-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_2219151-2459265

-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_1-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_299-T1
Valid prediction for Augustus_model.g244.t1
Valid prediction for Augustus_model.g224.t1
Valid prediction for Augustus_model.g237.t1
Valid prediction for GlimmerHMM_glimmerT_282-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_292-T1
Valid prediction for snap_scaffold_1-snap.388-T1
Valid prediction for GlimmerHMM_glimmerT_283-T1
Valid prediction for snap_scaffold_1-snap.362-T1
Valid prediction for Augustus_model.g227.t1
Valid prediction for snap_scaffold_1-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_298-T1
Valid prediction for GlimmerHMM_glimmerT_306-T1
Valid prediction for GlimmerHMM_glimmerT_280-T1
Valid prediction for GlimmerHMM_glimmerT_279-T1
Valid prediction for snap_scaffold_1-snap.364-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.381-T1
Valid prediction for Augustus_model.g236.t1
Valid prediction for GlimmerHMM_glimmerT_301-T1
Valid prediction for snap_scaffold_1-snap.391-T1
Valid prediction for snap_scaffold_1-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_295-T1
Valid prediction for snap_scaffold_1-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_303-T1
Valid prediction for Augustus_model.g229.t1
Valid prediction for GlimmerHMM_glimmerT_290-T1
Valid prediction for GlimmerHMM_glimmerT_304-T1
Valid prediction for GlimmerHMM_glimmerT_291-T1
Valid prediction for Augustus_model.g234.t1
Valid prediction for snap_scaffold_1-snap.380-T1
Valid prediction for snap_scaffold_1-snap.392-T1
Valid prediction for Augustus_model.g226.t1
Valid prediction for snap_scaffold_1-snap.386-T1
Valid prediction for GlimmerHMM_glimmerT_288-T1
Valid prediction for Augustus_model.g245.t1
Valid prediction for snap_scaffold_1-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_300-T1
Valid prediction for Augustus_model.g225.t1
Valid prediction for snap_scaffold_1-snap.363-T1
Valid prediction for Augustus_model.g246.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_296-T1
Valid prediction for snap_scaffold_1-snap.395-T1
Valid prediction for Augustus_model.g241.t1
Valid prediction for snap_scaffold_1-snap.368-T1
Valid prediction for snap_scaffold_1-snap.385-T1
Valid prediction for snap_scaffold_1-snap.371-T1
Valid prediction for Augustus_model.g235.t1
Valid prediction for snap_scaffold_1-snap.372-T1
Valid prediction for snap_scaffold_1-snap.366-T1
Valid prediction for Augustus_model.g230.t1
Valid prediction for snap_scaffold_1-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_294-T1
Valid prediction for CodingQuarry_transcript_2550-T1
Valid prediction for snap_scaffold_1-snap.374-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.373-T1
Valid prediction for Augustus_model.g223.t1
Valid prediction for Augustus_model.g242.t1
Valid prediction for Augustus_model.g231.t1
Valid prediction for Augustus_model.g228.t1
Valid prediction for snap_scaffold_1-snap.376-T1
Valid prediction for snap_scaffold_1-snap.367-T1
Couldn't classify 74212, 74325
Couldn't classify 75384, 75556
Sorry, prediction pasa_asmbl_118.p1 fails validation.
(CCC)	 AG	74212-74325	GT	GGG
(GTG)	 AG	74659-74869	GT	AGG
(TCC)	 AG	75098-75220	GT	AGG
(TGA)	 AG	75384-75556	GG	AAG
-recovered pasa_asmbl_118.p1, internal, 74212, 74325
-recovered pasa_asmbl_118.p1, internal, 74659, 74869
-recovered pasa_asmbl_118.p1, internal, 75098, 75220
Valid prediction for snap_scaffold_1-snap.377-T1
Valid prediction for Augustus_model.g240.t1
Valid prediction for snap_scaffold_1-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_305-T1
Valid prediction for GlimmerHMM_glimmerT_289-T1
Valid prediction for Augustus_model.g232.t1
Valid prediction for Augustus_model.g238.t1
Valid prediction for snap_scaffold_1-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_286-T1
Valid prediction for snap_scaffold_1-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_302-T1
Couldn't classify 72736, 72835
Couldn't classify 73733, 73894
Sorry, prediction pasa_asmbl_119.p1 fails validation.
(CGT)	 GC	72736-72835	GC	AGG
(AGT)	 AG	73028-73225	GT	CCG
(CCC)	 AG	73412-73482	GT	AGG
(CCT)	 AG	73733-73894	AT	CCA
-recovered pasa_asmbl_119.p1, internal, 73028, 73225
-recovered pasa_asmbl_119.p1, internal, 73412, 73482
Valid prediction for snap_scaffold_1-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_278-T1
Valid prediction for GlimmerHMM_glimmerT_281-T1
Couldn't classify 61137, 61234
Sorry, prediction pasa_asmbl_121.p1 fails validation.
(ATG)	 AG	55228-55321	GT	TCG
(TGA)	 AG	58171-58276	GT	ATG
(CTT)	 AG	60783-60979	GT	CAG
(AGG)	 AG	61137-61234	CC	CGC
-recovered pasa_asmbl_121.p1, initial, 55228, 55321
-recovered pasa_asmbl_121.p1, internal, 55228, 55321
-recovered pasa_asmbl_121.p1, internal, 58171, 58276
-recovered pasa_asmbl_121.p1, internal, 60783, 60979
Valid prediction for GlimmerHMM_glimmerT_287-T1
Valid prediction for snap_scaffold_1-snap.384-T1
Valid prediction for snap_scaffold_1-snap.382-T1
Valid prediction for Augustus_model.g233.t1
Valid prediction for snap_scaffold_1-snap.369-T1
Valid prediction for Augustus_model.g239.t1
Valid prediction for snap_scaffold_1-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_285-T1
Valid prediction for GlimmerHMM_glimmerT_284-T1
Valid prediction for Augustus_model.g243.t1
Valid prediction for GlimmerHMM_glimmerT_293-T1
Valid prediction for GlimmerHMM_glimmerT_297-T1
Valid prediction for snap_scaffold_1-snap.393-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 182364, rend_intergenic: 177896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199083, rend_intergenic: 195873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209064, rend_intergenic: 200571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219064, rend_intergenic: 210644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225029, rend_intergenic: 221011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240115
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 182364, rend_intergenic: 177896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199083, rend_intergenic: 195873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209064, rend_intergenic: 200571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219064, rend_intergenic: 210644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225029, rend_intergenic: 221011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 225297 - 240115
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 226545 - 240115
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 228195 - 240115
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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