-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_4307776-4497533

-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 snap_scaffold_10-snap.941-T1
Valid prediction for snap_scaffold_10-snap.953-T1
Valid prediction for snap_scaffold_10-snap.974-T1
Valid prediction for snap_scaffold_10-snap.961-T1
Valid prediction for pasa_asmbl_3122.p1
Valid prediction for snap_scaffold_10-snap.955-T1
Valid prediction for snap_scaffold_10-snap.934-T1
Valid prediction for snap_scaffold_10-snap.948-T1
Valid prediction for snap_scaffold_10-snap.933-T1
Valid prediction for GlimmerHMM_glimmerT_24597-T1
Valid prediction for GlimmerHMM_glimmerT_24574-T1
Valid prediction for snap_scaffold_10-snap.956-T1
Valid prediction for snap_scaffold_10-snap.943-T1
Valid prediction for snap_scaffold_10-snap.944-T1
Valid prediction for GlimmerHMM_glimmerT_24582-T1
Valid prediction for GlimmerHMM_glimmerT_24598-T1
Valid prediction for snap_scaffold_10-snap.971-T1
Valid prediction for Augustus_model.g16369.t1
Valid prediction for Augustus_model.g16378.t1
Valid prediction for GlimmerHMM_glimmerT_24587-T1
Valid prediction for GlimmerHMM_glimmerT_24599-T1
Valid prediction for snap_scaffold_10-snap.949-T1
Valid prediction for pasa_asmbl_3117.p1
Couldn't classify 17017, 17040
Couldn't classify 19497, 19502
Sorry, prediction pasa_asmbl_3120.p1 fails validation.
(ATC)	 AC	17017-17040	GT	AGG
(ACG)	 AG	17308-17418	GT	CGG
(CCT)	 AG	17591-17749	GT	AGG
(GAC)	 AG	17866-18055	GT	AGG
(AGT)	 AG	18134-18333	GT	AGG
(AAT)	 AG	18982-19068	GT	CGG
(GTT)	 AG	19212-19364	GT	AGG
(TGC)	 AG	19497-19502	GC	AGG
-recovered pasa_asmbl_3120.p1, internal, 17308, 17418
-recovered pasa_asmbl_3120.p1, internal, 17591, 17749
-recovered pasa_asmbl_3120.p1, internal, 17866, 18055
-recovered pasa_asmbl_3120.p1, internal, 18134, 18333
-recovered pasa_asmbl_3120.p1, internal, 18982, 19068
-recovered pasa_asmbl_3120.p1, internal, 19212, 19364
-recovered pasa_asmbl_3120.p1, internal, 19497, 19502
Valid prediction for Augustus_model.g16376.t1
Valid prediction for HiQ_model.g16373.t1
Valid prediction for GlimmerHMM_glimmerT_24578-T1
Couldn't classify 12434, 12733
Sorry, prediction pasa_asmbl_3118.p2 fails validation.
(GTT)	 AT	12434-12733	CC	AGC
Valid prediction for HiQ_model.g16366.t1
Valid prediction for CodingQuarry_transcript_5366-T1
Valid prediction for snap_scaffold_10-snap.967-T1
Valid prediction for snap_scaffold_10-snap.960-T1
Valid prediction for GlimmerHMM_glimmerT_24586-T1
Valid prediction for CodingQuarry_transcript_5364-T1
Valid prediction for Augustus_model.g16367.t1
Valid prediction for snap_scaffold_10-snap.970-T1
Valid prediction for snap_scaffold_10-snap.945-T1
Valid prediction for Augustus_model.g16379.t1
Valid prediction for snap_scaffold_10-snap.968-T1
Valid prediction for GlimmerHMM_glimmerT_24591-T1
Valid prediction for Augustus_model.g16375.t1
Valid prediction for Augustus_model.g16380.t1
Valid prediction for GlimmerHMM_glimmerT_24575-T1
Valid prediction for GlimmerHMM_glimmerT_24600-T1
Valid prediction for GlimmerHMM_glimmerT_24573-T1
Valid prediction for snap_scaffold_10-snap.936-T1
Valid prediction for snap_scaffold_10-snap.957-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_10-snap.954-T1
Valid prediction for snap_scaffold_10-snap.963-T1
Valid prediction for snap_scaffold_10-snap.973-T1
Valid prediction for snap_scaffold_10-snap.937-T1
Valid prediction for Augustus_model.g16377.t1
Valid prediction for GlimmerHMM_glimmerT_24594-T1
Valid prediction for snap_scaffold_10-snap.935-T1
Valid prediction for Augustus_model.g16371.t1
Valid prediction for snap_scaffold_10-snap.942-T1
Valid prediction for snap_scaffold_10-snap.947-T1
Valid prediction for snap_scaffold_10-snap.938-T1
Valid prediction for snap_scaffold_10-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_24590-T1
Valid prediction for snap_scaffold_10-snap.940-T1
Valid prediction for snap_scaffold_10-snap.966-T1
Valid prediction for GlimmerHMM_glimmerT_24576-T1
Valid prediction for GlimmerHMM_glimmerT_24593-T1
Valid prediction for snap_scaffold_10-snap.959-T1
Valid prediction for snap_scaffold_10-snap.952-T1
Valid prediction for snap_scaffold_10-snap.950-T1
Valid prediction for pasa_asmbl_4284.p1
Valid prediction for snap_scaffold_10-snap.965-T1
Valid prediction for snap_scaffold_10-snap.951-T1
Valid prediction for Augustus_model.g16374.t1
Valid prediction for Augustus_model.g16381.t1
Valid prediction for GlimmerHMM_glimmerT_24589-T1
Couldn't classify 158630, 159293
Sorry, prediction pasa_asmbl_4286.p1 fails validation.
