-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_2523310-2758818

-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.g34771.t1
Valid prediction for snap_scaffold_24-snap.583-T1
Valid prediction for snap_scaffold_24-snap.584-T1
Valid prediction for snap_scaffold_24-snap.626-T1
Valid prediction for snap_scaffold_24-snap.588-T1
Valid prediction for snap_scaffold_24-snap.600-T1
Valid prediction for GlimmerHMM_glimmerT_52174-T1
Valid prediction for CodingQuarry_transcript_37258-T1
Valid prediction for snap_scaffold_24-snap.597-T1
Valid prediction for Augustus_model.g34764.t1
Valid prediction for snap_scaffold_24-snap.603-T1
Valid prediction for snap_scaffold_24-snap.602-T1
Valid prediction for snap_scaffold_24-snap.617-T1
Valid prediction for HiQ_model.g34767.t1
Valid prediction for snap_scaffold_24-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_52173-T1
Valid prediction for snap_scaffold_24-snap.609-T1
Valid prediction for snap_scaffold_24-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_52182-T1
Valid prediction for snap_scaffold_24-snap.581-T1
Valid prediction for GlimmerHMM_glimmerT_52186-T1
Valid prediction for GlimmerHMM_glimmerT_52169-T1
Valid prediction for Augustus_model.g34757.t1
Valid prediction for Augustus_model.g34770.t1
Valid prediction for snap_scaffold_24-snap.621-T1
Valid prediction for pasa_asmbl_32105.p1
Valid prediction for Augustus_model.g34758.t1
Valid prediction for snap_scaffold_24-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_52163-T1
Valid prediction for snap_scaffold_24-snap.608-T1
Valid prediction for snap_scaffold_24-snap.577-T1
Valid prediction for snap_scaffold_24-snap.591-T1
Valid prediction for GlimmerHMM_glimmerT_52185-T1
Valid prediction for snap_scaffold_24-snap.613-T1
Valid prediction for GlimmerHMM_glimmerT_52177-T1
Valid prediction for snap_scaffold_24-snap.619-T1
Valid prediction for CodingQuarry_transcript_37257-T1
Couldn't classify 213531, 213699
Sorry, prediction pasa_asmbl_32106.p1 fails validation.
(GTG)	 CA	213531-213699	GT	AGG
(CTG)	 AG	214168-214276	GT	AGG
(CCC)	 AG	215268-215389	GT	AGG
(GGC)	 AG	215613-215720	GT	CGG
(GCT)	 AG	217083-217231	GA	GAG
-recovered pasa_asmbl_32106.p1, terminal, 217083, 217231
-recovered pasa_asmbl_32106.p1, internal, 214168, 214276
-recovered pasa_asmbl_32106.p1, internal, 215268, 215389
-recovered pasa_asmbl_32106.p1, internal, 215613, 215720
Valid prediction for snap_scaffold_24-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_52175-T1
Valid prediction for CodingQuarry_transcript_37260-T1
Valid prediction for GlimmerHMM_glimmerT_52180-T1
Valid prediction for GlimmerHMM_glimmerT_52167-T1
Valid prediction for snap_scaffold_24-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_52162-T1
Valid prediction for snap_scaffold_24-snap.616-T1
Valid prediction for GlimmerHMM_glimmerT_52183-T1
Valid prediction for CodingQuarry_transcript_37259-T1
Valid prediction for snap_scaffold_24-snap.582-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.614-T1
Valid prediction for snap_scaffold_24-snap.625-T1
Valid prediction for snap_scaffold_24-snap.623-T1
Valid prediction for GlimmerHMM_glimmerT_52172-T1
Valid prediction for snap_scaffold_24-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_52164-T1
Valid prediction for GlimmerHMM_glimmerT_52176-T1
Valid prediction for HiQ_model.g34768.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_52184-T1
Valid prediction for snap_scaffold_24-snap.601-T1
Valid prediction for GlimmerHMM_glimmerT_52166-T1
Valid prediction for snap_scaffold_24-snap.628-T1
Valid prediction for Augustus_model.g34759.t1
Valid prediction for GlimmerHMM_glimmerT_52161-T1
Valid prediction for snap_scaffold_24-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_52158-T1
Valid prediction for snap_scaffold_24-snap.620-T1
Valid prediction for snap_scaffold_24-snap.618-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_52159-T1
Valid prediction for snap_scaffold_24-snap.598-T1
Valid prediction for snap_scaffold_24-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_52171-T1
Valid prediction for snap_scaffold_24-snap.589-T1
Valid prediction for Augustus_model.g34756.t1
Valid prediction for Augustus_model.g34760.t1
Valid prediction for GlimmerHMM_glimmerT_52165-T1
Valid prediction for Augustus_model.g34763.t1
Valid prediction for snap_scaffold_24-snap.593-T1
Valid prediction for snap_scaffold_24-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_52181-T1
Valid prediction for GlimmerHMM_glimmerT_52179-T1
Valid prediction for snap_scaffold_24-snap.596-T1
Valid prediction for snap_scaffold_24-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_52160-T1
Valid prediction for Augustus_model.g34761.t1
Valid prediction for snap_scaffold_24-snap.578-T1
Valid prediction for snap_scaffold_24-snap.594-T1
Valid prediction for snap_scaffold_24-snap.612-T1
Valid prediction for Augustus_model.g34762.t1
Valid prediction for GlimmerHMM_glimmerT_52168-T1
Valid prediction for Augustus_model.g34769.t1
Valid prediction for GlimmerHMM_glimmerT_52178-T1
