-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_4928988-5107604

-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 HiQ_model.g7773.t1
Valid prediction for GlimmerHMM_glimmerT_11867-T1
Valid prediction for GlimmerHMM_glimmerT_11880-T1
Valid prediction for GlimmerHMM_glimmerT_11881-T1
Valid prediction for snap_scaffold_5-snap.990-T1
Valid prediction for pasa_asmbl_45331.p1
Valid prediction for snap_scaffold_5-snap.986-T1
Valid prediction for CodingQuarry_transcript_52052-T1
Couldn't classify 107346, 107516
Couldn't classify 107711, 107809
Sorry, prediction CodingQuarry_transcript_52046-T1 fails validation.
(ATG)	 TC	105710-105816	GT	AGG
(GAA)	 AG	106957-107170	GT	AGG
(GCC)	 AG	107346-107516	GG	GAG
(GGT)	 AT	107711-107809	AC	AGA
-recovered CodingQuarry_transcript_52046-T1, initial, 105710, 105816
-recovered CodingQuarry_transcript_52046-T1, internal, 106957, 107170
Valid prediction for CodingQuarry_transcript_52043-T1
Valid prediction for GlimmerHMM_glimmerT_11876-T1
Couldn't classify 121659, 121760
Sorry, prediction pasa_asmbl_45333.p1 fails validation.
(GCT)	 TA	121659-121760	GT	AGG
(GTG)	 AG	122116-122264	GT	GCG
(ATA)	 AG	125005-125052	GT	GCG
(GTA)	 AG	126604-126705	GT	AGG
(AAA)	 AG	128547-128595	GT	AGG
(GTG)	 AG	129022-129102	AG	GAA
-recovered pasa_asmbl_45333.p1, terminal, 129022, 129102
-recovered pasa_asmbl_45333.p1, internal, 122116, 122264
-recovered pasa_asmbl_45333.p1, internal, 125005, 125052
-recovered pasa_asmbl_45333.p1, internal, 126604, 126705
-recovered pasa_asmbl_45333.p1, internal, 128547, 128595
Valid prediction for snap_scaffold_5-snap.966-T1
Valid prediction for HiQ_model.g7775.t1
Valid prediction for snap_scaffold_5-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_11889-T1
Valid prediction for GlimmerHMM_glimmerT_11888-T1
Valid prediction for snap_scaffold_5-snap.995-T1
Valid prediction for Augustus_model.g7774.t1
Valid prediction for snap_scaffold_5-snap.991-T1
Couldn't classify 94064, 94286
Couldn't classify 94520, 94629
Sorry, prediction pasa_asmbl_46470.p2 fails validation.
(GAG)	 AC	94064-94286	GT	AGG
(TTG)	 AG	94520-94629	GG	GGG
Valid prediction for GlimmerHMM_glimmerT_11878-T1
Valid prediction for Augustus_model.g7766.t1
Valid prediction for snap_scaffold_5-snap.989-T1
Valid prediction for GlimmerHMM_glimmerT_11882-T1
Valid prediction for GlimmerHMM_glimmerT_11866-T1
Valid prediction for snap_scaffold_5-snap.987-T1
Valid prediction for GlimmerHMM_glimmerT_11870-T1
Valid prediction for Augustus_model.g7769.t1
Valid prediction for Augustus_model.g7771.t1
Valid prediction for CodingQuarry_transcript_52050-T1
Valid prediction for pasa_asmbl_45323.p1
Valid prediction for snap_scaffold_5-snap.993-T1
Valid prediction for CodingQuarry_transcript_52048-T1
Valid prediction for GlimmerHMM_glimmerT_11879-T1
Valid prediction for GlimmerHMM_glimmerT_11877-T1
Valid prediction for GlimmerHMM_glimmerT_11872-T1
Valid prediction for snap_scaffold_5-snap.975-T1
Valid prediction for GlimmerHMM_glimmerT_11885-T1
Couldn't classify 19773, 19791
Sorry, prediction pasa_asmbl_45317.p1 fails validation.
