-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_2822912-3028128

-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.g26615.t1
Valid prediction for snap_scaffold_17-snap.605-T1
Valid prediction for snap_scaffold_17-snap.615-T1
Valid prediction for snap_scaffold_17-snap.629-T1
Valid prediction for GlimmerHMM_glimmerT_39971-T1
Valid prediction for Augustus_model.g26626.t1
Valid prediction for snap_scaffold_17-snap.621-T1
Valid prediction for Augustus_model.g26616.t1
Valid prediction for snap_scaffold_17-snap.607-T1
Valid prediction for snap_scaffold_17-snap.634-T1
Couldn't classify 195829, 196323
Sorry, prediction pasa_asmbl_17790.p1 fails validation.
(CCT)	 TT	195829-196323	AT	AAA
Valid prediction for Augustus_model.g26632.t1
Valid prediction for GlimmerHMM_glimmerT_39974-T1
Valid prediction for GlimmerHMM_glimmerT_39985-T1
Valid prediction for snap_scaffold_17-snap.600-T1
Valid prediction for Augustus_model.g26620.t1
Valid prediction for snap_scaffold_17-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_39977-T1
Valid prediction for snap_scaffold_17-snap.614-T1
Valid prediction for snap_scaffold_17-snap.620-T1
Valid prediction for snap_scaffold_17-snap.623-T1
Valid prediction for GlimmerHMM_glimmerT_39976-T1
Valid prediction for GlimmerHMM_glimmerT_39970-T1
Valid prediction for snap_scaffold_17-snap.598-T1
Valid prediction for GlimmerHMM_glimmerT_39980-T1
Valid prediction for snap_scaffold_17-snap.630-T1
Valid prediction for snap_scaffold_17-snap.609-T1
Valid prediction for pasa_asmbl_18700.p1
Valid prediction for Augustus_model.g26625.t1
Valid prediction for Augustus_model.g26624.t1
Valid prediction for snap_scaffold_17-snap.612-T1
Valid prediction for pasa_asmbl_18696.p1
Valid prediction for CodingQuarry_transcript_21919-T1
Valid prediction for CodingQuarry_transcript_21920-T1
Valid prediction for Augustus_model.g26622.t1
Couldn't classify 184552, 184739
Sorry, prediction pasa_asmbl_18697.p1 fails validation.
(AGG)	 CC	184552-184739	GT	AGG
(CAT)	 AG	186851-187048	GT	AGG
(AAT)	 AG	187350-187514	GT	AGG
(GTG)	 AG	188673-189135	GT	AGG
(CTG)	 AG	190472-190660	TC	GAT
add_exon() Sorry, pasa_asmbl_18697.p1 187350-187514-terminal-1 is invalid.
-recovered pasa_asmbl_18697.p1, terminal, 187350, 187514
-recovered pasa_asmbl_18697.p1, terminal, 190472, 190660
-recovered pasa_asmbl_18697.p1, internal, 186851, 187048
-recovered pasa_asmbl_18697.p1, internal, 187350, 187514
-recovered pasa_asmbl_18697.p1, internal, 188673, 189135
Valid prediction for GlimmerHMM_glimmerT_39973-T1
Valid prediction for Augustus_model.g26619.t1
Valid prediction for GlimmerHMM_glimmerT_39966-T1
Valid prediction for snap_scaffold_17-snap.626-T1
Valid prediction for HiQ_model.g26630.t1
Valid prediction for GlimmerHMM_glimmerT_39967-T1
Valid prediction for snap_scaffold_17-snap.624-T1
Valid prediction for snap_scaffold_17-snap.608-T1
Valid prediction for Augustus_model.g26631.t1
Valid prediction for Augustus_model.g26618.t1
Valid prediction for snap_scaffold_17-snap.617-T1
Valid prediction for snap_scaffold_17-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_39984-T1
Valid prediction for GlimmerHMM_glimmerT_39962-T1
Valid prediction for snap_scaffold_17-snap.632-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_39978-T1
Valid prediction for Augustus_model.g26627.t1
Valid prediction for GlimmerHMM_glimmerT_39981-T1
Valid prediction for snap_scaffold_17-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_39964-T1
Valid prediction for GlimmerHMM_glimmerT_39975-T1
Valid prediction for snap_scaffold_17-snap.619-T1
Valid prediction for GlimmerHMM_glimmerT_39968-T1
Valid prediction for GlimmerHMM_glimmerT_39965-T1
Valid prediction for GlimmerHMM_glimmerT_39963-T1
Valid prediction for snap_scaffold_17-snap.606-T1
Valid prediction for Augustus_model.g26623.t1
Valid prediction for snap_scaffold_17-snap.610-T1
Valid prediction for snap_scaffold_17-snap.625-T1
Valid prediction for snap_scaffold_17-snap.628-T1
Valid prediction for snap_scaffold_17-snap.633-T1
Valid prediction for snap_scaffold_17-snap.603-T1
Valid prediction for snap_scaffold_17-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_39969-T1
Valid prediction for Augustus_model.g26629.t1
Valid prediction for snap_scaffold_17-snap.616-T1
Valid prediction for snap_scaffold_17-snap.602-T1
Valid prediction for Augustus_model.g26617.t1
Valid prediction for snap_scaffold_17-snap.631-T1
Valid prediction for Augustus_model.g26628.t1
Valid prediction for snap_scaffold_17-snap.627-T1
Valid prediction for Augustus_model.g26621.t1
Valid prediction for snap_scaffold_17-snap.613-T1
Valid prediction for snap_scaffold_17-snap.622-T1
Valid prediction for snap_scaffold_17-snap.618-T1
Valid prediction for GlimmerHMM_glimmerT_39983-T1
Valid prediction for snap_scaffold_17-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_39972-T1
Valid prediction for snap_scaffold_17-snap.601-T1
Valid prediction for GlimmerHMM_glimmerT_39979-T1
Valid prediction for GlimmerHMM_glimmerT_39982-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17604, rend_intergenic: 14063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48964, rend_intergenic: 44385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76233, rend_intergenic: 64712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82385, rend_intergenic: 77658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88583, rend_intergenic: 82536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96745, rend_intergenic: 91773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99965, rend_intergenic: 98285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102938, rend_intergenic: 100001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120041, rend_intergenic: 102960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130716, rend_intergenic: 126895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143970, rend_intergenic: 142153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154481, rend_intergenic: 150554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197786, rend_intergenic: 196446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201014, rend_intergenic: 199210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203253, rend_intergenic: 201491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205217
-exon list size: 341


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
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3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 17604, rend_intergenic: 14063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48964, rend_intergenic: 44385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76233, rend_intergenic: 64712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82385, rend_intergenic: 77658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88583, rend_intergenic: 82536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96745, rend_intergenic: 91773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99965, rend_intergenic: 98285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102938, rend_intergenic: 100001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120041, rend_intergenic: 102960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130716, rend_intergenic: 126895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143970, rend_intergenic: 142153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154481, rend_intergenic: 150554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197786, rend_intergenic: 196446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201014, rend_intergenic: 199210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203253, rend_intergenic: 201491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14207
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 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 1 - 14062
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 1 - 13850
-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
	-no exons in range 1 - 11556