-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_16931645-17124773

-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.g10968.t1
Valid prediction for GlimmerHMM_glimmerT_16350-T1
Valid prediction for snap_scaffold_6-snap.3603-T1
Valid prediction for snap_scaffold_6-snap.3617-T1
Valid prediction for GlimmerHMM_glimmerT_16354-T1
Valid prediction for snap_scaffold_6-snap.3588-T1
Valid prediction for GlimmerHMM_glimmerT_16365-T1
Valid prediction for snap_scaffold_6-snap.3609-T1
Valid prediction for HiQ_model.g10967.t1
Valid prediction for snap_scaffold_6-snap.3601-T1
Valid prediction for CodingQuarry_transcript_55394-T1
Valid prediction for GlimmerHMM_glimmerT_16368-T1
Valid prediction for GlimmerHMM_glimmerT_16364-T1
Valid prediction for GlimmerHMM_glimmerT_16369-T1
Valid prediction for snap_scaffold_6-snap.3594-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g10966.t1
Valid prediction for snap_scaffold_6-snap.3612-T1
Valid prediction for pasa_asmbl_47719.p1
Valid prediction for Augustus_model.g10963.t1
Valid prediction for snap_scaffold_6-snap.3606-T1
Valid prediction for snap_scaffold_6-snap.3597-T1
Valid prediction for pasa_asmbl_47723.p1
Valid prediction for snap_scaffold_6-snap.3615-T1
Valid prediction for Augustus_model.g10964.t1
Valid prediction for CodingQuarry_transcript_55393-T1
Valid prediction for snap_scaffold_6-snap.3621-T1
Valid prediction for GlimmerHMM_glimmerT_16345-T1
Valid prediction for Augustus_model.g10969.t1
Valid prediction for snap_scaffold_6-snap.3592-T1
Couldn't classify 111357, 111486
Sorry, prediction pasa_asmbl_47724.p1 fails validation.
(ATG)	 AG	107818-108003	GT	GTG
(GAA)	 AG	108766-108790	GT	AGG
(CTG)	 AG	109251-109306	GT	AGG
(GGA)	 AG	109701-109925	GT	AGG
(GAA)	 AG	110052-110200	GT	AGG
(GCC)	 AG	110326-110499	GT	AGG
(ACA)	 AG	111357-111486	TC	CCT
-recovered pasa_asmbl_47724.p1, initial, 107818, 108003
-recovered pasa_asmbl_47724.p1, internal, 107818, 108003
-recovered pasa_asmbl_47724.p1, internal, 108766, 108790
-recovered pasa_asmbl_47724.p1, internal, 109251, 109306
-recovered pasa_asmbl_47724.p1, internal, 109701, 109925
-recovered pasa_asmbl_47724.p1, internal, 110052, 110200
-recovered pasa_asmbl_47724.p1, internal, 110326, 110499
Valid prediction for snap_scaffold_6-snap.3620-T1
Valid prediction for pasa_asmbl_47721.p1
Valid prediction for Augustus_model.g10962.t1
Valid prediction for snap_scaffold_6-snap.3607-T1
Valid prediction for snap_scaffold_6-snap.3596-T1
Valid prediction for GlimmerHMM_glimmerT_16348-T1
Valid prediction for snap_scaffold_6-snap.3611-T1
Valid prediction for snap_scaffold_6-snap.3613-T1
Valid prediction for snap_scaffold_6-snap.3602-T1
Valid prediction for GlimmerHMM_glimmerT_16356-T1
Valid prediction for HiQ_model.g10961.t1
Valid prediction for GlimmerHMM_glimmerT_16359-T1
Valid prediction for CodingQuarry_transcript_55395-T1
Valid prediction for GlimmerHMM_glimmerT_16363-T1
Valid prediction for GlimmerHMM_glimmerT_16362-T1
Valid prediction for GlimmerHMM_glimmerT_16358-T1
Valid prediction for snap_scaffold_6-snap.3590-T1
Valid prediction for HiQ_model.g10960.t1
Couldn't classify 111964, 112294
Couldn't classify 113803, 113835
Sorry, prediction pasa_asmbl_47726.p1 fails validation.
