-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_1228048-1472934

-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.g19050.t1
Valid prediction for GlimmerHMM_glimmerT_28856-T1
Valid prediction for GlimmerHMM_glimmerT_28825-T1
Valid prediction for pasa_asmbl_7473.p1
Valid prediction for GlimmerHMM_glimmerT_28842-T1
Valid prediction for snap_scaffold_12-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_28859-T1
Valid prediction for snap_scaffold_12-snap.300-T1
Valid prediction for snap_scaffold_12-snap.303-T1
Valid prediction for snap_scaffold_12-snap.310-T1
Valid prediction for Augustus_model.g19049.t1
Valid prediction for GlimmerHMM_glimmerT_28850-T1
Valid prediction for snap_scaffold_12-snap.294-T1
Valid prediction for GlimmerHMM_glimmerT_28833-T1
Valid prediction for HiQ_model.g19053.t1
Couldn't classify 8337, 8747
Sorry, prediction pasa_asmbl_7465.p2 fails validation.
(GAC)	 CA	8337-8747	GG	GAG
Valid prediction for CodingQuarry_transcript_10129-T1
Valid prediction for GlimmerHMM_glimmerT_28860-T1
Valid prediction for GlimmerHMM_glimmerT_28836-T1
Valid prediction for snap_scaffold_12-snap.307-T1
Valid prediction for snap_scaffold_12-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_28845-T1
Valid prediction for GlimmerHMM_glimmerT_28844-T1
Valid prediction for snap_scaffold_12-snap.333-T1
Valid prediction for GlimmerHMM_glimmerT_28840-T1
Valid prediction for HiQ_model.g19056.t1
Valid prediction for snap_scaffold_12-snap.324-T1
Valid prediction for GlimmerHMM_glimmerT_28834-T1
Valid prediction for Augustus_model.g19057.t1
Valid prediction for GlimmerHMM_glimmerT_28831-T1
Valid prediction for CodingQuarry_transcript_10130-T1
Valid prediction for snap_scaffold_12-snap.326-T1
Valid prediction for snap_scaffold_12-snap.318-T1
Valid prediction for snap_scaffold_12-snap.336-T1
Valid prediction for snap_scaffold_12-snap.295-T1
Valid prediction for Augustus_model.g19046.t1
Valid prediction for Augustus_model.g19051.t1
Valid prediction for GlimmerHMM_glimmerT_28838-T1
Valid prediction for snap_scaffold_12-snap.305-T1
Couldn't classify 109862, 110017
Sorry, prediction pasa_asmbl_7468.p1 fails validation.
(ACT)	 GT	109862-110017	GT	AGG
(GTC)	 AG	110111-110204	GT	AGG
(AGA)	 AG	111281-111306	GT	AGG
(GAG)	 AG	113239-113331	GT	AGG
(GAA)	 AG	113731-113913	GT	TGG
(ACG)	 AG	114523-114614	GT	GGG
(TTC)	 AG	114791-115021	GT	AGG
(GTG)	 AG	115310-115414	GT	AGG
(GTC)	 AG	115694-115802	GT	AGG
(TGT)	 AG	116570-116672	GT	CTG
(CTG)	 AG	116949-116974	CC	GAC
-recovered pasa_asmbl_7468.p1, terminal, 116949, 116974
-recovered pasa_asmbl_7468.p1, internal, 110111, 110204
-recovered pasa_asmbl_7468.p1, internal, 111281, 111306
-recovered pasa_asmbl_7468.p1, internal, 113239, 113331
-recovered pasa_asmbl_7468.p1, internal, 113731, 113913
-recovered pasa_asmbl_7468.p1, internal, 114523, 114614
-recovered pasa_asmbl_7468.p1, internal, 114791, 115021
-recovered pasa_asmbl_7468.p1, internal, 115310, 115414
-recovered pasa_asmbl_7468.p1, internal, 115694, 115802
-recovered pasa_asmbl_7468.p1, internal, 116570, 116672
Valid prediction for pasa_asmbl_7471.p1
Valid prediction for snap_scaffold_12-snap.292-T1
Valid prediction for Augustus_model.g19048.t1
Valid prediction for snap_scaffold_12-snap.335-T1
Valid prediction for GlimmerHMM_glimmerT_28861-T1
Valid prediction for GlimmerHMM_glimmerT_28849-T1
Valid prediction for snap_scaffold_12-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_28839-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 Augustus_model.g19054.t1
Valid prediction for snap_scaffold_12-snap.315-T1
Valid prediction for snap_scaffold_12-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_28824-T1
Valid prediction for snap_scaffold_12-snap.293-T1
Valid prediction for snap_scaffold_12-snap.296-T1
Valid prediction for snap_scaffold_12-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_28827-T1
Valid prediction for snap_scaffold_12-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_28835-T1
Valid prediction for snap_scaffold_12-snap.334-T1
Valid prediction for snap_scaffold_12-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_28858-T1
Valid prediction for GlimmerHMM_glimmerT_28851-T1
Valid prediction for snap_scaffold_12-snap.321-T1
Valid prediction for snap_scaffold_12-snap.299-T1
Valid prediction for Augustus_model.g19055.t1
Valid prediction for GlimmerHMM_glimmerT_28852-T1
Couldn't classify 78238, 78253
Couldn't classify 81565, 81589
Sorry, prediction pasa_asmbl_8297.p1 fails validation.
