-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_1135546-1240589

-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 snap_scaffold_28-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_58104-T1
Valid prediction for snap_scaffold_28-snap.263-T1
Valid prediction for snap_scaffold_28-snap.251-T1
Valid prediction for snap_scaffold_28-snap.252-T1
Valid prediction for snap_scaffold_28-snap.257-T1
Valid prediction for snap_scaffold_28-snap.256-T1
Valid prediction for snap_scaffold_28-snap.267-T1
Valid prediction for GlimmerHMM_glimmerT_58103-T1
Valid prediction for GlimmerHMM_glimmerT_58106-T1
Valid prediction for snap_scaffold_28-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_58100-T1
Valid prediction for Augustus_model.g38467.t1
Valid prediction for snap_scaffold_28-snap.273-T1
Valid prediction for snap_scaffold_28-snap.270-T1
Valid prediction for snap_scaffold_28-snap.262-T1
Valid prediction for snap_scaffold_28-snap.254-T1
Valid prediction for snap_scaffold_28-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_58101-T1
Valid prediction for GlimmerHMM_glimmerT_58107-T1
Valid prediction for GlimmerHMM_glimmerT_58109-T1
Valid prediction for snap_scaffold_28-snap.265-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_28-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_58105-T1
Valid prediction for snap_scaffold_28-snap.261-T1
Couldn't classify 79815, 79924
Sorry, prediction pasa_asmbl_37979.p2 fails validation.
(ATG)	 GC	75460-75600	GT	AGG
(ATT)	 AG	76093-76155	GT	AGG
(ACC)	 AG	76801-76899	GT	TCG
(AAT)	 AG	77952-78048	GT	AGG
(ACC)	 AG	78432-78551	GT	CGG
(AGC)	 AG	79815-79924	GA	GCG
-recovered pasa_asmbl_37979.p2, initial, 75460, 75600
add_exon() Sorry, pasa_asmbl_37979.p2 77952-78048-terminal-3 is invalid.
-recovered pasa_asmbl_37979.p2, terminal, 77952, 78048
-recovered pasa_asmbl_37979.p2, internal, 76093, 76155
-recovered pasa_asmbl_37979.p2, internal, 76801, 76899
-recovered pasa_asmbl_37979.p2, internal, 77952, 78048
-recovered pasa_asmbl_37979.p2, internal, 78432, 78551
Valid prediction for GlimmerHMM_glimmerT_58108-T1
Valid prediction for snap_scaffold_28-snap.266-T1
Valid prediction for Augustus_model.g38466.t1
Valid prediction for Augustus_model.g38465.t1
Couldn't classify 85566, 85898
Sorry, prediction pasa_asmbl_37976.p1 fails validation.
(CTG)	 GT	85566-85898	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_58095-T1
Valid prediction for GlimmerHMM_glimmerT_58096-T1
Valid prediction for GlimmerHMM_glimmerT_58097-T1
Valid prediction for GlimmerHMM_glimmerT_58099-T1
Valid prediction for GlimmerHMM_glimmerT_58102-T1
Valid prediction for GlimmerHMM_glimmerT_58098-T1
Valid prediction for snap_scaffold_28-snap.269-T1
Valid prediction for snap_scaffold_28-snap.268-T1
Valid prediction for snap_scaffold_28-snap.255-T1
Valid prediction for Augustus_model.g38468.t1
Couldn't classify 80730, 80831
Couldn't classify 84568, 84627
Sorry, prediction pasa_asmbl_37978.p2 fails validation.
(GAG)	 GG	80730-80831	GT	CGG
(TGC)	 AG	81819-82032	GT	AGG
(CGG)	 AG	83774-83889	GT	AGG
(AAG)	 AG	84568-84627	CG	GCC
-recovered pasa_asmbl_37978.p2, internal, 81819, 82032
-recovered pasa_asmbl_37978.p2, internal, 83774, 83889
Valid prediction for GlimmerHMM_glimmerT_58094-T1
Valid prediction for Augustus_model.g38463.t1
Valid prediction for snap_scaffold_28-snap.253-T1
Valid prediction for snap_scaffold_28-snap.258-T1
Valid prediction for snap_scaffold_28-snap.264-T1
Valid prediction for Augustus_model.g38464.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12233, rend_intergenic: 8951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30656, rend_intergenic: 18627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32343, rend_intergenic: 30751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34046, rend_intergenic: 32924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45815, rend_intergenic: 34046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49881, rend_intergenic: 46576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56144, rend_intergenic: 49910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60414, rend_intergenic: 56160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70484, rend_intergenic: 67408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73342, rend_intergenic: 71706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75851, rend_intergenic: 74243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81985, rend_intergenic: 79323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90243, rend_intergenic: 84389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97171, rend_intergenic: 90387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 105044
-exon list size: 209