(GGA)	 CG	111964-112294	GT	GGG
(GTA)	 AG	112547-112717	GT	CAG
(TGT)	 AG	113091-113207	GT	AGG
(GTC)	 AG	113341-113537	GT	AGG
(TCC)	 AG	113803-113835	AC	ACA
-recovered pasa_asmbl_47726.p1, internal, 112547, 112717
-recovered pasa_asmbl_47726.p1, internal, 113091, 113207
-recovered pasa_asmbl_47726.p1, internal, 113341, 113537
Valid prediction for GlimmerHMM_glimmerT_16346-T1
Valid prediction for CodingQuarry_transcript_55392-T1
Valid prediction for GlimmerHMM_glimmerT_16349-T1
Valid prediction for GlimmerHMM_glimmerT_16360-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_6-snap.3610-T1
Valid prediction for snap_scaffold_6-snap.3626-T1
Valid prediction for snap_scaffold_6-snap.3587-T1
Valid prediction for snap_scaffold_6-snap.3616-T1
Valid prediction for snap_scaffold_6-snap.3595-T1
Valid prediction for snap_scaffold_6-snap.3622-T1
Valid prediction for snap_scaffold_6-snap.3618-T1
Valid prediction for GlimmerHMM_glimmerT_16367-T1
Valid prediction for GlimmerHMM_glimmerT_16343-T1
Valid prediction for GlimmerHMM_glimmerT_16351-T1
Valid prediction for snap_scaffold_6-snap.3605-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16344-T1
Valid prediction for GlimmerHMM_glimmerT_16353-T1
Valid prediction for snap_scaffold_6-snap.3625-T1
Valid prediction for snap_scaffold_6-snap.3599-T1
Valid prediction for GlimmerHMM_glimmerT_16370-T1
Valid prediction for GlimmerHMM_glimmerT_16357-T1
Valid prediction for snap_scaffold_6-snap.3589-T1
Valid prediction for GlimmerHMM_glimmerT_16366-T1
Valid prediction for GlimmerHMM_glimmerT_16361-T1
Valid prediction for snap_scaffold_6-snap.3593-T1
Valid prediction for snap_scaffold_6-snap.3600-T1
Valid prediction for GlimmerHMM_glimmerT_16371-T1
Valid prediction for Augustus_model.g10965.t1
Valid prediction for GlimmerHMM_glimmerT_16347-T1
Valid prediction for snap_scaffold_6-snap.3623-T1
Valid prediction for snap_scaffold_6-snap.3598-T1
Valid prediction for snap_scaffold_6-snap.3604-T1
Valid prediction for snap_scaffold_6-snap.3591-T1
Valid prediction for GlimmerHMM_glimmerT_16355-T1
Valid prediction for snap_scaffold_6-snap.3608-T1
Valid prediction for snap_scaffold_6-snap.3619-T1
Valid prediction for snap_scaffold_6-snap.3614-T1
Valid prediction for snap_scaffold_6-snap.3624-T1
Valid prediction for GlimmerHMM_glimmerT_16352-T1
Valid prediction for Augustus_model.g10970.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4235, rend_intergenic: 2826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10719, rend_intergenic: 5721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16343, rend_intergenic: 13951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23007, rend_intergenic: 18905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42747, rend_intergenic: 40606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76001, rend_intergenic: 59552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87890, rend_intergenic: 84001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115640, rend_intergenic: 114192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118999, rend_intergenic: 118739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126592, rend_intergenic: 120200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144254, rend_intergenic: 139958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151327, rend_intergenic: 144786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158236, rend_intergenic: 151652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169941, rend_intergenic: 164705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175234, rend_intergenic: 174554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189441, rend_intergenic: 177418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193129
-exon list size: 330


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
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    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
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    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
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    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 4235, rend_intergenic: 2826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10719, rend_intergenic: 5721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16343, rend_intergenic: 13951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23007, rend_intergenic: 18905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42747, rend_intergenic: 40606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76001, rend_intergenic: 59552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87890, rend_intergenic: 84001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115640, rend_intergenic: 114192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118999, rend_intergenic: 118739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126592, rend_intergenic: 120200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144254, rend_intergenic: 139958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151327, rend_intergenic: 144786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158236, rend_intergenic: 151652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169941, rend_intergenic: 164705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175234, rend_intergenic: 174554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189441, rend_intergenic: 177418  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