(CGG)	 GT	19773-19791	GT	CGG
(ATC)	 AG	20134-20218	GT	TGG
(CTC)	 AG	20361-20424	GT	AGG
(GTT)	 AG	20626-20697	GT	TGG
(GGC)	 AG	20909-20964	GT	AAG
(GAC)	 AG	21486-21495	AG	AAA
-recovered pasa_asmbl_45317.p1, terminal, 21486, 21495
-recovered pasa_asmbl_45317.p1, internal, 20134, 20218
-recovered pasa_asmbl_45317.p1, internal, 20361, 20424
-recovered pasa_asmbl_45317.p1, internal, 20626, 20697
-recovered pasa_asmbl_45317.p1, internal, 20909, 20964
Valid prediction for snap_scaffold_5-snap.1000-T1
Valid prediction for CodingQuarry_transcript_52047-T1
Valid prediction for Augustus_model.g7778.t1
Valid prediction for Augustus_model.g7770.t1
Valid prediction for snap_scaffold_5-snap.972-T1
Valid prediction for GlimmerHMM_glimmerT_11873-T1
Valid prediction for GlimmerHMM_glimmerT_11871-T1
Valid prediction for GlimmerHMM_glimmerT_11874-T1
Valid prediction for snap_scaffold_5-snap.1004-T1
Valid prediction for snap_scaffold_5-snap.970-T1
Valid prediction for pasa_asmbl_45340.p1
Valid prediction for Augustus_model.g7776.t1
Valid prediction for CodingQuarry_transcript_52045-T1
Valid prediction for snap_scaffold_5-snap.969-T1
Valid prediction for snap_scaffold_5-snap.998-T1
Valid prediction for CodingQuarry_transcript_52049-T1
Valid prediction for Augustus_model.g7768.t1
Valid prediction for CodingQuarry_transcript_52051-T1
Valid prediction for snap_scaffold_5-snap.1002-T1
Valid prediction for Augustus_model.g7767.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_11884-T1
Valid prediction for GlimmerHMM_glimmerT_11869-T1
Valid prediction for GlimmerHMM_glimmerT_11864-T1
Valid prediction for GlimmerHMM_glimmerT_11890-T1
Valid prediction for Augustus_model.g7782.t1
Valid prediction for snap_scaffold_5-snap.968-T1
Valid prediction for GlimmerHMM_glimmerT_11891-T1
Valid prediction for Augustus_model.g7780.t1
Valid prediction for CodingQuarry_transcript_52044-T1
Valid prediction for pasa_asmbl_44026.p1
Valid prediction for snap_scaffold_5-snap.999-T1
Valid prediction for snap_scaffold_5-snap.980-T1
Valid prediction for snap_scaffold_5-snap.971-T1
Valid prediction for snap_scaffold_5-snap.992-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11883-T1
Valid prediction for snap_scaffold_5-snap.988-T1
Valid prediction for snap_scaffold_5-snap.979-T1
Valid prediction for snap_scaffold_5-snap.983-T1
Valid prediction for CodingQuarry_transcript_52054-T1
Valid prediction for GlimmerHMM_glimmerT_11887-T1
Valid prediction for snap_scaffold_5-snap.965-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.997-T1
Valid prediction for HiQ_model.g7777.t1
Valid prediction for snap_scaffold_5-snap.978-T1
Valid prediction for snap_scaffold_5-snap.984-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1003-T1
Valid prediction for HiQ_model.g7772.t1
Valid prediction for snap_scaffold_5-snap.994-T1
Valid prediction for snap_scaffold_5-snap.985-T1
Valid prediction for snap_scaffold_5-snap.1001-T1
Valid prediction for CodingQuarry_transcript_52053-T1
Valid prediction for snap_scaffold_5-snap.1005-T1
Valid prediction for snap_scaffold_5-snap.977-T1
Valid prediction for GlimmerHMM_glimmerT_11875-T1
Valid prediction for Augustus_model.g7783.t1
Valid prediction for snap_scaffold_5-snap.982-T1
Valid prediction for snap_scaffold_5-snap.967-T1
Valid prediction for pasa_asmbl_44021.p1
Valid prediction for snap_scaffold_5-snap.981-T1
Valid prediction for snap_scaffold_5-snap.976-T1
Valid prediction for Augustus_model.g7779.t1
Valid prediction for GlimmerHMM_glimmerT_11865-T1
Valid prediction for GlimmerHMM_glimmerT_11886-T1
Valid prediction for Augustus_model.g7781.t1
Valid prediction for GlimmerHMM_glimmerT_11868-T1
Valid prediction for snap_scaffold_5-snap.974-T1
Valid prediction for Augustus_model.g7765.t1
Valid prediction for snap_scaffold_5-snap.996-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9548, rend_intergenic: 4968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26751, rend_intergenic: 22934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38535, rend_intergenic: 29398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39174, rend_intergenic: 38953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 39608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95006, rend_intergenic: 45605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99227, rend_intergenic: 96666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105669, rend_intergenic: 101820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108541, rend_intergenic: 105710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129372, rend_intergenic: 121719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146609, rend_intergenic: 139279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148964, rend_intergenic: 146721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154617, rend_intergenic: 151863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157663, rend_intergenic: 155548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163907, rend_intergenic: 163664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177996, rend_intergenic: 164488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178617
-exon list size: 510


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
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5.3    
5.5    
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5.9    
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6.6    
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7.0    
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7.6    
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8.0    
8.2    
8.4    
8.6    
8.8    
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10.9    
11.1    
11.3    
11.5    
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11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 9548, rend_intergenic: 4968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26751, rend_intergenic: 22934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38535, rend_intergenic: 29398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39174, rend_intergenic: 38953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 39608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95006, rend_intergenic: 45605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99227, rend_intergenic: 96666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105669, rend_intergenic: 101820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108541, rend_intergenic: 105710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129372, rend_intergenic: 121719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146609, rend_intergenic: 139279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148964, rend_intergenic: 146721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154617, rend_intergenic: 151863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157663, rend_intergenic: 155548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163907, rend_intergenic: 163664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177996, rend_intergenic: 164488  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