-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_2204324-2372563

-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 CodingQuarry_transcript_57446-T1
Valid prediction for Augustus_model.g11343.t1
Valid prediction for GlimmerHMM_glimmerT_17020-T1
Valid prediction for CodingQuarry_transcript_57447-T1
Valid prediction for snap_scaffold_7-snap.548-T1
Valid prediction for snap_scaffold_7-snap.556-T1
Valid prediction for Augustus_model.g11350.t1
Valid prediction for GlimmerHMM_glimmerT_17015-T1
Valid prediction for Augustus_model.g11346.t1
Valid prediction for GlimmerHMM_glimmerT_17000-T1
Valid prediction for Augustus_model.g11340.t1
Valid prediction for GlimmerHMM_glimmerT_17010-T1
Valid prediction for snap_scaffold_7-snap.534-T1
Valid prediction for snap_scaffold_7-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_16999-T1
Couldn't classify 158687, 158864
Sorry, prediction pasa_asmbl_49641.p1 fails validation.
(GAG)	 AG	158687-158864	GT	AGG
(GAT)	 AG	159758-159882	GT	AGG
(GTG)	 AG	160404-160540	GT	GGG
(GAA)	 AG	162653-162854	GG	GAG
-recovered pasa_asmbl_49641.p1, terminal, 162653, 162854
-recovered pasa_asmbl_49641.p1, internal, 158687, 158864
-recovered pasa_asmbl_49641.p1, internal, 159758, 159882
-recovered pasa_asmbl_49641.p1, internal, 160404, 160540
Valid prediction for snap_scaffold_7-snap.522-T1
Couldn't classify 105781, 105861
Couldn't classify 110470, 110484
Sorry, prediction pasa_asmbl_49631.p1 fails validation.
(CAG)	 TT	105781-105861	GT	AGG
(GTG)	 AG	107592-107662	GT	TCG
(GCC)	 AG	108746-108919	GT	AGG
(TTT)	 AG	109366-109492	GT	ATG
(GGT)	 AG	110470-110484	GT	TGG
-recovered pasa_asmbl_49631.p1, internal, 107592, 107662
-recovered pasa_asmbl_49631.p1, internal, 108746, 108919
-recovered pasa_asmbl_49631.p1, internal, 109366, 109492
-recovered pasa_asmbl_49631.p1, internal, 110470, 110484
Valid prediction for GlimmerHMM_glimmerT_17004-T1
Valid prediction for snap_scaffold_7-snap.542-T1
Valid prediction for Augustus_model.g11349.t1
Couldn't classify 115412, 115565
Couldn't classify 115767, 116092
Sorry, prediction pasa_asmbl_50545.p1 fails validation.
(GCC)	 GC	115412-115565	GT	GGG
(ACC)	 AG	115767-116092	GG	GGG
Valid prediction for GlimmerHMM_glimmerT_17018-T1
Valid prediction for GlimmerHMM_glimmerT_17017-T1
Valid prediction for GlimmerHMM_glimmerT_17001-T1
Valid prediction for snap_scaffold_7-snap.531-T1
Couldn't classify 117869, 117942
Sorry, prediction pasa_asmbl_49639.p1 fails validation.
(CCC)	 CG	117869-117942	GT	GGG
(GTT)	 AG	118099-118259	GT	CGG
(GTA)	 AG	118769-118860	GT	AGG
(AAC)	 AG	119150-119247	GT	AGG
(CTT)	 AG	119479-119630	GT	TGG
(GGC)	 AG	120249-120359	GT	TGG
(GTC)	 AG	120642-120755	GT	AGG
(GCC)	 AG	121522-121727	GG	AGG
-recovered pasa_asmbl_49639.p1, terminal, 121522, 121727
-recovered pasa_asmbl_49639.p1, internal, 118099, 118259
-recovered pasa_asmbl_49639.p1, internal, 118769, 118860
-recovered pasa_asmbl_49639.p1, internal, 119150, 119247
-recovered pasa_asmbl_49639.p1, internal, 119479, 119630
-recovered pasa_asmbl_49639.p1, internal, 120249, 120359
-recovered pasa_asmbl_49639.p1, internal, 120642, 120755
Valid prediction for snap_scaffold_7-snap.550-T1
Valid prediction for Augustus_model.g11341.t1
Valid prediction for Augustus_model.g11342.t1
Valid prediction for GlimmerHMM_glimmerT_17019-T1
Valid prediction for snap_scaffold_7-snap.530-T1
Valid prediction for snap_scaffold_7-snap.524-T1
Valid prediction for snap_scaffold_7-snap.528-T1
Valid prediction for snap_scaffold_7-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_17007-T1
Valid prediction for snap_scaffold_7-snap.545-T1
Valid prediction for Augustus_model.g11339.t1
Valid prediction for snap_scaffold_7-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_17012-T1
Valid prediction for Augustus_model.g11347.t1
Valid prediction for Augustus_model.g11351.t1
Couldn't classify 116900, 117796
Sorry, prediction pasa_asmbl_49638.p1 fails validation.
