergenic: 37020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46262, rend_intergenic: 44870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47768, rend_intergenic: 46505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54118, rend_intergenic: 47945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141354, rend_intergenic: 138627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163360, rend_intergenic: 157978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188668
-exon list size: 176


building trellis

0.6    
1.1    
1.7    
2.2    
2.8    
3.4    
3.9    
4.5    
5.1    
5.6    
6.2    
6.7    
7.3    
7.9    
8.4    
9.0    
9.6    
10.1    
10.7    
11.2    
11.8    
12.4    
12.9    
13.5    
14.0    
14.6    
15.2    
15.7    
16.3    
16.9    
17.4    
18.0    
18.5    
19.1    
19.7    
20.2    
20.8    
21.3    
21.9    
22.5    
23.0    
23.6    
24.2    
24.7    
25.3    
25.8    
26.4    
27.0    
27.5    
28.1    
28.7    
29.2    
29.8    
30.3    
30.9    
31.5    
32.0    
32.6    
33.1    
33.7    
34.3    
34.8    
35.4    
36.0    
36.5    
37.1    
37.6    
38.2    
38.8    
39.3    
39.9    
40.4    
41.0    
41.6    
42.1    
42.7    
43.3    
43.8    
44.4    
44.9    
45.5    
46.1    
46.6    
47.2    
47.8    
48.3    
48.9    
49.4    
50.0    
50.6    
51.1    
51.7    
52.2    
52.8    
53.4    
53.9    
54.5    
55.1    
55.6    
56.2    
56.7    
57.3    
57.9    
58.4    
59.0    
59.6    
60.1    
60.7    
61.2    
61.8    
62.4    
62.9    
63.5    
64.0    
64.6    
65.2    
65.7    
66.3    
66.9    
67.4    
68.0    
68.5    
69.1    
69.7    
70.2    
70.8    
71.3    
71.9    
72.5    
73.0    
73.6    
74.2    
74.7    
75.3    
75.8    
76.4    
77.0    
77.5    
78.1    
78.7    
79.2    
79.8    
80.3    
80.9    
81.5    
82.0    
82.6    
83.1    
83.7    
84.3    
84.8    
85.4    
86.0    
86.5    
87.1    
87.6    
88.2    
88.8    
89.3    
89.9    
90.4    
91.0    
91.6    
92.1    
92.7    
93.3    
93.8    
94.4    
94.9    
95.5    
96.1    
96.6    
97.2    
97.8    
98.3    
98.9    
99.4    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 16696, rend_intergenic: 10444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21927, rend_intergenic: 17048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41774, rend_intergenic: 37020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46262, rend_intergenic: 44870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47768, rend_intergenic: 46505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54118, rend_intergenic: 47945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141354, rend_intergenic: 138627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163360, rend_intergenic: 157978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support