-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_6412093-6584820

-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 GlimmerHMM_glimmerT_47283-T1
Valid prediction for snap_scaffold_20-snap.1432-T1
Valid prediction for snap_scaffold_20-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_47282-T1
Valid prediction for snap_scaffold_20-snap.1440-T1
Valid prediction for GlimmerHMM_glimmerT_47297-T1
Valid prediction for snap_scaffold_20-snap.1431-T1
Valid prediction for Augustus_model.g31529.t1
Valid prediction for GeneMark_model.82652_t
Valid prediction for snap_scaffold_20-snap.1449-T1
Valid prediction for snap_scaffold_20-snap.1429-T1
Valid prediction for Augustus_model.g31534.t1
Valid prediction for Augustus_model.g31530.t1
Valid prediction for Augustus_model.g31536.t1
Valid prediction for snap_scaffold_20-snap.1436-T1
Valid prediction for Augustus_model.g31533.t1
Valid prediction for snap_scaffold_20-snap.1439-T1
Valid prediction for GeneMark_model.82630_t
Valid prediction for Augustus_model.g31535.t1
Valid prediction for GeneMark_model.82647_t
Valid prediction for Augustus_model.g31526.t1
Valid prediction for GlimmerHMM_glimmerT_47294-T1
Valid prediction for GeneMark_model.82659_t
Valid prediction for snap_scaffold_20-snap.1451-T1
Couldn't classify 132462, 132619
Sorry, prediction pasa_asmbl_25815.p1 fails validation.
(GTG)	 TA	132462-132619	GT	TTG
(CAA)	 AG	132974-133108	GT	TGG
(GTA)	 AG	133994-134087	GT	AGG
(GTA)	 AG	136184-136258	TT	GAT
-recovered pasa_asmbl_25815.p1, terminal, 136184, 136258
-recovered pasa_asmbl_25815.p1, internal, 132974, 133108
-recovered pasa_asmbl_25815.p1, internal, 133994, 134087
Valid prediction for GeneMark_model.82663_t
Valid prediction for GlimmerHMM_glimmerT_47311-T1
Valid prediction for GlimmerHMM_glimmerT_47287-T1
Valid prediction for GeneMark_model.82635_t
Valid prediction for GlimmerHMM_glimmerT_47309-T1
Valid prediction for Augustus_model.g31528.t1
Valid prediction for GeneMark_model.82628_t
Valid prediction for GeneMark_model.82661_t
Valid prediction for GlimmerHMM_glimmerT_47307-T1
Valid prediction for GeneMark_model.82638_t
Valid prediction for GeneMark_model.82640_t
Valid prediction for GlimmerHMM_glimmerT_47303-T1
Valid prediction for snap_scaffold_20-snap.1441-T1
Valid prediction for GeneMark_model.82667_t
Valid prediction for GeneMark_model.82664_t
Valid prediction for GeneMark_model.82639_t
Valid prediction for GlimmerHMM_glimmerT_47290-T1
Valid prediction for GeneMark_model.82631_t
Valid prediction for snap_scaffold_20-snap.1445-T1
Valid prediction for Augustus_model.g31531.t1
Valid prediction for GeneMark_model.82634_t
Valid prediction for GlimmerHMM_glimmerT_47302-T1
Valid prediction for snap_scaffold_20-snap.1447-T1
Valid prediction for GeneMark_model.82632_t
Valid prediction for GlimmerHMM_glimmerT_47295-T1
Valid prediction for GeneMark_model.82657_t
Valid prediction for GeneMark_model.82655_t
Valid prediction for snap_scaffold_20-snap.1437-T1
Valid prediction for GeneMark_model.82645_t
Valid prediction for GlimmerHMM_glimmerT_47305-T1
Valid prediction for GeneMark_model.82649_t
Valid prediction for GlimmerHMM_glimmerT_47293-T1
Valid prediction for snap_scaffold_20-snap.1438-T1
Valid prediction for GlimmerHMM_glimmerT_47281-T1
Valid prediction for snap_scaffold_20-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_47298-T1
Valid prediction for Augustus_model.g31538.t1
Valid prediction for snap_scaffold_20-snap.1427-T1
Valid prediction for snap_scaffold_20-snap.1416-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_20-snap.1418-T1
Valid prediction for GeneMark_model.82633_t
Valid prediction for GlimmerHMM_glimmerT_47285-T1
Valid prediction for GeneMark_model.82648_t
Valid prediction for snap_scaffold_20-snap.1433-T1
Valid prediction for snap_scaffold_20-snap.1423-T1
Valid prediction for snap_scaffold_20-snap.1428-T1
Valid prediction for Augustus_model.g31537.t1
Valid prediction for snap_scaffold_20-snap.1417-T1
Valid prediction for snap_scaffold_20-snap.1443-T1
Valid prediction for CodingQuarry_transcript_30470-T1
Valid prediction for snap_scaffold_20-snap.1435-T1
Valid prediction for snap_scaffold_20-snap.1448-T1
Valid prediction for GeneMark_model.82646_t
Valid prediction for GeneMark_model.82665_t
Valid prediction for snap_scaffold_20-snap.1444-T1
Valid prediction for GeneMark_model.82643_t
Valid prediction for GlimmerHMM_glimmerT_47308-T1
Valid prediction for snap_scaffold_20-snap.1446-T1
Valid prediction for snap_scaffold_20-snap.1422-T1
Valid prediction for GeneMark_model.82653_t
Valid prediction for GlimmerHMM_glimmerT_47291-T1
Valid prediction for GeneMark_model.82637_t
Valid prediction for Augustus_model.g31527.t1
Valid prediction for GeneMark_model.82662_t
Valid prediction for GlimmerHMM_glimmerT_47292-T1
Valid prediction for GlimmerHMM_glimmerT_47286-T1
Valid prediction for Augustus_model.g31525.t1
Valid prediction for GlimmerHMM_glimmerT_47289-T1
Valid prediction for GlimmerHMM_glimmerT_47288-T1
Valid prediction for GlimmerHMM_glimmerT_47301-T1
Valid prediction for GlimmerHMM_glimmerT_47299-T1
Valid prediction for GlimmerHMM_glimmerT_47306-T1
Valid prediction for GeneMark_model.82651_t
Valid prediction for snap_scaffold_20-snap.1425-T1
Valid prediction for GeneMark_model.82658_t
Valid prediction for GeneMark_model.82641_t
Valid prediction for Augustus_model.g31532.t1
Valid prediction for GeneMark_model.82644_t
Valid prediction for GeneMark_model.82636_t
