-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_4238610-4433028

-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_19-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_43989-T1
Valid prediction for Augustus_model.g29158.t1
Valid prediction for snap_scaffold_19-snap.901-T1
Valid prediction for GlimmerHMM_glimmerT_43990-T1
Valid prediction for snap_scaffold_19-snap.921-T1
Couldn't classify 28307, 28339
Sorry, prediction pasa_asmbl_21940.p1 fails validation.
(ATG)	 CA	26878-26952	GT	AGG
(GTC)	 AG	27365-27500	GT	AGG
(GAG)	 AG	27767-27858	GT	AGG
(GAT)	 AG	28307-28339	GA	AAG
-recovered pasa_asmbl_21940.p1, initial, 26878, 26952
add_exon() Sorry, pasa_asmbl_21940.p1 27365-27500-terminal-3 is invalid.
-recovered pasa_asmbl_21940.p1, terminal, 27365, 27500
-recovered pasa_asmbl_21940.p1, internal, 27365, 27500
-recovered pasa_asmbl_21940.p1, internal, 27767, 27858
Valid prediction for GlimmerHMM_glimmerT_43985-T1
Valid prediction for GlimmerHMM_glimmerT_43971-T1
Valid prediction for snap_scaffold_19-snap.928-T1
Valid prediction for GlimmerHMM_glimmerT_43981-T1
Valid prediction for Augustus_model.g29157.t1
Valid prediction for snap_scaffold_19-snap.902-T1
Valid prediction for snap_scaffold_19-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_43968-T1
Valid prediction for snap_scaffold_19-snap.927-T1
Valid prediction for snap_scaffold_19-snap.898-T1
Valid prediction for snap_scaffold_19-snap.906-T1
Valid prediction for snap_scaffold_19-snap.907-T1
Valid prediction for Augustus_model.g29161.t1
Valid prediction for snap_scaffold_19-snap.933-T1
Valid prediction for snap_scaffold_19-snap.913-T1
Valid prediction for GlimmerHMM_glimmerT_43969-T1
Valid prediction for GlimmerHMM_glimmerT_43979-T1
Valid prediction for GlimmerHMM_glimmerT_43975-T1
Valid prediction for snap_scaffold_19-snap.934-T1
Valid prediction for snap_scaffold_19-snap.925-T1
Valid prediction for CodingQuarry_transcript_25637-T1
Valid prediction for snap_scaffold_19-snap.915-T1
Valid prediction for GlimmerHMM_glimmerT_43980-T1
Couldn't classify 30345, 30692
Sorry, prediction pasa_asmbl_21341.p2 fails validation.
(TCC)	 CC	30345-30692	TG	GAT
Valid prediction for snap_scaffold_19-snap.909-T1
Valid prediction for snap_scaffold_19-snap.932-T1
Valid prediction for snap_scaffold_19-snap.937-T1
Valid prediction for Augustus_model.g29159.t1
Valid prediction for snap_scaffold_19-snap.905-T1
Valid prediction for Augustus_model.g29162.t1
Valid prediction for GlimmerHMM_glimmerT_43970-T1
Valid prediction for Augustus_model.g29156.t1
Valid prediction for snap_scaffold_19-snap.919-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_43976-T1
Valid prediction for GlimmerHMM_glimmerT_43967-T1
Valid prediction for GlimmerHMM_glimmerT_43986-T1
Valid prediction for GlimmerHMM_glimmerT_43988-T1
Valid prediction for Augustus_model.g29160.t1
Valid prediction for snap_scaffold_19-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_43983-T1
Valid prediction for snap_scaffold_19-snap.914-T1
Valid prediction for snap_scaffold_19-snap.923-T1
Valid prediction for snap_scaffold_19-snap.903-T1
Valid prediction for snap_scaffold_19-snap.924-T1
Valid prediction for snap_scaffold_19-snap.926-T1
Valid prediction for snap_scaffold_19-snap.931-T1
Valid prediction for snap_scaffold_19-snap.935-T1
Valid prediction for snap_scaffold_19-snap.916-T1
Valid prediction for snap_scaffold_19-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_43978-T1
Valid prediction for snap_scaffold_19-snap.922-T1
Valid prediction for snap_scaffold_19-snap.920-T1
Valid prediction for snap_scaffold_19-snap.938-T1
Valid prediction for snap_scaffold_19-snap.904-T1
Valid prediction for snap_scaffold_19-snap.936-T1
Valid prediction for snap_scaffold_19-snap.899-T1
Valid prediction for GlimmerHMM_glimmerT_43973-T1
Valid prediction for GlimmerHMM_glimmerT_43982-T1
Valid prediction for snap_scaffold_19-snap.917-T1
Valid prediction for snap_scaffold_19-snap.910-T1
Valid prediction for snap_scaffold_19-snap.930-T1
Valid prediction for GlimmerHMM_glimmerT_43987-T1
Valid prediction for snap_scaffold_19-snap.912-T1
Valid prediction for GlimmerHMM_glimmerT_43972-T1
Valid prediction for GlimmerHMM_glimmerT_43974-T1
Valid prediction for GlimmerHMM_glimmerT_43984-T1
Valid prediction for snap_scaffold_19-snap.908-T1
Valid prediction for GlimmerHMM_glimmerT_43977-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8427, rend_intergenic: 3319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17515, rend_intergenic: 9277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23848, rend_intergenic: 23460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46961, rend_intergenic: 41220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51111, rend_intergenic: 47634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65678, rend_intergenic: 65106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67575, rend_intergenic: 65870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79046, rend_intergenic: 68394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133494, rend_intergenic: 132420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157002, rend_intergenic: 148223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173595, rend_intergenic: 171387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189096, rend_intergenic: 188544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194419
-exon list size: 223