building trellis

0.5    
0.9    
1.4    
1.9    
2.4    
2.8    
3.3    
3.8    
4.3    
4.7    
5.2    
5.7    
6.2    
6.6    
7.1    
7.6    
8.1    
8.5    
9.0    
9.5    
10.0    
10.4    
10.9    
11.4    
11.8    
12.3    
12.8    
13.3    
13.7    
14.2    
14.7    
15.2    
15.6    
16.1    
16.6    
17.1    
17.5    
18.0    
18.5    
19.0    
19.4    
19.9    
20.4    
20.9    
21.3    
21.8    
22.3    
22.7    
23.2    
23.7    
24.2    
24.6    
25.1    
25.6    
26.1    
26.5    
27.0    
27.5    
28.0    
28.4    
28.9    
29.4    
29.9    
30.3    
30.8    
31.3    
31.8    
32.2    
32.7    
33.2    
33.6    
34.1    
34.6    
35.1    
35.5    
36.0    
36.5    
37.0    
37.4    
37.9    
38.4    
38.9    
39.3    
39.8    
40.3    
40.8    
41.2    
41.7    
42.2    
42.7    
43.1    
43.6    
44.1    
44.5    
45.0    
45.5    
46.0    
46.4    
46.9    
47.4    
47.9    
48.3    
48.8    
49.3    
49.8    
50.2    
50.7    
51.2    
51.7    
52.1    
52.6    
53.1    
53.6    
54.0    
54.5    
55.0    
55.5    
55.9    
56.4    
56.9    
57.3    
57.8    
58.3    
58.8    
59.2    
59.7    
60.2    
60.7    
61.1    
61.6    
62.1    
62.6    
63.0    
63.5    
64.0    
64.5    
64.9    
65.4    
65.9    
66.4    
66.8    
67.3    
67.8    
68.2    
68.7    
69.2    
69.7    
70.1    
70.6    
71.1    
71.6    
72.0    
72.5    
73.0    
73.5    
73.9    
74.4    
74.9    
75.4    
75.8    
76.3    
76.8    
77.3    
77.7    
78.2    
78.7    
79.1    
79.6    
80.1    
80.6    
81.0    
81.5    
82.0    
82.5    
82.9    
83.4    
83.9    
84.4    
84.8    
85.3    
85.8    
86.3    
86.7    
87.2    
87.7    
88.2    
88.6    
89.1    
89.6    
90.0    
90.5    
91.0    
91.5    
91.9    
92.4    
92.9    
93.4    
93.8    
94.3    
94.8    
95.3    
95.7    
96.2    
96.7    
97.2    
97.6    
98.1    
98.6    
99.1    
99.5    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 12233, rend_intergenic: 8951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30656, rend_intergenic: 18627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32343, rend_intergenic: 30751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34046, rend_intergenic: 32924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45815, rend_intergenic: 34046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49881, rend_intergenic: 46576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56144, rend_intergenic: 49910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60414, rend_intergenic: 56160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70484, rend_intergenic: 67408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73342, rend_intergenic: 71706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75851, rend_intergenic: 74243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81985, rend_intergenic: 79323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90243, rend_intergenic: 84389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97171, rend_intergenic: 90387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 6 predictions persist after filtering for low support