Valid prediction for snap_scaffold_20-snap.1430-T1
Valid prediction for snap_scaffold_20-snap.1450-T1
Couldn't classify 115295, 115397
Sorry, prediction pasa_asmbl_26756.p1 fails validation.
(GGA)	 GA	115295-115397	GT	AGG
(TGT)	 AG	115723-115899	GT	TCG
(CAA)	 AG	116282-116378	GT	GGG
(ATA)	 AG	116471-116547	GT	AGG
(CTG)	 AG	116660-116851	GT	TGG
(AGG)	 AG	117093-117272	GT	AGG
(CCC)	 AG	117546-117743	GT	GGG
(AAC)	 AG	117887-117996	AG	AAA
-recovered pasa_asmbl_26756.p1, terminal, 117887, 117996
-recovered pasa_asmbl_26756.p1, internal, 115723, 115899
-recovered pasa_asmbl_26756.p1, internal, 116282, 116378
-recovered pasa_asmbl_26756.p1, internal, 116471, 116547
-recovered pasa_asmbl_26756.p1, internal, 116660, 116851
-recovered pasa_asmbl_26756.p1, internal, 117093, 117272
-recovered pasa_asmbl_26756.p1, internal, 117546, 117743
Valid prediction for GlimmerHMM_glimmerT_47310-T1
Valid prediction for GeneMark_model.82650_t
Valid prediction for snap_scaffold_20-snap.1424-T1
Valid prediction for snap_scaffold_20-snap.1442-T1
Valid prediction for GeneMark_model.82660_t
Valid prediction for GlimmerHMM_glimmerT_47296-T1
Valid prediction for GeneMark_model.82666_t
Valid prediction for GeneMark_model.82627_t
Valid prediction for snap_scaffold_20-snap.1420-T1
Valid prediction for GeneMark_model.82656_t
Valid prediction for GlimmerHMM_glimmerT_47284-T1
Valid prediction for GeneMark_model.82629_t
Valid prediction for GlimmerHMM_glimmerT_47280-T1
Valid prediction for snap_scaffold_20-snap.1415-T1
Valid prediction for CodingQuarry_transcript_30471-T1
Valid prediction for snap_scaffold_20-snap.1419-T1
Valid prediction for GlimmerHMM_glimmerT_47300-T1
Valid prediction for snap_scaffold_20-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_47304-T1
Valid prediction for GeneMark_model.82626_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41193, rend_intergenic: 36869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80774, rend_intergenic: 78658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87913, rend_intergenic: 85636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101133, rend_intergenic: 98338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130209, rend_intergenic: 125802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135719, rend_intergenic: 131437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145236, rend_intergenic: 138810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158743, rend_intergenic: 147983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167088, rend_intergenic: 165889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172728
-exon list size: 503


building trellis

0.2    
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6.1    
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7.1    
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9.3    
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9.9    
10.1    
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11.1    
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12.9    
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13.7    
13.9    
14.1    
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23.4    
23.6    
23.8    
24.0    
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24.8    
25.0    
25.1    
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25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
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    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
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    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
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    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
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    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
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    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
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    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
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    
85.1    
85.3    
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    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 41193, rend_intergenic: 36869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80774, rend_intergenic: 78658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87913, rend_intergenic: 85636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101133, rend_intergenic: 98338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130209, rend_intergenic: 125802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135719, rend_intergenic: 131437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145236, rend_intergenic: 138810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158743, rend_intergenic: 147983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167088, rend_intergenic: 165889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17702
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 2 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 - 15006
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 - 14497
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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

-building DP trellis

-building trellis in range 1 - 14146
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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