-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_171590-328846

-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 GeneMark_model.14280_t
Valid prediction for snap_scaffold_4-snap.50-T1
Valid prediction for GeneMark_model.14247_t
Valid prediction for GlimmerHMM_glimmerT_8772-T1
Valid prediction for snap_scaffold_4-snap.54-T1
Valid prediction for GeneMark_model.14250_t
Valid prediction for GlimmerHMM_glimmerT_8780-T1
Valid prediction for Augustus_model.g5771.t1
Valid prediction for snap_scaffold_4-snap.45-T1
Valid prediction for snap_scaffold_4-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_8777-T1
Valid prediction for GlimmerHMM_glimmerT_8775-T1
Valid prediction for GlimmerHMM_glimmerT_8770-T1
Valid prediction for pasa_asmbl_42419.p1
Valid prediction for GeneMark_model.14254_t
Valid prediction for GeneMark_model.14277_t
Valid prediction for snap_scaffold_4-snap.49-T1
Valid prediction for GeneMark_model.14271_t
Valid prediction for snap_scaffold_4-snap.61-T1
Valid prediction for Augustus_model.g5772.t1
Valid prediction for GeneMark_model.14273_t
Valid prediction for GlimmerHMM_glimmerT_8779-T1
Valid prediction for snap_scaffold_4-snap.35-T1
Valid prediction for GeneMark_model.14259_t
Valid prediction for GlimmerHMM_glimmerT_8781-T1
Valid prediction for snap_scaffold_4-snap.52-T1
Valid prediction for snap_scaffold_4-snap.42-T1
Valid prediction for snap_scaffold_4-snap.44-T1
Valid prediction for GlimmerHMM_glimmerT_8789-T1
Valid prediction for snap_scaffold_4-snap.40-T1
Valid prediction for GeneMark_model.14249_t
Valid prediction for GeneMark_model.14252_t
Valid prediction for snap_scaffold_4-snap.38-T1
Valid prediction for GeneMark_model.14267_t
Valid prediction for GeneMark_model.14256_t
Valid prediction for snap_scaffold_4-snap.58-T1
Valid prediction for GeneMark_model.14278_t
Valid prediction for snap_scaffold_4-snap.62-T1
Valid prediction for snap_scaffold_4-snap.37-T1
Valid prediction for GeneMark_model.14275_t
Valid prediction for GeneMark_model.14263_t
Valid prediction for snap_scaffold_4-snap.59-T1
Valid prediction for GeneMark_model.14265_t
Valid prediction for Augustus_model.g5767.t1
Valid prediction for GlimmerHMM_glimmerT_8785-T1
Valid prediction for GeneMark_model.14261_t