(ATC)	 TC	78238-78253	GT	AGG
(GGA)	 AG	80290-80468	GT	AGG
(ATA)	 AG	80754-80854	GT	AGG
(GTT)	 AG	81024-81170	GT	AGG
(TTG)	 AG	81565-81589	GG	GGG
-recovered pasa_asmbl_8297.p1, internal, 80290, 80468
-recovered pasa_asmbl_8297.p1, internal, 80754, 80854
-recovered pasa_asmbl_8297.p1, internal, 81024, 81170
Valid prediction for snap_scaffold_12-snap.320-T1
Valid prediction for snap_scaffold_12-snap.327-T1
Valid prediction for GlimmerHMM_glimmerT_28855-T1
Valid prediction for snap_scaffold_12-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_28853-T1
Valid prediction for snap_scaffold_12-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_28854-T1
Valid prediction for snap_scaffold_12-snap.337-T1
Valid prediction for snap_scaffold_12-snap.312-T1
Valid prediction for Augustus_model.g19052.t1
Valid prediction for Augustus_model.g19058.t1
Valid prediction for GlimmerHMM_glimmerT_28857-T1
Valid prediction for snap_scaffold_12-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_28826-T1
Valid prediction for GlimmerHMM_glimmerT_28841-T1
Valid prediction for GlimmerHMM_glimmerT_28832-T1
Valid prediction for snap_scaffold_12-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_28848-T1
Valid prediction for snap_scaffold_12-snap.301-T1
Valid prediction for snap_scaffold_12-snap.298-T1
Valid prediction for snap_scaffold_12-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_28830-T1
Valid prediction for GlimmerHMM_glimmerT_28828-T1
Valid prediction for snap_scaffold_12-snap.329-T1
Valid prediction for snap_scaffold_12-snap.323-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28829-T1
Valid prediction for snap_scaffold_12-snap.314-T1
Valid prediction for snap_scaffold_12-snap.316-T1
Valid prediction for snap_scaffold_12-snap.330-T1
Valid prediction for snap_scaffold_12-snap.332-T1
Valid prediction for snap_scaffold_12-snap.304-T1
Valid prediction for snap_scaffold_12-snap.309-T1
Valid prediction for GlimmerHMM_glimmerT_28843-T1
Valid prediction for snap_scaffold_12-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_28847-T1
Valid prediction for GlimmerHMM_glimmerT_28837-T1
Valid prediction for GlimmerHMM_glimmerT_28846-T1
Valid prediction for Augustus_model.g19047.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11194, rend_intergenic: 9927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35301, rend_intergenic: 23354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35997, rend_intergenic: 35459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43389, rend_intergenic: 36322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45928, rend_intergenic: 43608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57108, rend_intergenic: 48040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79321, rend_intergenic: 59327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91096, rend_intergenic: 81707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117566, rend_intergenic: 91302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142031, rend_intergenic: 130536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166069, rend_intergenic: 163213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166710, rend_intergenic: 166069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173379, rend_intergenic: 169006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174359, rend_intergenic: 173734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197185, rend_intergenic: 192727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199654, rend_intergenic: 197298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203568, rend_intergenic: 201624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242865, rend_intergenic: 241195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244887
-exon list size: 389


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 11194, rend_intergenic: 9927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35301, rend_intergenic: 23354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35997, rend_intergenic: 35459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43389, rend_intergenic: 36322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45928, rend_intergenic: 43608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57108, rend_intergenic: 48040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79321, rend_intergenic: 59327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91096, rend_intergenic: 81707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117566, rend_intergenic: 91302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142031, rend_intergenic: 130536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166069, rend_intergenic: 163213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166710, rend_intergenic: 166069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173379, rend_intergenic: 169006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174359, rend_intergenic: 173734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197185, rend_intergenic: 192727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199654, rend_intergenic: 197298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203568, rend_intergenic: 201624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242865, rend_intergenic: 241195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support