Valid prediction for snap_scaffold_24-snap.592-T1
Valid prediction for snap_scaffold_24-snap.627-T1
Valid prediction for snap_scaffold_24-snap.607-T1
Valid prediction for snap_scaffold_24-snap.622-T1
Valid prediction for snap_scaffold_24-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_52170-T1
Valid prediction for snap_scaffold_24-snap.585-T1
Valid prediction for snap_scaffold_24-snap.615-T1
Valid prediction for Augustus_model.g34765.t1
Valid prediction for snap_scaffold_24-snap.610-T1
Valid prediction for Augustus_model.g34766.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9661, rend_intergenic: 4715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19906, rend_intergenic: 14830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35346, rend_intergenic: 28536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48927, rend_intergenic: 38692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49686, rend_intergenic: 49023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55188, rend_intergenic: 53501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65950, rend_intergenic: 55464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68509, rend_intergenic: 66543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77891, rend_intergenic: 70007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105744, rend_intergenic: 81321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115990, rend_intergenic: 108170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122346, rend_intergenic: 116029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141383, rend_intergenic: 123272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146067, rend_intergenic: 142410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148077, rend_intergenic: 146502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157370, rend_intergenic: 148222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161912, rend_intergenic: 157658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165265, rend_intergenic: 161927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173050, rend_intergenic: 169736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185342, rend_intergenic: 173296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192263, rend_intergenic: 185508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198567, rend_intergenic: 194597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209957, rend_intergenic: 207747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215781, rend_intergenic: 213537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217965, rend_intergenic: 216688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233184, rend_intergenic: 225099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235509
-exon list size: 374


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9661, rend_intergenic: 4715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19906, rend_intergenic: 14830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35346, rend_intergenic: 28536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48927, rend_intergenic: 38692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49686, rend_intergenic: 49023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55188, rend_intergenic: 53501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65950, rend_intergenic: 55464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68509, rend_intergenic: 66543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77891, rend_intergenic: 70007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105744, rend_intergenic: 81321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115990, rend_intergenic: 108170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122346, rend_intergenic: 116029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141383, rend_intergenic: 123272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146067, rend_intergenic: 142410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148077, rend_intergenic: 146502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157370, rend_intergenic: 148222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161912, rend_intergenic: 157658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165265, rend_intergenic: 161927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173050, rend_intergenic: 169736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185342, rend_intergenic: 173296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192263, rend_intergenic: 185508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198567, rend_intergenic: 194597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209957, rend_intergenic: 207747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215781, rend_intergenic: 213537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217965, rend_intergenic: 216688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233184, rend_intergenic: 225099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support