-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 GeneMark_model.14266_t
Valid prediction for GlimmerHMM_glimmerT_8768-T1
Valid prediction for GlimmerHMM_glimmerT_8788-T1
Valid prediction for snap_scaffold_4-snap.46-T1
Valid prediction for pasa_asmbl_41068.p1
Valid prediction for GlimmerHMM_glimmerT_8771-T1
Valid prediction for snap_scaffold_4-snap.57-T1
Valid prediction for GeneMark_model.14274_t
Valid prediction for snap_scaffold_4-snap.43-T1
Valid prediction for GeneMark_model.14269_t
Couldn't classify 125135, 125665
Sorry, prediction pasa_asmbl_41057.p2 fails validation.
(ATG)	 CA	125135-125665	AT	ATA
Valid prediction for CodingQuarry_transcript_48771-T1
Valid prediction for GlimmerHMM_glimmerT_8776-T1
Valid prediction for GeneMark_model.14255_t
Valid prediction for GeneMark_model.14248_t
Valid prediction for GlimmerHMM_glimmerT_8786-T1
Couldn't classify 87034, 87088
Sorry, prediction pasa_asmbl_41061.p1 fails validation.
(ACA)	 GT	87034-87088	GT	AGG
(GTA)	 AG	87478-87821	GC	AGG
(GTG)	 AG	89810-89907	GT	AGG
(GGG)	 AG	90376-90568	GT	CGG
(GCA)	 AG	91293-91439	CC	GAC
-recovered pasa_asmbl_41061.p1, terminal, 91293, 91439
-recovered pasa_asmbl_41061.p1, internal, 87478, 87821
-recovered pasa_asmbl_41061.p1, internal, 89810, 89907
-recovered pasa_asmbl_41061.p1, internal, 90376, 90568
Valid prediction for GeneMark_model.14253_t
Valid prediction for GlimmerHMM_glimmerT_8787-T1
Valid prediction for Augustus_model.g5773.t1
Valid prediction for snap_scaffold_4-snap.53-T1
Valid prediction for snap_scaffold_4-snap.48-T1
Valid prediction for snap_scaffold_4-snap.34-T1
Valid prediction for snap_scaffold_4-snap.55-T1
Valid prediction for HiQ_model.g5770.t1
Valid prediction for GlimmerHMM_glimmerT_8774-T1
Valid prediction for snap_scaffold_4-snap.60-T1
Valid prediction for GlimmerHMM_glimmerT_8773-T1
Valid prediction for GlimmerHMM_glimmerT_8782-T1
Valid prediction for GeneMark_model.14262_t
Valid prediction for GeneMark_model.14257_t
Valid prediction for GlimmerHMM_glimmerT_8769-T1
Valid prediction for HiQ_model.g5776.t1
Valid prediction for GlimmerHMM_glimmerT_8790-T1
Couldn't classify 96310, 96654
Sorry, prediction pasa_asmbl_41058.p1 fails validation.
(ATG)	 AG	96310-96654	AG	AGA
Valid prediction for GeneMark_model.14272_t
Valid prediction for GlimmerHMM_glimmerT_8778-T1
Valid prediction for GeneMark_model.14276_t
Valid prediction for GeneMark_model.14281_t
Valid prediction for Augustus_model.g5768.t1
Valid prediction for GeneMark_model.14258_t
Valid prediction for GeneMark_model.14279_t
Valid prediction for GlimmerHMM_glimmerT_8784-T1
Valid prediction for snap_scaffold_4-snap.51-T1
Valid prediction for Augustus_model.g5775.t1
Valid prediction for pasa_asmbl_41054.p1
Valid prediction for Augustus_model.g5774.t1
Valid prediction for HiQ_model.g5766.t1
Valid prediction for snap_scaffold_4-snap.39-T1
Valid prediction for snap_scaffold_4-snap.47-T1
Valid prediction for GeneMark_model.14268_t
Valid prediction for GeneMark_model.14251_t
Valid prediction for CodingQuarry_transcript_48768-T1
Valid prediction for GeneMark_model.14264_t
Valid prediction for GlimmerHMM_glimmerT_8783-T1
Valid prediction for snap_scaffold_4-snap.36-T1
Valid prediction for GeneMark_model.14270_t
Valid prediction for snap_scaffold_4-snap.41-T1
Valid prediction for GeneMark_model.14260_t
Valid prediction for Augustus_model.g5769.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12399, rend_intergenic: 9847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29941, rend_intergenic: 28221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34639, rend_intergenic: 31612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39928, rend_intergenic: 35228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60864, rend_intergenic: 59212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69784, rend_intergenic: 62268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73725, rend_intergenic: 72566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85284, rend_intergenic: 81121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94678, rend_intergenic: 86707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107234, rend_intergenic: 105556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109854, rend_intergenic: 107649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126006, rend_intergenic: 122957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134402, rend_intergenic: 127405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157257
-exon list size: 555


building trellis

0.2    
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3.8    
3.9    
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4.5    
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4.8    
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5.7    
5.9    
6.1    
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6.5    
6.6    
6.8    
7.0    
7.2    
7.4    
7.5    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.8    
11.0    
11.1    
11.3    
11.5    
11.7    
11.8    
12.0    
12.2    
12.4    
12.6    
12.7    
12.9    
13.1    
13.3    
13.5    
13.6    
13.8    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
16.0    
16.2    
16.3    
16.5    
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16.9    
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17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
21.2    
21.4    
21.5    
21.7    
21.9    
22.1    
22.3    
22.4    
22.6    
22.8    
23.0    
23.2    
23.3    
23.5    
23.7    
23.9    
24.1    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.6    
26.8    
26.9    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.2    
35.4    
35.5    
35.7    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.2    
37.3    
37.5    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.8    
39.0    
39.1    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.8    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.1    
43.3    
43.4    
43.6    
43.8    
44.0    
44.2    
44.3    
44.5    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.8    
47.9    
48.1    
48.3    
48.5    
48.7    
48.8    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.2    
51.3    
51.5    
51.7    
51.9    
52.1    
52.2    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.4    
56.6    
56.7    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.2    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 12399, rend_intergenic: 9847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29941, rend_intergenic: 28221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34639, rend_intergenic: 31612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39928, rend_intergenic: 35228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60864, rend_intergenic: 59212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69784, rend_intergenic: 62268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73725, rend_intergenic: 72566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85284, rend_intergenic: 81121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94678, rend_intergenic: 86707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107234, rend_intergenic: 105556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109854, rend_intergenic: 107649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126006, rend_intergenic: 122957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134402, rend_intergenic: 127405  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

-building DP trellis

-building trellis in range 143800 - 157257
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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