(TCC)	 CC	158630-159293	GT	AGG
(GTA)	 AG	159399-159586	GT	GTG
(GTG)	 AG	161602-161745	AC	AGA
-recovered pasa_asmbl_4286.p1, terminal, 161602, 161745
-recovered pasa_asmbl_4286.p1, internal, 159399, 159586
Valid prediction for GlimmerHMM_glimmerT_24585-T1
Couldn't classify 157811, 158365
Sorry, prediction pasa_asmbl_4288.p1 fails validation.
(ATG)	 AC	156864-157619	GT	CTG
(AGC)	 AG	157811-158365	AC	CCA
-recovered pasa_asmbl_4288.p1, initial, 156864, 157619
Valid prediction for GlimmerHMM_glimmerT_24584-T1
Valid prediction for CodingQuarry_transcript_5365-T1
Valid prediction for GlimmerHMM_glimmerT_24583-T1
Valid prediction for snap_scaffold_10-snap.972-T1
Valid prediction for GlimmerHMM_glimmerT_24588-T1
Valid prediction for snap_scaffold_10-snap.939-T1
Valid prediction for snap_scaffold_10-snap.962-T1
Valid prediction for Augustus_model.g16372.t1
Valid prediction for Augustus_model.g16370.t1
Valid prediction for snap_scaffold_10-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_24592-T1
Valid prediction for GlimmerHMM_glimmerT_24579-T1
Valid prediction for GlimmerHMM_glimmerT_24595-T1
Valid prediction for GlimmerHMM_glimmerT_24596-T1
Valid prediction for snap_scaffold_10-snap.946-T1
Valid prediction for GlimmerHMM_glimmerT_24577-T1
Valid prediction for snap_scaffold_10-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_24580-T1
Valid prediction for HiQ_model.g16368.t1
Valid prediction for GlimmerHMM_glimmerT_24581-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40607, rend_intergenic: 32144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45097, rend_intergenic: 43261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61281, rend_intergenic: 47907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64306, rend_intergenic: 63041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75400, rend_intergenic: 64377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94150, rend_intergenic: 75549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99890, rend_intergenic: 96018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101356, rend_intergenic: 99948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109251, rend_intergenic: 101444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115540, rend_intergenic: 111075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123167, rend_intergenic: 115847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167351, rend_intergenic: 124737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169631, rend_intergenic: 167674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175016, rend_intergenic: 174813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180186, rend_intergenic: 175017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184648, rend_intergenic: 180366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187541, rend_intergenic: 185081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189758
-exon list size: 393


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
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3.5    
3.8    
4.1    
4.3    
4.6    
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5.1    
5.3    
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5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
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63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
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68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 40607, rend_intergenic: 32144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45097, rend_intergenic: 43261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61281, rend_intergenic: 47907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64306, rend_intergenic: 63041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75400, rend_intergenic: 64377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94150, rend_intergenic: 75549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99890, rend_intergenic: 96018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101356, rend_intergenic: 99948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109251, rend_intergenic: 101444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115540, rend_intergenic: 111075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123167, rend_intergenic: 115847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167351, rend_intergenic: 124737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169631, rend_intergenic: 167674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175016, rend_intergenic: 174813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180186, rend_intergenic: 175017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184648, rend_intergenic: 180366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187541, rend_intergenic: 185081  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