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.7    
3.1    
3.6    
4.0    
4.4    
4.9    
5.3    
5.8    
6.2    
6.7    
7.1    
7.6    
8.0    
8.4    
8.9    
9.3    
9.8    
10.2    
10.7    
11.1    
11.6    
12.0    
12.4    
12.9    
13.3    
13.8    
14.2    
14.7    
15.1    
15.6    
16.0    
16.4    
16.9    
17.3    
17.8    
18.2    
18.7    
19.1    
19.6    
20.0    
20.4    
20.9    
21.3    
21.8    
22.2    
22.7    
23.1    
23.6    
24.0    
24.4    
24.9    
25.3    
25.8    
26.2    
26.7    
27.1    
27.6    
28.0    
28.4    
28.9    
29.3    
29.8    
30.2    
30.7    
31.1    
31.6    
32.0    
32.4    
32.9    
33.3    
33.8    
34.2    
34.7    
35.1    
35.6    
36.0    
36.4    
36.9    
37.3    
37.8    
38.2    
38.7    
39.1    
39.6    
40.0    
40.4    
40.9    
41.3    
41.8    
42.2    
42.7    
43.1    
43.6    
44.0    
44.4    
44.9    
45.3    
45.8    
46.2    
46.7    
47.1    
47.6    
48.0    
48.4    
48.9    
49.3    
49.8    
50.2    
50.7    
51.1    
51.6    
52.0    
52.4    
52.9    
53.3    
53.8    
54.2    
54.7    
55.1    
55.6    
56.0    
56.4    
56.9    
57.3    
57.8    
58.2    
58.7    
59.1    
59.6    
60.0    
60.4    
60.9    
61.3    
61.8    
62.2    
62.7    
63.1    
63.6    
64.0    
64.4    
64.9    
65.3    
65.8    
66.2    
66.7    
67.1    
67.6    
68.0    
68.4    
68.9    
69.3    
69.8    
70.2    
70.7    
71.1    
71.6    
72.0    
72.4    
72.9    
73.3    
73.8    
74.2    
74.7    
75.1    
75.6    
76.0    
76.4    
76.9    
77.3    
77.8    
78.2    
78.7    
79.1    
79.6    
80.0    
80.4    
80.9    
81.3    
81.8    
82.2    
82.7    
83.1    
83.6    
84.0    
84.4    
84.9    
85.3    
85.8    
86.2    
86.7    
87.1    
87.6    
88.0    
88.4    
88.9    
89.3    
89.8    
90.2    
90.7    
91.1    
91.6    
92.0    
92.4    
92.9    
93.3    
93.8    
94.2    
94.7    
95.1    
95.6    
96.0    
96.4    
96.9    
97.3    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 8427, rend_intergenic: 3319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17515, rend_intergenic: 9277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23848, rend_intergenic: 23460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46961, rend_intergenic: 41220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51111, rend_intergenic: 47634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65678, rend_intergenic: 65106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67575, rend_intergenic: 65870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79046, rend_intergenic: 68394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133494, rend_intergenic: 132420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157002, rend_intergenic: 148223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173595, rend_intergenic: 171387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189096, rend_intergenic: 188544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 172845 - 194419
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 172845 - 188602
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 2 predictions from path traversal

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

-building DP trellis

-building trellis in range 172845 - 183941
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 2 predictions from path traversal

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