(CAG)	 TC	116900-117796	CC	CCC
Valid prediction for snap_scaffold_7-snap.552-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.553-T1
Valid prediction for Augustus_model.g11345.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_7-snap.560-T1
Valid prediction for snap_scaffold_7-snap.558-T1
Valid prediction for snap_scaffold_7-snap.527-T1
Valid prediction for snap_scaffold_7-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_17014-T1
Valid prediction for snap_scaffold_7-snap.543-T1
Valid prediction for snap_scaffold_7-snap.554-T1
Valid prediction for snap_scaffold_7-snap.532-T1
Valid prediction for snap_scaffold_7-snap.557-T1
Valid prediction for GlimmerHMM_glimmerT_17002-T1
Valid prediction for snap_scaffold_7-snap.549-T1
Valid prediction for snap_scaffold_7-snap.539-T1
Valid prediction for snap_scaffold_7-snap.533-T1
Valid prediction for snap_scaffold_7-snap.546-T1
Valid prediction for Augustus_model.g11348.t1
Valid prediction for GlimmerHMM_glimmerT_17008-T1
Valid prediction for snap_scaffold_7-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_17009-T1
Valid prediction for GlimmerHMM_glimmerT_17013-T1
Valid prediction for snap_scaffold_7-snap.526-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_17003-T1
Valid prediction for snap_scaffold_7-snap.536-T1
Valid prediction for snap_scaffold_7-snap.555-T1
Valid prediction for snap_scaffold_7-snap.529-T1
Valid prediction for GlimmerHMM_glimmerT_17011-T1
Valid prediction for snap_scaffold_7-snap.525-T1
Valid prediction for snap_scaffold_7-snap.523-T1
Valid prediction for GlimmerHMM_glimmerT_17016-T1
Valid prediction for Augustus_model.g11344.t1
Valid prediction for snap_scaffold_7-snap.551-T1
Valid prediction for snap_scaffold_7-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_17006-T1
Valid prediction for snap_scaffold_7-snap.544-T1
Valid prediction for GlimmerHMM_glimmerT_17005-T1
Valid prediction for snap_scaffold_7-snap.541-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11034, rend_intergenic: 8526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29823, rend_intergenic: 15538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45698, rend_intergenic: 34000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58054, rend_intergenic: 46105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69182, rend_intergenic: 61943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77379, rend_intergenic: 74439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81235, rend_intergenic: 78442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86394, rend_intergenic: 84261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102892, rend_intergenic: 96930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113942, rend_intergenic: 106408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114968, rend_intergenic: 114279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121727, rend_intergenic: 115763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130905, rend_intergenic: 127564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133055, rend_intergenic: 130970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138649, rend_intergenic: 134059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148383, rend_intergenic: 144251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151316, rend_intergenic: 148748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162854, rend_intergenic: 151648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167074, rend_intergenic: 165123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168240
-exon list size: 412


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.1    
3.4    
3.6    
3.9    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.0    
6.3    
6.5    
6.8    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.9    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 11034, rend_intergenic: 8526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29823, rend_intergenic: 15538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45698, rend_intergenic: 34000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58054, rend_intergenic: 46105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69182, rend_intergenic: 61943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77379, rend_intergenic: 74439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81235, rend_intergenic: 78442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86394, rend_intergenic: 84261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102892, rend_intergenic: 96930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113942, rend_intergenic: 106408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114968, rend_intergenic: 114279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121727, rend_intergenic: 115763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130905, rend_intergenic: 127564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133055, rend_intergenic: 130970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138649, rend_intergenic: 134059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148383, rend_intergenic: 144251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151316, rend_intergenic: 148748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162854, rend_intergenic: 151648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167074, rend_intergenic: 165123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12565
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 - 12405
-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 1 - 11265
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support